@article{hislop_luby_loarca_humann_hummer_bassil_zhao_sheehan_casa_billings_et al._2024, title={A Blueberry (<i> Vaccinium</i> L.) Crop Ontology to Enable Standardized Phenotyping for Blueberry Breeding and Research}, volume={59}, ISSN={["2327-9834"]}, DOI={10.21273/HORTSCI17676-23}, abstractNote={Breeding programs around the world continually collect data on large numbers of individuals. To be able to combine data collected across regions, years, and experiments, research communities develop standard operating procedures for data collection and measurement. One such method is a crop ontology, or a standardized vocabulary for collecting data on commonly measured traits. The ontology is also computer readable to facilitate the use of data management systems such as databases. Blueberry breeders and researchers across the United States have come together to develop the first standardized crop ontology in blueberry ( Vaccinium spp.). We provide an overview and report on the construction of the first blueberry crop ontology and the 178 traits and methods included within. Researchers of Vaccinium species—such as other blueberry species, cranberry, lingonberry, and bilberry—can use the described crop ontology to collect phenotypic data of greater quality and consistency, interoperability, and computer readability. Crop ontologies, as a shared data language, benefit the entire worldwide research community by enabling collaborative meta-analyses that can be used with genomic data for quantitative trait loci, genome-wide association studies, and genomic selection analysis.}, number={10}, journal={HORTSCIENCE}, author={Hislop, Lillian M. and Luby, Claire H. and Loarca, Jenyne and Humann, Jodi and Hummer, Kim E. and Bassil, Nahla and Zhao, Dongyan and Sheehan, Moira J. and Casa, Alexandra M. and Billings, Grant T. and et al.}, year={2024}, month={Oct}, pages={1433–1442} }
 @article{mengist_pottorff_mackey_ferrao_casorzo_lila_luby_giongo_perkins-veazie_bassil_et al._2024, title={Assessing predictability of post-storage texture and appearance characteristics in blueberry at breeding population level}, volume={214}, ISSN={["1873-2356"]}, DOI={10.1016/j.postharvbio.2024.112964}, journal={POSTHARVEST BIOLOGY AND TECHNOLOGY}, author={Mengist, Molla F. and Pottorff, Marti and Mackey, Ted and Ferrao, Felipe and Casorzo, Gonzalo and Lila, Mary Ann and Luby, Claire and Giongo, Lara and Perkins-Veazie, Penelope and Bassil, Nahla and et al.}, year={2024}, month={Aug} }
 @article{seth_iorizzo_maritim_sharma_2024, title={Editorial: Epigenetic and gene regulation underlying crosstalk in plant development and stress responses}, volume={15}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2024.1427102}, abstractNote={Editorial: Epigenetic and gene regulation underlying crosstalk in plant development and stress responses}, journal={FRONTIERS IN GENETICS}, author={Seth, Romit and Iorizzo, Massimo and Maritim, Tony Kipkoech and Sharma, Ram Kumar}, year={2024}, month={Jul} }
 @article{munoz_hayes_perkins-veazie_gillitt_munoz_kay_lila_ferruzzi_iorizzo_2024, title={Genotype and ripening method affect carotenoid content and bio-accessibility in banana}, volume={3}, ISSN={["2042-650X"]}, url={https://doi.org/10.1039/D3FO04632J}, DOI={10.1039/d3fo04632j}, abstractNote={This study concludes that the genotype, ripening methods (natural vs. exogenous ethylene application), and carotenoid bioaccessible content should be considered when setting a nutrition goal for vitamin A biofortification in banana-breeding programs.}, journal={FOOD & FUNCTION}, author={Munoz, Bryan and Hayes, Micaela and Perkins-Veazie, Penelope and Gillitt, Nicholas and Munoz, Miguel and Kay, Colin D. and Lila, Mary Ann and Ferruzzi, Mario G. and Iorizzo, Massimo}, year={2024}, month={Mar} }
 @article{ivarsson_bennett_ferrara_strauch_vallase_iorizzo_pecorelli_lila_valacchi_2024, title={Gut-derived wild blueberry phenolic acid metabolites modulate extrinsic cutaneous damage}, volume={6}, ISSN={["2042-650X"]}, url={https://doi.org/10.1039/D4FO01874E}, DOI={10.1039/d4fo01874e}, abstractNote={As the first line of defense, the skin is equipped with various physiological mechanisms positioned to prevent incoming oxidative damage from numerous environmental insults. With persistent exposure to the environment, understanding ways to augment the skin defenses is paramount in protecting from premature aging. In this study, we investigated the ability of five dietary phenolic metabolites, typically found in the bloodstream after wild blueberry consumption, to successfully defend the skin from UV light exposure in a novel}, journal={FOOD & FUNCTION}, author={Ivarsson, John and Bennett, Abby and Ferrara, Francesca and Strauch, Renee and Vallase, Andrea and Iorizzo, Massimo and Pecorelli, Alessandra and Lila, Mary Ann and Valacchi, Giuseppe}, year={2024}, month={Jun} }
 @article{ivarsson_bennett_ferrara_strauch_vallese_iorizzo_pecorelli_lila_valacchi_2024, title={Gut-derived wild blueberry phenolic acid metabolites modulate extrinsic cutaneous damage (vol 15, pg 7849, 2024)}, volume={10}, ISSN={["2042-650X"]}, DOI={10.1039/d4fo90097a}, abstractNote={Correction for ‘Gut-derived wild blueberry phenolic acid metabolites modulate extrinsic cutaneous damage’ by John Ivarsson et al. , Food Funct. , 2024, 15 , 7849–7864, https://doi.org/10.1039/D4FO01874E.}, journal={FOOD & FUNCTION}, author={Ivarsson, John and Bennett, Abby and Ferrara, Francesca and Strauch, Renee and Vallese, Andrea and Iorizzo, Massimo and Pecorelli, Alessandra and Lila, Mary Ann and Valacchi, Giuseppe}, year={2024}, month={Oct} }
 @article{ferrao_azevedo_benevenuto_mengist_luby_pottorff_casorzo_mackey_lila_giongo_et al._2024, title={Inference of the genetic basis of fruit texture in highbush blueberries using genome-wide association analyses}, volume={11}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhae233}, abstractNote={Abstract The global production and consumption of blueberry (Vaccinium spp.), a specialty crop known for its abundant bioactive and antioxidant compounds, has more than doubled over the last decade. To hold this momentum, plant breeders have begun to use quantitative genetics and molecular breeding to guide their decisions and select new cultivars that are improved for fruit quality. In this study, we leveraged our inferences on the genetic basis of fruit texture and chemical components by surveying large breeding populations from northern highbush blueberries (NHBs) and southern highbush blueberries (SHBs), the two dominant cultivated blueberries. After evaluating 1065 NHB genotypes planted at the Oregon State University, and 992 SHB genotypes maintained at the University of Florida for 17 texture-related traits, evaluated over multiple years, our contributions consist of the following: (i) we drew attention to differences between NHB and SHB materials and showed that both blueberry types can be differentiated using texture traits; (ii) we computed genetic parameters and shed light on the genetic architecture of important texture attributes, indicating that most traits had a complex nature with low to moderate heritability; (iii) using molecular breeding, we emphasized that prediction could be performed across populations; and finally (iv) the genomic association analyses pinpointed some genomic regions harboring potential candidate genes for texture that could be used for further validation studies. Altogether, the methods and approaches used here can guide future breeding efforts focused on maximizing texture improvements in blueberries.}, number={10}, journal={HORTICULTURE RESEARCH}, author={Ferrao, Luis Felipe V and Azevedo, Camila and Benevenuto, Juliana and Mengist, Molla Fentie and Luby, Claire and Pottorff, Marti and Casorzo, Gonzalo I. P. and Mackey, Ted and Lila, Mary Ann and Giongo, Lara and et al.}, year={2024}, month={Oct} }
 @article{lopez-moreno_phillips_diaz-garcia_torres-meraz_jarquin_loarca_ikeda_giongo_grygleski_iorizzo_et al._2024, title={Multiparametric Cranberry (<i>Vaccinium macrocarpon</i> Ait.) Fruit Textural Trait Development for Harvest and Postharvest Evaluation in Representative Cultivars}, volume={55}, ISSN={["1745-4603"]}, DOI={10.1111/jtxs.12866}, abstractNote={ABSTRACT Fruit texture is a priority trait that guarantees the long‐term economic sustainability of the cranberry industry through value‐added products such as sweetened dried cranberries (SDCs). To develop a standard methodology to measure texture, we conducted a comparative analysis of 22 textural traits using five different methods under both harvest and postharvest conditions in 10 representative cranberry cultivars. A set of textural traits from the 10%‐strain compression and puncture methods were identified that differentiate between cultivars primarily based on hardness/stiffness and elasticity properties. The complementary use of both methodologies allowed for a detailed evaluation by capturing the effect of key texture‐determining factors such as structure, flesh, and skin. Furthermore, the high effectiveness of this approach in different conditions and its ability to capture high phenotypic variation in cultivars highlights its great potential for applicability in various areas of the value chain and research. Therefore, this study provides an informed reference for unifying future efforts to enhance cranberry fruit texture and quality.}, number={5}, journal={JOURNAL OF TEXTURE STUDIES}, author={Lopez-Moreno, Hector and Phillips, Matthew and Diaz-Garcia, Luis and Torres-Meraz, Maria and Jarquin, Diego and Loarca, Jenyne and Ikeda, Shinya and Giongo, Lara and Grygleski, Edward and Iorizzo, Massimo and et al.}, year={2024}, month={Oct} }
 @article{maule_loarca_diaz-garcia_lopez-moreno_johnson-cicalese_vorsa_iorizzo_neyhart_zalapa_2024, title={Of buds and bits: a meta-QTL study identifies stable QTL for berry quality and yield traits in cranberry mapping populations (<i>Vaccinium macrocarpon</i> Ait.)}, volume={15}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2024.1294570}, abstractNote={Introduction For nearly two centuries, cranberry ( Vaccinium macrocarpon Ait.) breeders have improved fruit quality and yield by selecting traits on fruiting stems, termed “reproductive uprights.” Crop improvement is accelerating rapidly in contemporary breeding programs due to modern genetic tools and high-throughput phenotyping methods, improving selection efficiency and accuracy. Methods We conducted genotypic evaluation on 29 primary traits encompassing fruit quality, yield, and chemical composition in two full-sib cranberry breeding populations— CNJ02 ( n = 168) and CNJ04 ( n = 67)—over 3 years. Genetic characterization was further performed on 11 secondary traits derived from these primary traits. Results For CNJ02 , 170 major quantitative trait loci (QTL; R 2 ≥ 0.10) were found with interval mapping, 150 major QTL were found with model mapping, and 9 QTL were found to be stable across multiple years. In CNJ04 , 69 major QTL were found with interval mapping, 81 major QTL were found with model mapping, and 4 QTL were found to be stable across multiple years. Meta-QTL represent stable genomic regions consistent across multiple years, populations, studies, or traits. Seven multi-trait meta-QTL were found in CNJ02 , one in CNJ04 , and one in the combined analysis of both populations. A total of 22 meta-QTL were identified in cross-study, cross-population analysis using digital traits for berry shape and size (8 meta-QTL), digital images for berry color (2 meta-QTL), and three-study cross-analysis (12 meta-QTL). Discussion Together, these meta-QTL anchor high-throughput fruit quality phenotyping techniques to traditional phenotyping methods, validating state-of-the-art methods in cranberry phenotyping that will improve breeding accuracy, efficiency, and genetic gain in this globally significant fruit crop.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Maule, Andrew F. and Loarca, Jenyne and Diaz-Garcia, Luis and Lopez-Moreno, Hector and Johnson-Cicalese, Jennifer and Vorsa, Nicholi and Iorizzo, Massimo and Neyhart, Jeffrey L. and Zalapa, Juan E.}, year={2024}, month={Sep} }
 @article{oh_stapleton_giongo_johanningsmeier_mollinari_mainland_perkins-veazie_iorizzo_2024, title={Prediction of blueberry sensory texture attributes by integrating multiple instrumental measurements}, volume={218}, ISSN={["1873-2356"]}, DOI={10.1016/j.postharvbio.2024.113160}, journal={POSTHARVEST BIOLOGY AND TECHNOLOGY}, author={Oh, Heeduk and Stapleton, Lee and Giongo, Lara and Johanningsmeier, Suzanne and Mollinari, Marcelo and Mainland, Charles M. and Perkins-Veazie, Penelope and Iorizzo, Massimo}, year={2024}, month={Dec} }
 @article{canales_gallardo_iorizzo_munoz_ferra_luby_bassil_pottorff_perkins-veazie_sandefur_et al._2024, title={Willingness to Pay for Blueberries: Sensory Attributes, Fruit Quality Traits, and Consumers' Characteristics}, volume={59}, ISSN={["2327-9834"]}, DOI={10.21273/HORTSCI17947-24}, abstractNote={Understanding consumers’ preferences for fruit quality attributes is key to informing breeding efforts, meeting consumer preferences, and promoting increased market demand. The objective of this study was to assess the effect of fruit quality traits and hedonic sensory evaluation on consumers’ willingness to pay (WTP) for a selection of fresh northern and southern highbush blueberry cultivars. The WTP was elicited by using a double-bounded contingent valuation conducted in conjunction with a consumer sensory test. Two types of models were estimated using either sensory evaluations (i.e., consumer preference and consumer intensity) or instrumental measurement data (i.e., measures of soluble solids, titratable acidity, sugars, acids, and firmness) as explanatory variables to model WTP. Results using sensory evaluations indicated that flavor liking, flavor intensity, and sweetness intensity are key factors that influence consumers’ acceptance and WTP for blueberries. A regression analysis using instrumental measurements indicated that measures related to sweetness and acidity traits are important factors that determine WTP. Higher WTP was associated with higher total sugar content across different levels of total organic acid. The WTP increases with organic acid content, because this is needed for enhanced flavor; however, WTP declines at high concentrations of organic acid. Except for extreme values of firmness, the WTP increased as measures of fruit firmness increased, indicating a consumer preference for firmer blueberries. Overall, the results provided new insights into the relationships between consumer preference and WTP and fruit quality benchmarks to select for improved quality.}, number={8}, journal={HORTSCIENCE}, author={Canales, Elizabeth and Gallardo, R. Karina and Iorizzo, Massimo and Munoz, Patricio and Ferra, Luis Felipe and Luby, Claire and Bassil, Nahla and Pottorff, Marti and Perkins-Veazie, Penelope and Sandefur, Paul and et al.}, year={2024}, month={Aug}, pages={1207–1218} }
 @article{ma_gallardo_canales_atucha_zalapa_iorizzo_2024, title={Would consumers accept CRISPR fruit crops if the benefit has health implications? An application to cranberry products}, ISSN={["2372-2614"]}, DOI={10.1017/age.2023.38}, abstractNote={Abstract
	  Cranberry products are perceived as healthy due to their high antioxidant content yet adding sugars to increase their palatability deters consumption. Plant breeding technologies such as gene editing, specifically the clustered regularly interspaced palindromic repeats (CRISPR), offer a plausible alternative to develop cranberries with desired traits (e.g., lower acidity and increased sweetness). We estimated consumers’ willingness to pay for sugar content, CRISPR, and cranberry flavor intensity for two cranberry products under different health-related information treatments. Respondents stated a discount for regular sugar content favoring reduced sugar products, for CRISPR compared to conventional breeding, and for weak/bland compared to full/intense cranberry flavor. Compensated valuation analysis of products with different attribute levels indicates that consumers were willing to pay a premium for cranberry products with reduced sugar content, CRISPR-bred, and full/intense cranberry flavor relative to products with regular sugar content, conventionally bred, and weak/bland flavor. Information treatments highlighting cranberries’ health benefits and recommendations to limit sugar intake increased consumers’ discounts for regular sugar content, surpassing the discount for CRISPR. This research underscores the importance of the conditions under which breeding technologies might gain public acceptance. This information will benefit the scientific community and industry seeking to use CRISPR to develop improved cranberry cultivars.}, journal={AGRICULTURAL AND RESOURCE ECONOMICS REVIEW}, author={Ma, Xueying and Gallardo, Rosa Karina and Canales, Elizabeth and Atucha, Amaya and Zalapa, Juan and Iorizzo, Massimo}, year={2024}, month={Jan} }
 @article{lopez-moreno_phillips_diaz-garcia_torres-meraz_la torre_berro_loarca_mura_ikeda_atucha_et al._2023, title={A Survey of Key Methods, Traits, Parameters, and Conditions for Measuring Texture in Cranberry (Vaccinium macrocarpon Ait.)}, volume={9}, ISSN={["2311-7524"]}, DOI={10.3390/horticulturae9040479}, abstractNote={In the cranberry (Vaccinium macrocarpon Ait.) industry, the textural properties and firmness of the fruit are priority traits for producing processed products, such as sweetened dried cranberry (SDC), which have gained popularity in recent years. However, there is currently no reliable methodology for screening these traits in breeding programs. In this study, we examine the key methodologies, textural traits, parameters, and conditions that are necessary to accurately and efficiently measure the texture of cranberry fruit. Double compression, single compression, puncture, shearing and Kramer shear cell methodologies were successfully implemented in cranberry, resulting in a total of 47 textural features. These features allowed the evaluation of the texture of the cranberry fruit based on key factors such as flesh, structure, and skin. This study also examined factors than can affect the performance of texture measurements, including the optimal sample size, storage time, fruit texture-size correlation, fruit temperature and orientation, optimal speed/strain combinations, and the effect of probe diameter. The results of the study suggests that certain texture traits of the compression and puncture methodologies could potentially be used to test varieties and aid in breeding programs.}, number={4}, journal={HORTICULTURAE}, author={Lopez-Moreno, Hector and Phillips, Matthew and Diaz-Garcia, Luis and Torres-Meraz, Maria A. and La Torre, Fernando and Berro, Ines and Loarca, Jenyne and Mura, Jyostna and Ikeda, Shinya and Atucha, Amaya and et al.}, year={2023}, month={Apr} }
 @article{trandel-hayse_johanningsmeier_oh_iorizzo_perkins-veazie_2023, title={Blueberry Cell Wall Polysaccharide Composition of Three Distinct Fruit Firmness Phenotypes}, volume={3}, ISSN={["2692-1944"]}, DOI={10.1021/acsfoodscitech.3c00284}, abstractNote={Blueberry (Vaccinium corymbosum) cultivars vary in firmness, and these phenotypic differences may be associated with peel and pulp cell wall polysaccharides. Three blueberry cultivars of distinctive texture phenotypes, Indigocrisp (crisp), Emerald (firm, industry standard), and Jewel (soft), were evaluated for cell wall polysaccharide composition. Alcohol-insoluble residues (AIRs) from both peel and pulp were reduced, methylated, hydrolyzed, acetylated, and quantified using gas chromatography–mass spectrometry (GC-MS). Monosaccharide composition (μg·mg–1 AIR) differed among cultivars, with "Indigocrisp" pulp highest in glucuronic acid (22.23), "Emerald" pulp highest in glucose (106.31), and "Jewel" peel highest in arabinose (38.73) and mannose (11.88). Forty-five cell wall polysaccharide linkages were identified, and specific linkages were associated with blueberry peel and pulp among the texture phenotypes. Polysaccharide classifications were then estimated from the 45 cell wall polysaccharide linkages. "Indigocrisp" and "Emerald" pulp were highest in arabinan and type II arabinogalactan, which are less susceptible to depolymerization. "Indigocrisp" pulp had a greater abundance of heteromannan, xyloglucan, and cellulose, while "Jewel" was highest in rhamnogalacturonan I, which typically depolymerizes first. The greater abundances of arabinan and type II arabinogalactan in the pulp of the firm and crisp cultivars likely contribute to the texture characteristics of these phenotypes.}, number={11}, journal={ACS FOOD SCIENCE & TECHNOLOGY}, author={Trandel-Hayse, Marlee and Johanningsmeier, Suzanne and Oh, Heeduk and Iorizzo, Massimo and Perkins-Veazie, Penelope}, year={2023}, month={Nov}, pages={1920–1930} }
 @article{yocca_platts_alger_teresi_mengist_benevenuto_ferrao_jacobs_babinski_magallanes-lundback_et al._2023, title={Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts}, volume={10}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhad202}, abstractNote={Abstract
               Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence–absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium—a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.}, number={11}, journal={HORTICULTURE RESEARCH}, author={Yocca, Alan E. and Platts, Adrian and Alger, Elizabeth and Teresi, Scott and Mengist, Molla F. and Benevenuto, Juliana and Ferrao, Luis Felipe V and Jacobs, MacKenzie and Babinski, Michal and Magallanes-Lundback, Maria and et al.}, year={2023}, month={Nov} }
 @article{perez_carvajal_beretta_bannoud_fangio_berli_fontana_salomon_gonzalez_valerga_et al._2023, title={Characterization of Purple Carrot Germplasm for Antioxidant Capacity and Root Concentration of Anthocyanins, Phenolics, and Carotenoids}, volume={12}, ISSN={["2223-7747"]}, DOI={10.3390/plants12091796}, abstractNote={The present study characterized a genetically and phenotypically diverse collection of 27 purple and two non-purple (one orange and one yellow) carrot accessions for concentration of root anthocyanins, phenolics, and carotenoids, and antioxidant capacity estimated by four different methods (ORAC, DPPH, ABTS, FRAP), in a partially replicated experimental design comprising data from two growing seasons (2018 and 2019). Broad and significant (p < 0.0001) variation was found among the accessions for all the traits. Acylated anthocyanins (AA) predominated over non-acylated anthocyanins (NAA) in all the accessions and years analyzed, with AA accounting for 55.5–100% of the total anthocyanin content (TAC). Anthocyanins acylated with ferulic acid and coumaric acid were the most abundant carrot anthocyanins. In general, black or solid purple carrots had the greatest TAC and total phenolic content (TPC), and the strongest antioxidant capacities, measured by all methods. Antioxidant capacity, estimated by all methods, was significantly, positively, and moderately-to-strongly correlated with the content of all individual anthocyanins pigments, TAC, and TPC, in both years (r = 0.59–0.90, p < 0.0001), but not with the carotenoid pigments lutein and β-carotene; suggesting that anthocyanins and other phenolics, but not carotenoids, are major contributors of the antioxidant capacity in purple carrots. We identified accessions with high concentration of chemically stable AA, with potential value for the production of food dyes, and accessions with relatively high content of bioavailable NAA that can be selected for increased nutraceutical value (e.g., for fresh consumption).}, number={9}, journal={PLANTS-BASEL}, author={Perez, Maria Belen and Carvajal, Sofia and Beretta, Vanesa and Bannoud, Florencia and Fangio, Maria Florencia and Berli, Federico and Fontana, Ariel and Salomon, Maria Victoria and Gonzalez, Roxana and Valerga, Lucia and et al.}, year={2023}, month={Apr} }
 @article{yow_laosuntisuk_young_doherty_gillitt_perkins-veazie_jenny xiang_iorizzo_2023, title={Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-45722-y}, abstractNote={AbstractPineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Laosuntisuk, Kanjana and Young, Roberto A. and Doherty, Colleen J. and Gillitt, Nicholas and Perkins-Veazie, Penelope and Jenny Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Nov} }
 @article{oh_pottorff_giongo_mainland_iorizzo_perkins-veazie_2024, title={Exploring shelf-life predictability of appearance traits and fruit texture in blueberry}, volume={208}, ISSN={["1873-2356"]}, DOI={10.1016/j.postharvbio.2023.112643}, abstractNote={Improving the shelf-life of blueberries (Vaccinium spp.) has become a crucial breeding priority for the industry. However, the breeders have sparse empirical data to select genotypes with extended shelf-life. In this study, a large set of cultivars was evaluated for mechanical texture and appearance characteristics at harvest and after storage to understand their relationship and test multiple statistical models to assess the predictability of shelf-life. Blueberries harvested from 61 cultivars with extensive phenotypic variation were stored at 2 oC and 80% relative humidity (RH) for six weeks. The results indicated that weight loss, texture change, and fruit wrinkling could be predicted using fruit characteristics measured at harvest (T0) or two weeks post-harvest (T2). The berry size at T0 was able to predict postharvest weight loss with high accuracy; the larger the initial berry size, the less weight loss. This trend plateaued with berries larger than 18 mm in diameter. For texture, the measurements at T0 and six weeks after storage (T6) were positively correlated in all mechanical texture parameters, indicating that the initial texture is highly related to the final texture after storage. The overall change of texture could be best predicted using the texture parameter 'distance to maximum force' (DFM) measured at T0. Although the prediction accuracy was relatively low (R2 = 0.34), the model still effectively predicted the cultivars with the most texture change and those with the least. Interestingly, the prediction power improved to a moderate level (R2 = 0.45–0.66) when using all the texture and appearance parameters measured at T0 and T2. Wrinkling was best predicted by either the initial fruit size or the texture parameter 'force linear distance' (FLD) with low accuracy (R2 = 0.35–0.37); the larger the berry or FLD at T0, the less wrinkle after storage. These findings provide empirical data that blueberry breeders could use to select for shelf-life in blueberry. Predicting the variation of shelf-life indicators in a germplasm can substantially reduce the cost and time required to phenotype shelf-life performance.}, journal={POSTHARVEST BIOLOGY AND TECHNOLOGY}, author={Oh, Heeduk and Pottorff, Marti and Giongo, Lara and Mainland, Charles M. and Iorizzo, Massimo and Perkins-Veazie, Penelope}, year={2024}, month={Feb} }
 @article{d'amelia_curaba_abid_esposito_cavagnaro_carputo_iorizzo_2023, title={Functional characterization of DcMYB11, an R2R3 MYB associated with the purple pigmentation of carrot petiole}, volume={258}, ISSN={["1432-2048"]}, DOI={10.1007/s00425-023-04200-5}, number={3}, journal={PLANTA}, author={D'Amelia, Vincenzo and Curaba, Julien and Abid, Muhammad Ali and Esposito, Salvatore and Cavagnaro, Pablo and Carputo, Domenico and Iorizzo, Massimo}, year={2023}, month={Sep} }
 @article{yow_bostan_young_valacchi_gillitt_perkins-veazie_xiang_iorizzo_2023, title={Identification of bromelain subfamily proteases encoded in the pineapple genome}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-38907-y}, abstractNote={AbstractPapain (aka C1A) family proteases, including bromelain enzymes, are widespread across the plant kingdom and play critical regulatory functions in protein turnover during development. The proteolytic activity exhibited by papain family proteases has led to their increased usage for a wide range of cosmetic, therapeutic, and medicinal purposes. Bromelain enzymes, or bromelains in short, are members of the papain family that are specific to the bromeliad plant family. The only major commercial extraction source of bromelain is pineapple. The importance of C1A family and bromelain subfamily proteases in pineapple development and their increasing economic importance led several researchers to utilize available genomic resources to identify protease-encoding genes in the pineapple genome. To date, studies are lacking in screening bromelain genes for targeted use in applied science studies. In addition, the bromelain genes coding for the enzymes present in commercially available bromelain products have not been identified and their evolutionary origin has remained unclear. Here, using the newly developed MD2 v2 pineapple genome, we aimed to identify bromelain-encoding genes and elucidate their evolutionary origin. Orthologous and phylogenetic analyses of all papain-family proteases encoded in the pineapple genome revealed a single orthogroup (189) and phylogenetic clade (XIII) containing the bromelain subfamily. Duplication mode and synteny analyses provided insight into the origin and expansion of the bromelain subfamily in pineapple. Proteomic analysis identified four bromelain enzymes present in two commercially available bromelain products derived from pineapple stem, corresponding to products of four putative bromelain genes. Gene expression analysis using publicly available transcriptome data showed that 31 papain-family genes identified in this study were up-regulated in specific tissues, including stem, fruit, and floral tissues. Some of these genes had higher expression in earlier developmental stages of different tissues. Similar expression patterns were identified by RT-qPCR analysis with leaf, stem, and fruit. Our results provide a strong foundation for future applicable studies on bromelain, such as transgenic approaches to increase bromelain content in pineapple, development of bromelain-producing bioreactors, and studies that aim to determine the medicinal and/or therapeutic viability of individual bromelain enzymes.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Bostan, Hamed and Young, Roberto and Valacchi, Giuseppe and Gillitt, Nicholas and Perkins-Veazie, Penelope and Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Jul} }
 @article{farneti_giongo_emanuelli_toivonen_folta_iorizzo_2023, title={Interdisciplinary approaches to improve quality of soft fruit berries, volume II}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1341519}, abstractNote={EDITORIAL article Front. Plant Sci., 07 December 2023Sec. Crop and Product Physiology Volume 14 - 2023 | https://doi.org/10.3389/fpls.2023.1341519}, journal={FRONTIERS IN PLANT SCIENCE}, author={Farneti, Brian and Giongo, Lara and Emanuelli, Francesco and Toivonen, Peter and Folta, Kevin and Iorizzo, Massimo}, year={2023}, month={Dec} }
 @article{coe_bostan_rolling_turner-hissong_macko-podgorni_senalik_liu_seth_curaba_mengist_et al._2023, title={Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots}, volume={9}, ISSN={["2055-0278"]}, url={https://doi.org/10.1038/s41477-023-01526-6}, DOI={10.1038/s41477-023-01526-6}, abstractNote={AbstractHere an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and β-carotene orange phenotype. All three genes control high α- and β-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.}, journal={NATURE PLANTS}, author={Coe, Kevin and Bostan, Hamed and Rolling, William and Turner-Hissong, Sarah and Macko-Podgorni, Alicja and Senalik, Douglas and Liu, Su and Seth, Romit and Curaba, Julien and Mengist, Molla Fentie and et al.}, year={2023}, month={Sep} }
 @article{herniter_kim_wang_havill_johnson-cicalese_muehlbauer_iorizzo_vorsa_2023, title={Trait Mapping of Phenolic Acids in an Interspecific (Vaccinium corymbosum var. caesariense x V. darrowii) Diploid Blueberry Population}, volume={12}, ISSN={["2223-7747"]}, DOI={10.3390/plants12061346}, abstractNote={Blueberries (Vaccinium sect. Cyanococcus) are a dietary source of phenolic acids, including chlorogenic acid (CGA) and related compounds such as acetylated caffeoylquinic acid (ACQA) and caffeoylarbutin (CA). These compounds are known to be potent antioxidants with potential health benefits. While the chemistry of these compounds has been extensively studied, the genetic analysis has lagged behind. Understanding the genetic basis for traits with potential health implications may be of great use in plant breeding. By characterizing genetic variation related to fruit chemistry, breeders can make more efficient use of plant diversity to develop new cultivars with higher concentrations of these potentially beneficial compounds. Using a large interspecific F1 population, developed from a cross between the temperate V. corymbosum var. ceasariense and the subtropical V. darrowii, with 1025 individuals genotyped using genotype-by-sequencing methods, of which 289 were phenotyped for phenolic acid content, with data collected across 2019 and 2020, we have identified loci associated with phenolic acid content. Loci for the compounds clustered on the proximal arm of Vc02, suggesting that a single gene or several closely associated genes are responsible for the biosynthesis of all four tested compounds. Within this region are multiple gene models similar to hydroxycinnamoyl CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) and UDP glucose:cinnamate glucosyl transferase (UGCT), genes known to be involved in the CGA biosynthesis pathway. Additional loci on Vc07 and Vc12 were associated with caffeoylarbutin content, suggesting a more complicated biosynthesis of that compound.}, number={6}, journal={PLANTS-BASEL}, author={Herniter, Ira A. and Kim, Yurah and Wang, Yifei and Havill, Joshua S. and Johnson-Cicalese, Jennifer and Muehlbauer, Gary J. and Iorizzo, Massimo and Vorsa, Nicholi}, year={2023}, month={Mar} }
 @article{albert_iorizzo_mengist_montanari_zalapa_maule_edger_yocca_platts_pucker_et al._2023, title={Vaccinium as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit}, ISSN={["1532-2548"]}, DOI={10.1093/plphys/kiad250}, abstractNote={Abstract
               The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops, including blueberry, cranberry, bilberry, and lingonberry. Consumption of Vaccinium berries is strongly associated with various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids, including the anthocyanins that provide the attractive red and blue berry colors. Because these phytochemicals are increasingly appealing to consumers, they have become a crop breeding target. There has been substantial recent progress in Vaccinium genomics and genetics together with new functional data on the transcriptional regulation of flavonoids. This is helping to unravel the developmental control of flavonoids and identify genetic regions and genes that can be selected for to further improve Vaccinium crops and advance our understanding of flavonoid regulation and biosynthesis across a broader range of fruit crops. In this update we consider the recent progress in understanding flavonoid regulation in fruit crops, using Vaccinium as an example and highlighting the significant gains in both genomic tools and functional analysis.}, journal={PLANT PHYSIOLOGY}, author={Albert, Nick W. and Iorizzo, Massimo and Mengist, Molla F. and Montanari, Sara and Zalapa, Juan and Maule, Andrew and Edger, Patrick P. and Yocca, Alan E. and Platts, Adrian E. and Pucker, Boas and et al.}, year={2023}, month={May} }
 @article{mengist_bostan_de paola_teresi_platts_cremona_qi_mackey_bassil_ashrafi_et al._2022, title={Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)}, volume={9}, ISSN={["1469-8137"]}, url={https://doi.org/10.1111/nph.18428}, DOI={10.1111/nph.18428}, abstractNote={Summary


Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter‐specific, and inter‐ploidy admixture of its genome and lack of in depth genome‐wide inheritance and comparative structural studies.

Here we describe a new high‐quality, phased, chromosome‐scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high‐density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species.

Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr‐6 and one of chr‐10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter‐crossable wild diploid species.

These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.

}, journal={NEW PHYTOLOGIST}, author={Mengist, Molla F. and Bostan, Hamed and De Paola, Domenico and Teresi, Scott J. and Platts, Adrian E. and Cremona, Gaetana and Qi, Xinpeng and Mackey, Ted and Bassil, Nahla V and Ashrafi, Hamid and et al.}, year={2022}, month={Sep} }
 @article{hayes_mohamedshah_chadwick-corbin_hoskin_iorizzo_lila_neilson_ferruzzi_2022, title={Bioaccessibility and intestinal cell uptake of carotenoids and chlorophylls differ in powdered spinach by the ingredient form as measured using in vitro gastrointestinal digestion and anaerobic fecal fermentation models}, volume={13}, ISSN={["2042-650X"]}, url={https://doi.org/10.1039/D2FO00051B}, DOI={10.1039/d2fo00051b}, abstractNote={Insights into food matrix factors impacting bioavailability of bioactive carotenoids and chlorophylls from fruits and vegetable ingredients are essential to understanding their ability to promote health.}, number={7}, journal={FOOD & FUNCTION}, publisher={Royal Society of Chemistry (RSC)}, author={Hayes, Micaela and Mohamedshah, Zulfiqar and Chadwick-Corbin, Sydney and Hoskin, Roberta and Iorizzo, Massimo and Lila, Mary Ann and Neilson, Andrew P. and Ferruzzi, Mario G.}, year={2022}, month={Mar} }
 @article{lila_hoskin_grace_xiong_strauch_ferruzzi_iorizzo_kay_2022, title={Boosting the Bioaccessibility of Dietary Bioactives by Delivery as Protein-Polyphenol Aggregate Particles}, volume={4}, ISSN={["1520-5118"]}, url={https://doi.org/10.1021/acs.jafc.2c00398}, DOI={10.1021/acs.jafc.2c00398}, abstractNote={Protein-polyphenol aggregate particles concurrently fortify a functional food product with healthy dietary proteins and concentrated polyphenols. However, what impact does ingestion of aggregate particles have on ultimate health relevance of either the polyphenolic molecules in the matrix or the protein molecules? Because human health benefits are contingent on bioavailability after ingestion, the fate of these molecules during transit in the gastrointestinal tract (GIT) will dictate their utility as functional food ingredients. This brief review explores diverse applications of protein-polyphenol particles in the food industry and the bioaccessibility of both bioactive polyphenolic compounds and edible proteins. Evidence to date suggests that complexation of phytoactive polyphenolics effectively enhances their health-relevant impacts, specifically because the phytoactives are protected in the protein matrix during transit in the GIT, allowing intact, non-degraded molecules to reach the colon for catabolism at the gut microbiome level, a prerequisite to realize the health benefits of these active compounds.}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Lila, Mary Ann and Hoskin, Roberta Targino and Grace, Mary H. and Xiong, Jia and Strauch, Renee and Ferruzzi, Mario and Iorizzo, Massimo and Kay, Colin}, year={2022}, month={Apr} }
 @article{rolling_senalik_iorizzo_ellison_van deynze_simon_2022, title={CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)}, volume={2022}, ISSN={["1758-0463"]}, DOI={10.1093/database/baac079}, abstractNote={AbstractCarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research. CarrotOmics was developed using resources available at the MainLab Bioinformatics core (https://www.bioinfo.wsu.edu/) and is implemented using Tripal with Drupal modules. The database delivers access to download or visualize the carrot reference genome with gene predictions, gene annotations and sequence assembly. Other genomic resources include information for 11 224 genetic markers from 73 linkage maps or genotyping-by-sequencing and descriptions of 371 mapped loci. There are records for 1601 Apiales species (or subspecies) and descriptions of 9408 accessions from 11 germplasm collections representing more than 600 of these species. Additionally, 204 Apiales species have phenotypic information, totaling 28 517 observations from 10 041 biological samples. Resources on CarrotOmics are freely available, search functions are provided to find data of interest and video tutorials are available to describe the search functions and genomic tools. CarrotOmics is a timely resource for the Apiaceae research community and for carrot geneticists developing improved cultivars with novel traits addressing challenges including an expanding acreage in tropical climates, an evolving consumer interested in sustainably grown vegetables and a dynamic environment due to climate change. Data from CarrotOmics can be applied in genomic-assisted selection and genetic research to improve basic research and carrot breeding efficiency.Database URLhttps://carrotomics.org/}, journal={DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION}, author={Rolling, William R. and Senalik, Douglas and Iorizzo, Massimo and Ellison, Shelby and Van Deynze, Allen and Simon, Philipp W.}, year={2022}, month={Sep} }
 @article{mengist_grace_mackey_munoz_pucker_bassil_luby_ferruzzi_lila_iorizzo_2022, title={Dissecting the genetic basis of bioactive metabolites and fruit quality traits in blueberries (Vaccinium corymbosum L.)}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.964656}, abstractNote={Blueberry is well-recognized as a healthy fruit with functionality derived largely from anthocyanin and chlorogenic acid. Despite their importance, no study to date has evaluated the genetic basis of these bioactives in blueberries and their relationship with fruit quality traits. Hence, to fill this gap, a mapping population including 196 F1 individuals was phenotyped for anthocyanin and chlorogenic acid concentration and fruit quality traits (titratable acidity, pH, and total soluble solids) over 3 years and data were used for QTL mapping and correlation analysis. Total soluble solids and chlorogenic acid were positively correlated with glycosylated anthocyanin and total anthocyanin, respectively, indicating that parallel selection for these traits is possible. Across all the traits, a total of 188 QTLs were identified on chromosomes 1, 2, 4, 8, 9, 11 and 12. Notably, four major regions with overlapping major-effect QTLs were identified on chromosomes 1, 2, 4 and 8, and were responsible for acylation and glycosylation of anthocyanins in a substrate and sugar donor specific manner. Through comparative transcriptome analysis, multiple candidate genes were identified for these QTLs, including glucosyltransferases and acyltransferases. Overall, the study provides the first insights into the genetic basis controlling anthocyanins accumulation and composition, chlorogenic acid and fruit quality traits, and establishes a framework to advance genetic studies and molecular breeding for anthocyanins in blueberry.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Mengist, Molla Fentie and Grace, Mary H. and Mackey, Ted and Munoz, Bryan and Pucker, Boas and Bassil, Nahla and Luby, Claire and Ferruzzi, Mario and Lila, Mary Ann and Iorizzo, Massimo}, year={2022}, month={Sep} }
 @article{perez_hamparsomian_gonzalez_denoya_dominguez_barboza_iorizzo_simon_vaudagna_cavagnaro_2022, title={Physicochemical properties, degradation kinetics, and antioxidant capacity of aqueous anthocyanin-based extracts from purple carrots compared to synthetic and natural food colorants}, volume={387}, ISSN={["1873-7072"]}, DOI={10.1016/j.foodchem.2022.132893}, abstractNote={As a means to evaluate the potential of carrot anthocyanins as food colorants and nutraceutical agents, we investigated the physicochemical stability and antioxidant capacity of purple carrot extracts under different pH (2.5-7.0) and temperature (4-40 °C) conditions, in comparison to a commercial synthetic (E131) and a natural grape-based (GRP) colorant. During incubation, the colorants were weekly-monitored for various color parameters, concentration of anthocyanins and phenolics, and antioxidant capacity. Carrot colorants were more stable than GRP; and their thermal stability was equal (at 4 °C) or higher than that of E131 (at 25-40 °C). Carrot anthocyanins had lower degradation rate at low pH and temperature, with acylated anthocyanins (AA) being significantly more stable than non-acylated anthocyanins (NAA). Anthocyanins acylated with feruloyl and coumaroyl glycosides were the most stable carrot pigments. The higher stability of carrot colorants is likely due to their richness in AA and -to a lesser extent- copigmentation with other phenolics.}, journal={FOOD CHEMISTRY}, author={Perez, Maria B. and Hamparsomian, Maria J. Da Pena and Gonzalez, Roxana E. and Denoya, Gabriela I. and Dominguez, Deolindo L. E. and Barboza, Karina and Iorizzo, Massimo and Simon, Philipp W. and Vaudagna, Sergio R. and Cavagnaro, Pablo F.}, year={2022}, month={Sep} }
 @article{grace_hoskin_hayes_iorizzo_kay_ferruzzi_lila_2022, title={Spray-dried and freeze-dried protein-spinach particles; effect of drying technique and protein type on the bioaccessibility of carotenoids, chlorophylls, and phenolics}, volume={388}, ISSN={["1873-7072"]}, DOI={10.1016/j.foodchem.2022.133017}, abstractNote={The effects of protein carrier and drying technique on the concentration and bioaccessibility of lipophilic compounds (lutein, β-carotene, chlorophylls a and b) and hydrophilic flavonoids in freeze-dried (FD) or spray-dried (SD) spinach juice and protein-spinach particles were investigated. Carotenoid and chlorophyll contents were highest in FD spinach juice without protein (147 and 1355 mg/100 g, respectively). For both SD and FD protein-spinach particles, SPI best protected carotenoids and chlorophylls (123 and 1160 mg/g, respectively), although the bioaccessibility of lipophilic compounds in WPI particles was higher than SPI particles (p < 0.05). For flavonoids, the drying technique was more important than the type of carrier, since FD particles had higher total flavonoids than SD. However, SD particles had higher bioaccessibility for most flavonoids (40-90 %) compared to FD (<20 %). The drying method and protein carrier can be designed to produce protein-spinach ingredients with desired concentration of compounds and bioaccessibility.}, journal={FOOD CHEMISTRY}, author={Grace, Mary H. and Hoskin, Roberta T. and Hayes, Micaela and Iorizzo, Massimo and Kay, Colin and Ferruzzi, Mario G. and Lila, Mary Ann}, year={2022}, month={Sep} }
 @article{edger_iorizzo_bassil_benevenuto_ferrao_giongo_hummer_lawas_leisner_li_et al._2022, title={There and back again; historical perspective and future directions for Vaccinium breeding and research studies}, volume={9}, ISSN={["2052-7276"]}, DOI={10.1093/hr/uhac083}, abstractNote={Abstract
               The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops’ relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.}, journal={HORTICULTURE RESEARCH}, author={Edger, Patrick P. and Iorizzo, Massimo and Bassil, Nahla V and Benevenuto, Juliana and Ferrao, Luis Felipe V and Giongo, Lara and Hummer, Kim and Lawas, Lovely Mae F. and Leisner, Courtney P. and Li, Changying and et al.}, year={2022}, month={Jan} }
 @article{hulse-kemp_bostan_chen_ashrafi_stoffel_sanseverino_li_cheng_schatz_garvin_et al._2021, title={An anchored chromosome-scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids}, volume={6}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20101}, abstractNote={AbstractSpinach (Spinacia oleracea L.) is a member of the Caryophyllales family, a basal eudicot asterid that consists of sugar beet (Beta vulgaris L. subsp. vulgaris), quinoa (Chenopodium quinoa Willd.), and amaranth (Amaranthus hypochondriacus L.). With the introduction of baby leaf types, spinach has become a staple food in many homes. Production issues focus on yield, nitrogen‐use efficiency and resistance to downy mildew (Peronospora effusa). Although genomes are available for the above species, a chromosome‐level assembly exists only for quinoa, allowing for proper annotation and structural analyses to enhance crop improvement. We independently assembled and annotated genomes of the cultivar Viroflay using short‐read strategy (Illumina) and long‐read strategies (Pacific Biosciences) to develop a chromosome‐level, genetically anchored assembly for spinach. Scaffold N50 for the Illumina assembly was 389 kb, whereas that for Pacific BioSciences was 4.43 Mb, representing 911 Mb (93% of the genome) in 221 scaffolds, 80% of which are anchored and oriented on a sequence‐based genetic map, also described within this work. The two assemblies were 99.5% collinear. Independent annotation of the two assemblies with the same comprehensive transcriptome dataset show that the quality of the assembly directly affects the annotation with significantly more genes predicted (26,862 vs. 34,877) in the long‐read assembly. Analysis of resistance genes confirms a bias in resistant gene motifs more typical of monocots. Evolutionary analysis indicates that Spinacia is a paleohexaploid with a whole‐genome triplication followed by extensive gene rearrangements identified in this work. Diversity analysis of 75 lines indicate that variation in genes is ample for hypothesis‐driven, genomic‐assisted breeding enabled by this work.}, journal={PLANT GENOME}, author={Hulse-Kemp, Amanda M. and Bostan, Hamed and Chen, Shiyu and Ashrafi, Hamid and Stoffel, Kevin and Sanseverino, Walter and Li, Linzhou and Cheng, Shifeng and Schatz, Michael C. and Garvin, Tyler and et al.}, year={2021}, month={Jun} }
 @article{diaz-garcia_garcia-ortega_gonzalez-rodriguez_delaye_iorizzo_zalapa_2021, title={Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.633310}, abstractNote={The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Diaz-Garcia, Luis and Garcia-Ortega, Luis Fernando and Gonzalez-Rodriguez, Maria and Delaye, Luis and Iorizzo, Massimo and Zalapa, Juan}, year={2021}, month={Feb} }
 @article{giongo_ajelli_pottorff_perkins-veazie_iorizzo_2022, title={Comparative multi-parameters approach to dissect texture subcomponents of highbush blueberry cultivars at harvest and postharvest}, volume={183}, ISSN={["1873-2356"]}, DOI={10.1016/j.postharvbio.2021.111696}, abstractNote={Fruit texture and firmness are important cues of blueberry quality for the fresh market. These attributes contribute to consumer acceptance, resistance to bruising during harvesting and transportation, and shelf-life. Thus, fruit firmness and texture are major priorities for blueberry breeders, producers and distributors. In this study, the discriminative power of texture analysis was examined using penetration tests with different probes and double compression for texture profile analysis (TPA). Mechanical parameters taken from the force deformation curves used to dissect texture subcomponents in blueberries that are associated with specific tissue layers. Principal component analysis (PCA) allows to filter and identify mechanical parameters that significantly discern the most variation amongst 24 blueberry genotypes and showed that texture in this crop is multi-trait and cultivar-dependent. Texture analysis was used also on blueberries stored over six weeks to identify mechanical parameters that could be used as predictors for long shelf life. Additionally, the mechanical parameters were correlated with dynamometer data to determine the utility and accuracy of a simple handheld device to measure fruit firmness in blueberries. This study provides a framework for the identification and characterization of the subcomponents of texture in highbush blueberry.}, journal={POSTHARVEST BIOLOGY AND TECHNOLOGY}, author={Giongo, Lara and Ajelli, Matteo and Pottorff, Marti and Perkins-Veazie, Penelope and Iorizzo, Massimo}, year={2022}, month={Jan} }
 @article{bannoud_carvajal_ellison_senalik_gomez talquenca_iorizzo_simon_cavagnaro_2021, title={Genetic and Transcription Profile Analysis of Tissue-Specific Anthocyanin Pigmentation in Carrot Root Phloem}, volume={12}, ISSN={["2073-4425"]}, DOI={10.3390/genes12101464}, abstractNote={In purple carrots, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns. Within the phloem, purple pigmentation can be found in the outer phloem (OP) (also called the cortex) and inner phloem (IP), or it can be confined exclusively to the OP. In this work, the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root OP and IP tissues was investigated by means of linkage mapping and transcriptome (RNA-seq) and phylogenetic analyses; followed by gene expression (RT-qPCR) evaluations in two genetic backgrounds, an F2 population (3242) and the inbred B7262. Genetic mapping of ‘root outer phloem anthocyanin pigmentation’ (ROPAP) and inner phloem pigmentation (RIPAP) revealed colocalization of ROPAP with the P1 and P3 genomic regions previously known to condition pigmentation in different genetic stocks, whereas RIPAP co-localized with P3 only. Transcriptome analysis of purple OP (POP) vs. non-purple IP (NPIP) tissues, along with linkage and phylogenetic data, allowed an initial identification of 28 candidate genes, 19 of which were further evaluated by RT-qPCR in independent root samples of 3242 and B7262, revealing 15 genes consistently upregulated in the POP in both genetic backgrounds, and two genes upregulated in the POP in specific backgrounds. These include seven transcription factors, seven anthocyanin structural genes, and two genes involved in cellular transport. Altogether, our results point at DcMYB7, DcMYB113, and a MADS-box (DCAR_010757) as the main candidate genes conditioning ROPAP in 3242, whereas DcMYB7 and MADS-box condition RIPAP in this background. In 7262, DcMYB113 conditions ROPAP.}, number={10}, journal={GENES}, author={Bannoud, Florencia and Carvajal, Sofia and Ellison, Shelby and Senalik, Douglas and Gomez Talquenca, Sebastian and Iorizzo, Massimo and Simon, Philipp W. and Cavagnaro, Pablo F.}, year={2021}, month={Oct} }
 @article{qi_ogden_bostan_sargent_ward_gilbert_iorizzo_rowland_2021, title={High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population}, volume={12}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2021.692628}, abstractNote={Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowiiFla4B × diploidV. corymbosumW85–20) with the parent W85–23 (diploidV. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Qi, Xinpeng and Ogden, Elizabeth L. and Bostan, Hamed and Sargent, Daniel J. and Ward, Judson and Gilbert, Jessica and Iorizzo, Massimo and Rowland, Lisa J.}, year={2021}, month={Jun} }
 @article{mengist_bostan_young_kay_gillitt_ballington_kay_ferruzzi_ashrafi_lila_et al._2021, title={High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry}, volume={8}, ISSN={["2052-7276"]}, url={https://doi.org/10.1038/s41438-021-00605-z}, DOI={10.1038/s41438-021-00605-z}, abstractNote={AbstractFruit quality traits play a significant role in consumer preferences and consumption in blueberry (Vaccinium corymbosumL). The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry. A total of 287 F1individuals derived from a cross between two southern highbush blueberry cultivars, ‘Reveille’ and ‘Arlen’, were phenotyped over three years (2016–2018) for fruit quality-related traits, including titratable acidity, pH, total soluble solids, and fruit weight. A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers. The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM. The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits, including seven loci for fruit weight, three loci for titratable acidity, five loci for pH, and three loci for total soluble solids. Ten of these loci were detected in more than one year. These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid, and 8–13% for pH. However, the loci identified for fruit weight did not explain more than 10% of the phenotypic variance. We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits. Organic acids, citric acid, and quinic acid were significantly (P < 0.05) and positively correlated with titratable acidity. Sugar molecules showed a strong and positive correlation with total soluble solids. Overall, the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.}, number={1}, journal={HORTICULTURE RESEARCH}, author={Mengist, Molla F. and Bostan, Hamed and Young, Elisheba and Kay, Kristine L. and Gillitt, Nicholas and Ballington, James and Kay, Colin D. and Ferruzzi, Mario G. and Ashrafi, Hamid and Lila, Mary Ann and et al.}, year={2021}, month={Dec} }
 @article{yow_bostan_castanera_ruggieri_mengist_curaba_young_gillitt_iorizzo_2022, title={Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family}, volume={13}, ISSN={["2073-4425"]}, url={https://doi.org/10.3390/genes13010052}, DOI={10.3390/genes13010052}, abstractNote={Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.}, number={1}, journal={GENES}, author={Yow, Ashley G. and Bostan, Hamed and Castanera, Raul and Ruggieri, Valentino and Mengist, Molla F. and Curaba, Julien and Young, Roberto and Gillitt, Nicholas and Iorizzo, Massimo}, year={2022}, month={Jan} }
 @article{kulkarni_vorsa_natarajan_elavarthi_iorizzo_reddy_melmaiee_2021, title={Admixture Analysis Using Genotyping-by-Sequencing Reveals Genetic Relatedness and Parental Lineage Distribution in Highbush Blueberry Genotypes and Cross Derivatives}, volume={22}, ISSN={["1422-0067"]}, DOI={10.3390/ijms22010163}, abstractNote={Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single-nucleotide polymorphisms, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.}, number={1}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Kulkarni, Krishnanand P. and Vorsa, Nicholi and Natarajan, Purushothaman and Elavarthi, Sathya and Iorizzo, Massimo and Reddy, Umesh K. and Melmaiee, Kalpalatha}, year={2021}, month={Jan} }
 @misc{iorizzo_curaba_pottorff_ferruzzi_simon_cavagnaro_2020, title={Carrot Anthocyanins Genetics and Genomics: Status and Perspectives to Improve Its Application for the Food Colorant Industry}, volume={11}, ISSN={["2073-4425"]}, DOI={10.3390/genes11080906}, abstractNote={Purple or black carrots (Daucus carota ssp. sativus var. atrorubens Alef) are characterized by their dark purple- to black-colored roots, owing their appearance to high anthocyanin concentrations. In recent years, there has been increasing interest in the use of black carrot anthocyanins as natural food dyes. Black carrot roots contain large quantities of mono-acylated anthocyanins, which impart a measure of heat-, light- and pH-stability, enhancing the color-stability of food products over their shelf-life. The genetic pathway controlling anthocyanin biosynthesis appears well conserved among land plants; however, different variants of anthocyanin-related genes between cultivars results in tissue-specific accumulations of purple pigments. Thus, broad genetic variations of anthocyanin profile, and tissue-specific distributions in carrot tissues and organs, can be observed, and the ratio of acylated to non-acylated anthocyanins varies significantly in the purple carrot germplasm. Additionally, anthocyanins synthesis can also be influenced by a wide range of external factors, such as abiotic stressors and/or chemical elicitors, directly affecting the anthocyanin yield and stability potential in food and beverage applications. In this study, we critically review and discuss the current knowledge on anthocyanin diversity, genetics and the molecular mechanisms controlling anthocyanin accumulation in carrots. We also provide a view of the current knowledge gaps and advancement needs as regards developing and applying innovative molecular tools to improve the yield, product performance and stability of carrot anthocyanin for use as a natural food colorant.}, number={8}, journal={GENES}, author={Iorizzo, Massimo and Curaba, Julien and Pottorff, Marti and Ferruzzi, Mario G. and Simon, Philipp and Cavagnaro, Pablo F.}, year={2020}, month={Aug} }
 @article{mengist_burtch_debelo_pottorff_bostan_nunn_corbin_kay_bassil_hummer_et al._2020, title={Development of a genetic framework to improve the efficiency of bioactive delivery from blueberry}, volume={10}, ISSN={["2045-2322"]}, url={https://europepmc.org/articles/PMC7560831}, DOI={10.1038/s41598-020-74280-w}, abstractNote={AbstractIn the present study, we applied a novel high-throughput in vitro gastrointestinal digestion model to phenotype bioaccessibility of phenolics in a diverse germplasm collection representing cultivated highbush blueberries. Results revealed significant (P < 0.05) differences between accessions, years, and accession by year interaction for relative and absolute bioaccessibility of flavonoids and phenolic acids. Broad sense heritability estimates revealed low to moderate inheritances of relative and absolute bioaccessibility, suggesting that besides environmental variables, genetics factors could control bioaccessibility of phenolics. Acylated anthocyanins had significantly higher relative bioaccessibility than non-acylated anthocyanins. Correlation analysis indicated that relative bioaccessibility did not show significant association with fruit quality or raw concentration of metabolites. The study also identified accessions that have high relative and absolute bioaccessibility values. Overall, combining the bioaccessibility of phenolics with genetic and genomic approaches will enable the identification of genotypes and genetic factors influencing these traits in blueberry.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Mengist, Molla F. and Burtch, Haley and Debelo, Hawi and Pottorff, Marti and Bostan, Hamed and Nunn, Candace and Corbin, Sydney and Kay, Colin D. and Bassil, Nahla and Hummer, Kim and et al.}, year={2020}, month={Oct} }
 @article{farneti_emanuelli_giongo_toivonen_iorizzo_folta_finn_2020, title={Editorial: Interdisciplinary Approaches to Improve Quality of Soft Fruit Berries}, volume={11}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2020.592222}, abstractNote={1 Genomics and Biology of Fruit Crop Department, Fondazione Edmund Mach, San Michele all’Adige, Italy, 2 Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada, 3 Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States, 4 Horticultural Sciences Department, University of Florida, Gainesville, FL, United States, 5 Horticultural Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States}, journal={FRONTIERS IN PLANT SCIENCE}, author={Farneti, Brian and Emanuelli, Francesco and Giongo, Lara and Toivonen, Peter and Iorizzo, Massimo and Folta, Kevin and Finn, Chad}, year={2020}, month={Sep} }
 @article{curaba_bostan_cavagnaro_senalik_mengist_zhao_simon_iorizzo_2020, title={Identification of an SCPL Gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root}, volume={10}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2019.01770}, abstractNote={Anthocyanins are natural health promoting pigments that can be produced in large quantities in some purple carrot cultivars. Decoration patterns of anthocyanins, such as acylation, can greatly influence their stability and biological properties and use in the food industry as nutraceuticals and natural colorants. Despite recent advances made toward understanding the genetic control of anthocyanin accumulation in purple carrot, the genetic mechanism controlling acylation of anthocyanin in carrot root have not been studied yet. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify the genetic factor conditioning the accumulation of non-acylated (Cy3XGG) versus acylated (Cy3XFGG and Cy3XSGG) cyanidin derivatives, in three carrot populations. Segregation and mapping analysis pointed to a single gene with dominant effect controlling anthocyanin acylation in the root, located in a 576kb region containing 29 predicted genes. Orthologous and phylogenetic analyses enabled the identification of a cluster of three SCPL-acyltransferases coding genes within this region. Comparative transcriptome analysis indicated that only one of these three genes, DcSCPL1, was always expressed in association with anthocyanin pigmentation in the root and was co-expressed with DcMYB7, a gene known to activate anthocyanin biosynthetic genes in carrot. DcSCPL1 sequence analysis, in root tissue containing a low level of acylated anthocyanins, demonstrated the presence of an insertion causing an abnormal splicing of the 3rd exon during mRNA editing, likely resulting in the production of a non-functional acyltransferase and explaining the reduced acylation phenotype. This study provides strong linkage-mapping and functional evidences for the candidacy of DcSCPL1 as a primary regulator of anthocyanin acylation in carrot storage root.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Curaba, Julien and Bostan, Hamed and Cavagnaro, Pablo F. and Senalik, Douglas and Mengist, Molla Fentie and Zhao, Yunyang and Simon, Philipp W. and Iorizzo, Massimo}, year={2020}, month={Jan} }
 @article{iorizzo_cavagnaro_bostan_zhao_zhang_simon_2019, title={A Cluster of MYB Transcription Factors Regulates Anthocyanin Biosynthesis in Carrot (Daucus carota L.) Root and Petiole}, volume={9}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2018.01927}, abstractNote={Purple carrots can accumulate large quantities of anthocyanins in their roots and –in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these “root pigmentation” regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Iorizzo, Massimo and Cavagnaro, Pablo F. and Bostan, Hamed and Zhao, Yunyang and Zhang, Jianhui and Simon, Philipp W.}, year={2019}, month={Jan} }
 @article{cavagnaro_iorizzo_2019, title={Carrot Anthocyanin Diversity, Genetics, and Genomics}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_15}, abstractNote={Purple carrots (Daucus carota ssp. sativus var. atrorubens Alef.) accumulate anthocyanins in their roots, petioles, and other plant parts. These flavonoid pigments represent an excellent dietary source of antioxidant and anti-inflammatory agents. In addition, carrot anthocyanins are also used as food dyes. Compositional variation in carrot root, mainly with regard to the content of acylated (AA) and non-acylated anthocyanins (NAA), strongly influences the bioavailability and chemical stability of these pigments, therefore conditioning their potential use as nutraceutical agents or as food colorants. In this context, genetic diversity analysis for root anthocyanin composition is relevant for selecting materials for either purpose. Also, knowledge on the genetic basis underlying anthocyanin biosynthesis and modification is expected to aid in the development of new varieties with high nutraceutical or for extracting food dyes. In the last decades, germplasm collections have been characterized for anthocyanin content and composition. Various simply inherited traits for root and petiole anthocyanin pigmentation and acylation, including P1, P3 and Raa1, and QTL for root anthocyanins, have been described and mapped to two regions of chromosome 3, in different genetic backgrounds. Recent advances in high-throughput sequencing and bioinformatic analyses have facilitated the discovery of candidate regulatory genes for root and petiole pigmentation associated with the P3 region in chromosome 3, as well as structural genes involved in anthocyanin glycosylation and acylation. In this chapter, we reviewed recent advances in diversity, genetic, and genomic studies related to carrot anthocyanin pigmentation.}, journal={CARROT GENOME}, author={Cavagnaro, Pablo F. and Iorizzo, Massimo}, year={2019}, pages={261–277} }
 @article{simon_geoffriau_ellison_iorizzo_2019, title={Carrot Carotenoid Genetics and Genomics}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_14}, abstractNote={Carotenoids are essential for photosynthesis, and they are the ultimate source of all dietary vitamin A. They account for the striking diversity of orange, yellow, and red carrot storage root color, and this likely contributes to the fact that carotenoids are the most extensively studied class of compounds in carrot, where their biosynthesis and accumulation have been evaluated across diverse genetic backgrounds and environments. Many genes in the 2-C-methyl-D-erythritol-4-phosphate pathway (MEP) and carotenoid biosynthetic pathways have been identified and characterized in carrot, and genes in those pathways are expressed in carrot roots of all colors, including white carrots which contain at most trace amounts of carotenoids. The active functioning of genes in the carotenoid pathway in carrot roots of all colors should be expected since pathway products serve as precursors for hormones important in plant development. 1-Deoxy-d-xylulose-5-phosphate synthase (DXS) in the MEP pathway and the phytoene synthase and lycopene β-cyclase (PSY, LCYB) genes in the carotenoid pathway provide some level of overall regulation or modulation of these respective pathways, and these genes are incrementally upregulated in carrots with higher carotenoid content but variation in their expression does not account for the diverse content and composition of carotenoids in different colors of carrots. In contrast, genetic polymorphism in the Y and Y2 genes accounts for much for the variation in carotenoids accumulated in white, yellow, and orange carrots, and with the sequencing of the carrot genome, the genetic basis for these genes is becoming revealed. A candidate for the Y gene, DCAR_032551, is not a member of either the MEP or carotenoid biosynthesis pathway but rather a regulator of photosystem development and carotenoid storage. A clear candidate for the Y2 gene has not been identified, but no carotenoid biosynthetic gene was found in the genomic region defined by fine mapping of Y2. The Or gene, which regulates chromoplast development in other crops, was also recently associated with the presence of carotenoids in carrot. The discovery of genes outside the carotenoid biosynthetic pathway that contributes to carotenoid colors of carrots is but one exciting consequence of sequencing the carrot genome.}, journal={CARROT GENOME}, author={Simon, Philipp W. and Geoffriau, Emmanuel and Ellison, Shelby and Iorizzo, Massimo}, year={2019}, pages={247–260} }
 @article{bostan_senalik_simon_iorizzo_2019, title={Carrot Genetics, Omics and Breeding Toolboxes}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_13}, abstractNote={Today, researchers routinely generate and analyze large and complex omics, genetics and breeding datasets for both model and nonmodel crop species including carrot. This has resulted in the massive production and availability of omics data, which opened multiple challenges to store, organize and make those data available to the research and breeding communities. The value of these resources increases significantly when it is organized, annotated, effectively integrated with other data and made available to browse, query and analyze. In this chapter, we summarize the available omics, genetics and breeding resources for carrot and other Daucus species in different public and private databases. We also discuss the challenges for collecting, integrating and interpreting this data with a focus on the lack of dedicated, centralized and user-friendly bioinformatics platforms, breeding toolboxes and infrastructures for the carrot genome.}, journal={CARROT GENOME}, author={Bostan, Hamed and Senalik, Douglas and Simon, Philipp W. and Iorizzo, Massimo}, year={2019}, pages={225–245} }
 @article{iorizzo_ellison_pottorff_cavagnaro_2019, title={Carrot Molecular Genetics and Mapping}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_7}, abstractNote={Carrot (Daucus carota L.) is an important root vegetable crop that is consumed worldwide and is appreciated for its taste and nutritional content (e.g., provitamin A carotenoids, anthocyanins, vitamins, and other minerals). Carrot genetic research has improved vastly over the past few decades due to advancements in molecular genomic resources developed for carrot. The increasing availability of DNA sequences such as expressed sequence tags (ESTs), creation of a physical map, sequencing of the carrot genome, and the numerous advancements in DNA genotyping has enabled the study of phenotypic variation of crop traits through the development of genetic linkage maps, which enable the ability to identify QTLs and their underlying genetic basis. In addition, the creation of genetic and genomic tools for carrot has enabled the study of diversity within carrot populations and germplasm collections, enabled genome-wide association studies (GWASs), characterization of populations at the species level, and comparative genomics with other crops and model species. Combined, these tools will advance the breeding process for carrot by enabling a targeted approach to improving traits by utilizing marker-assisted selection (MAS) strategies.}, journal={CARROT GENOME}, author={Iorizzo, Massimo and Ellison, Shelby and Pottorff, Marti and Cavagnaro, Pablo F.}, year={2019}, pages={101–117} }
 @article{spooner_simon_senalik_iorizzo_2019, title={Carrot Organelle Genomes: Organization, Diversity, and Inheritance}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_12}, abstractNote={Cultivated carrot (Daucus carota subsp. sativus) is one of about 25–40 related wild species in the genus Daucus depending on the classification. It is part of a widely distributed and taxonomically complex family Apiaceae (Umbelliferae) containing 466 genera and 3820 species that is one of the largest families of seed plants. Members of the Apiaceae, particularly the genus Daucus, have been the subject of intensive recent molecular studies on the structure and genetics of plastids and mitochondria. This chapter summarizes organellar (plastids and mitochondria) structure, function, mutational rates, and inter-organelle DNA transfer in the Apiaceae and inheritance in the genus Daucus, with a wider focus on the Apiaceae and the sister family Araliaceae, and places these data in the context of other studies in the angiosperms.}, journal={CARROT GENOME}, author={Spooner, David M. and Simon, Philipp W. and Senalik, Douglas and Iorizzo, Massimo}, year={2019}, pages={205–223} }
 @article{bannoud_ellison_paolinelli_horejsi_senalik_fanzone_iorizzo_simon_cavagnaro_2019, title={Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.)}, volume={132}, ISSN={["1432-2242"]}, DOI={10.1007/s00122-019-03366-5}, abstractNote={Inheritance, QTL mapping, phylogenetic, and transcriptome (RNA-Seq) analyses provide insight into the genetic control underlying carrot root and leaf tissue-specific anthocyanin pigmentation and identify candidate genes for root phloem pigmentation. Purple carrots can accumulate large quantities of anthocyanins in their root tissues, as well as in other plant parts. This work investigated the genetic control underlying tissue-specific anthocyanin pigmentation in the carrot root phloem and xylem, and in leaf petioles. Inheritance of anthocyanin pigmentation in these three tissues was first studied in segregating F 2  and F 4  populations, followed by QTL mapping of phloem and xylem anthocyanin pigments (independently) onto two genotyping by sequencing-based linkage maps, to reveal two regions in chromosome 3, namely P 1  and P 3 , controlling pigmentation in these three tissues. Both P 1  and P 3  condition pigmentation in the phloem, with P 3  also conditioning pigmentation in the xylem and petioles. By means of linkage mapping, phylogenetic analysis, and comparative transcriptome (RNA-Seq) analysis among carrot roots with differing purple pigmentation phenotypes, we identified candidate genes conditioning pigmentation in the phloem, the main tissue influencing total anthocyanin levels in the root. Among them, a MYB transcription factor, DcMYB7, and two cytochrome CYP450 genes with putative flavone synthase activity were identified as candidates regulating both the presence/absence of pigmentation and the concentration of anthocyanins in the root phloem. Concomitant expression patterns of DcMYB7 and eight anthocyanin structural genes were found, suggesting that DcMYB7 regulates transcription levels in the latter. Another MYB, DcMYB6, was upregulated in specific purple-rooted samples, suggesting a genotype-specific regulatory activity for this gene. These data contribute to the understanding of anthocyanin regulation in the carrot root at a tissue-specific level and maybe instrumental for improving carrot nutritional value.}, number={9}, journal={THEORETICAL AND APPLIED GENETICS}, author={Bannoud, Florencia and Ellison, Shelby and Paolinelli, Marcos and Horejsi, Thomas and Senalik, Douglas and Fanzone, Martin and Iorizzo, Massimo and Simon, Philipp W. and Cavagnaro, Pablo F.}, year={2019}, month={Sep}, pages={2485–2507} }
 @article{iorizzo_macko-podgorni_senalik_van deynze_simon_2019, title={The Carrot Nuclear Genome and Comparative Analysis}, ISBN={["978-3-030-03388-0"]}, ISSN={["2199-479X"]}, DOI={10.1007/978-3-030-03389-7_11}, abstractNote={The first draft of the carrot genome of an orange inbred line, “DC-27,” was published in 2014. However, the genome assembly was fragmented and not assembled to the chromosome level, which limited its application for comprehensive genetic and genomic analyses. In 2016, a high-quality chromosome level, genome assembly of a doubled-haploid orange carrot DH1 was published, which rapidly advanced carrot genetic and genomic studies. The sequenced genome enabled the ability to identify candidate genes underlying important agronomic and nutrition-related traits such as root development, the accumulation of terpenoids, β-carotenes, and anthocyanins. Genome-level contributions include the clarification of phylogenetic relationships within carrot germplasm and the elucidation of the evolutionary history within the Euasterid II and Euasterid I clades. In this chapter, a description of the history of efforts made to characterize the carrot genome in the pre- and post-genomic era and the partners involved in the development of the high-quality carrot genome assembly are also described.}, journal={CARROT GENOME}, author={Iorizzo, Massimo and Macko-Podgorni, Alicja and Senalik, Douglas and Van Deynze, Allen and Simon, Philipp W.}, year={2019}, pages={187–204} }
 @article{strauch_mengist_pan_yousef_iorizzo_brown_lila_2019, title={Variation in anthocyanin profiles of 27 genotypes of red cabbage over two growing seasons}, volume={301}, ISSN={["1873-7072"]}, url={https://doi.org/10.1016/j.foodchem.2019.125289}, DOI={10.1016/j.foodchem.2019.125289}, abstractNote={Acylated anthocyanins, such as those found in red cabbage, are more heat-, light-, and alkaline pH-stable than non-acylated anthocyanins, making them attractive for a variety of commercial applications. A UPLC-DAD-MSE method with an optimized chromatographic strategy was used to identify 29 red cabbage anthocyanins, predominantly acylated and glucosylated cyanidin derivatives. Anthocyanin profiles of 27 red cabbage genotypes harvested in consecutive growing seasons were measured and assessed for variation. Three unique anthocyanin profile fingerprints were identified through hierarchical clustering analysis. PCA analysis identified anthocyanin accumulation traits and genotypes with high diversity which can be utilized in future investigations into the genetic and molecular basis for anthocyanin production, acylation, and diversity.}, journal={FOOD CHEMISTRY}, publisher={Elsevier BV}, author={Strauch, Renee C. and Mengist, Molla F. and Pan, Kevin and Yousef, Gad G. and Iorizzo, Massimo and Brown, Allan F. and Lila, Mary Ann}, year={2019}, month={Dec} }
 @article{villano_esposito_carucci_iorizzo_frusciante_carputo_aversano_2019, title={High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding}, volume={39}, ISSN={1380-3743 1572-9788}, url={http://dx.doi.org/10.1007/S11032-018-0912-0}, DOI={10.1007/s11032-018-0912-0}, number={1}, journal={Molecular Breeding}, publisher={Springer Science and Business Media LLC}, author={Villano, Clizia and Esposito, Salvatore and Carucci, Francesca and Iorizzo, Massimo and Frusciante, Luigi and Carputo, Domenico and Aversano, Riccardo}, year={2019}, month={Jan} }
 @article{macko-podgorni_machaj_stelmach_senalik_grzebelus_iorizzo_simon_grzebelus_2017, title={Characterization of a Genomic Region under Selection in Cultivated Carrot (Daucus carota subsp sativus) Reveals a Candidate Domestication Gene}, volume={8}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2017.00012}, abstractNote={Carrot is one of the most important vegetables worldwide, owing to its capability to develop fleshy, highly nutritious storage roots. It was domesticated ca. 1,100 years ago in Central Asia. No systematic knowledge about the molecular mechanisms involved in the domestication syndrome in carrot are available, however, the ability to form a storage root is undoubtedly the essential transition from the wild Daucus carota to the cultivated carrot. Here, we expand on the results of a previous study which identified a polymorphism showing a significant signature for selection upon domestication. We mapped the region under selection to the distal portion of the long arm of carrot chromosome 2, confirmed that it had been selected, as reflected in both the lower nucleotide diversity in the cultivated gene pool, as compared to the wild (πw/πc = 7.4 vs. 1.06 for the whole genome), and the high FST (0.52 vs. 0.12 for the whole genome). We delimited the region to ca. 37 kb in length and identified a candidate domestication syndrome gene carrying three non-synonymous single nucleotide polymorphisms and one indel systematically differentiating the wild and the cultivated accessions. This gene, DcAHLc1, belongs to the AT-hook motif nuclear localized (AHL) family of plant regulatory genes which are involved in the regulation of organ development, including root tissue patterning. AHL genes work through direct interactions with other AHL family proteins and a range of other proteins that require intercellular protein movement. Based on QTL data on root thickening we speculate that DcAHLc1 might be involved in the development of the carrot storage root, as the localization of the gene overlapped with one of the QTLs. According to haplotype information we propose that the ‘cultivated’ variant of DcAHLc1 has been selected from wild Central Asian carrot populations upon domestication and it is highly predominant in the western cultivated carrot gene pool. However, some primitive eastern landraces and the derived B7262 purple inbred line still carry the ‘wild’ variant, reflecting a likely complexity of the genetic determination of the formation of carrot storage roots.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Macko-Podgorni, Alicja and Machaj, Gabriela and Stelmach, Katarzyna and Senalik, Douglas and Grzebelus, Ewa and Iorizzo, Massimo and Simon, Philipp W. and Grzebelus, Dariusz}, year={2017}, month={Jan} }
 @article{schlautman_covarrubias-pazaran_diaz-garcia_iorizzo_polashock_grygleski_vorsa_zalapa_2017, title={Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping}, volume={7}, ISSN={["2160-1836"]}, DOI={10.1534/g3.116.037556}, abstractNote={AbstractThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.}, number={4}, journal={G3-GENES GENOMES GENETICS}, author={Schlautman, Brandon and Covarrubias-Pazaran, Giovanny and Diaz-Garcia, Luis and Iorizzo, Massimo and Polashock, James and Grygleski, Edward and Vorsa, Nicholi and Zalapa, Juan}, year={2017}, month={Apr}, pages={1177–1189} }
 @article{spooner_ruess_iorizzo_senalik_simon_2017, title={Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid(1)}, volume={104}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.1600415}, abstractNote={PREMISE OF THE STUDY:We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences.METHODS:We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP).KEY RESULTS:Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations.CONCLUSIONS:Our data have allowed us to (1) produce a well‐resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.}, number={2}, journal={AMERICAN JOURNAL OF BOTANY}, author={Spooner, David M. and Ruess, Holly and Iorizzo, Massimo and Senalik, Douglas and Simon, Philipp}, year={2017}, month={Feb}, pages={296–312} }
 @article{ellison_senalik_bostan_iorizzo_simon_2017, title={Fine Mapping, Transcriptome Analysis, and Marker Development for Y-2, the Gene That Conditions beta-Carotene Accumulation in Carrot (Daucus carota L.)}, volume={7}, ISSN={["2160-1836"]}, DOI={10.1534/g3.117.043067}, abstractNote={Abstract
               Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y2 locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y2. Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot.}, number={8}, journal={G3-GENES GENOMES GENETICS}, author={Ellison, Shelby and Senalik, Douglas and Bostan, Hamed and Iorizzo, Massimo and Simon, Philipp}, year={2017}, month={Aug}, pages={2665–2675} }
 @article{iorizzo_ellison_senalik_zeng_satapoomin_huang_bowman_iovene_sanseverino_cavagnaro_et al._2016, title={A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution}, volume={48}, ISSN={["1546-1718"]}, DOI={10.1038/ng.3565}, abstractNote={Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events. We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.}, number={6}, journal={NATURE GENETICS}, publisher={Springer Nature}, author={Iorizzo, Massimo and Ellison, Shelby and Senalik, Douglas and Zeng, Peng and Satapoomin, Pimchanok and Huang, Jiaying and Bowman, Megan and Iovene, Marina and Sanseverino, Walter and Cavagnaro, Pablo and et al.}, year={2016}, month={Jun}, pages={657-+} }
 @article{covarrubias-pazaran_diaz-garcia_schlautman_deutsch_salazar_hernandez-ochoa_grygleski_steffan_iorizzo_polashock_et al._2016, title={Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping}, volume={17}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-016-2802-3}, abstractNote={The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS).}, journal={BMC GENOMICS}, author={Covarrubias-Pazaran, Giovanny and Diaz-Garcia, Luis and Schlautman, Brandon and Deutsch, Joseph and Salazar, Walter and Hernandez-Ochoa, Miguel and Grygleski, Edward and Steffan, Shawn and Iorizzo, Massimo and Polashock, James and et al.}, year={2016}, month={Jun} }
 @article{mandel_ramsey_iorizzo_simon_2016, title={Patterns of Gene Flow between Crop and Wild Carrot, Daucus carota (Apiaceae) in the United States}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0161971}, abstractNote={Studies of gene flow between crops and their wild relatives have implications for both management practices for cultivation and understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene flow for wild relatives of crop species. Moreover, the comparison of genetic markers with different modes of inheritance, or transmission, such as those of the nuclear and chloroplast genomes, can inform the relative risk of transgene escape via pollen versus seed. Here we investigate patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in two regions of the United States. We employed 15 nuclear simple sequence repeat (SSR) markers and one polymorphic chloroplast marker. Further, we utilized both conventional population genetic metrics along with Shannon diversity indices as the latter have been proposed to be more sensitive to allele frequency changes and differentiation. We found that populations in both regions that were proximal to crop fields showed lower levels of differentiation to the crops than populations that were located farther away. We also found that Shannon measures were more sensitive to differences in both genetic diversity and differentiation in our study. Finally, we found indirect evidence of paternal transmission of chloroplast DNA and accompanying lower than expected levels of chloroplast genetic structure amongst populations as might be expected if chloroplast DNA genes flow through both seed and pollen. Our findings of substantial gene flow for both nuclear and chloroplast markers demonstrate the efficiency of both pollen and seed to transfer genetic information amongst populations of carrot.}, number={9}, journal={PLOS ONE}, author={Mandel, Jennifer R. and Ramsey, Adam J. and Iorizzo, Massimo and Simon, Philipp W.}, year={2016}, month={Sep} }
 @article{villano_miraglia_iorizzo_aversano_carputo_2016, title={Combined Use of Molecular Markers and High-Resolution Melting (HRM) to Assess Chromosome Dosage in Potato Hybrids}, volume={107}, ISSN={["1465-7333"]}, DOI={10.1093/jhered/esv094}, abstractNote={In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n = 2x = 24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of 5 interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding program or following transformation techniques.}, number={2}, journal={JOURNAL OF HEREDITY}, author={Villano, Clizia and Miraglia, Valeria and Iorizzo, Massimo and Aversano, Riccardo and Carputo, Domenico}, year={2016}, month={Mar}, pages={187–192} }
 @article{schlautman_covarrubias-pazaran_diaz-garcia_johnson-cicalese_iorrizo_rodriguez-bonilla_bougie_bougie_wiesman_steffan_et al._2015, title={Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection}, volume={35}, ISSN={["1572-9788"]}, DOI={10.1007/s11032-015-0367-5}, number={8}, journal={MOLECULAR BREEDING}, author={Schlautman, Brandon and Covarrubias-Pazaran, Giovanny and Diaz-Garcia, Luis A. and Johnson-Cicalese, Jennifer and Iorrizo, Massimo and Rodriguez-Bonilla, Lorraine and Bougie, Tierney and Bougie, Tiffany and Wiesman, Eric and Steffan, Shawn and et al.}, year={2015}, month={Aug} }
 @article{parsons_matthews_iorizzo_roberts_simon_2015, title={Meloidogyne incognita nematode resistance QTL in carrot}, volume={35}, ISSN={1380-3743 1572-9788}, url={http://dx.doi.org/10.1007/S11032-015-0309-2}, DOI={10.1007/S11032-015-0309-2}, number={5}, journal={Molecular Breeding}, publisher={Springer Science and Business Media LLC}, author={Parsons, Joshua and Matthews, William and Iorizzo, Massimo and Roberts, Philip and Simon, Philipp}, year={2015}, month={Apr} }
 @article{muccillo_gambuti_frusciante_iorizzo_moio_raieta_rinaldi_colantuoni_aversano_2014, title={Biochemical features of native red wines and genetic diversity of the corresponding grape varieties from Campania region}, volume={143}, ISSN={0308-8146}, url={http://dx.doi.org/10.1016/J.FOODCHEM.2013.07.133}, DOI={10.1016/J.FOODCHEM.2013.07.133}, abstractNote={Campania region has always been considered one of the most appreciated Italian districts for wine production. Wine distinctiveness arises from their native grapevines. To better define the chemical profile of Campania autochthonous red grape varieties, we analysed the phenolic composition of Aglianico di Taurasi, Aglianico del Vulture, Aglianico del Taburno, Piedirosso wines, and a minor native variety, Lingua di Femmina in comparison with Merlot and Cabernet Sauvignon, as reference cultivars. A genetic profiling was also carried out using microsatellite molecular markers with high polymorphic and unambiguous profiles. Principal component analysis applied to 72 wines based on the 18 biochemical parameters, explained 77.6% of the total variance and highlighted important biological entities providing insightful patterns. Moreover, comparison of SSR-based data with phenylpropanoid molecules exhibited a statistically significant correlation. Our approach might be reasonably adopted for future characterisations and traceability of grapevines and corresponding wines.}, journal={Food Chemistry}, publisher={Elsevier BV}, author={Muccillo, Livio and Gambuti, Angelita and Frusciante, Luigi and Iorizzo, Massimo and Moio, Luigi and Raieta, Katia and Rinaldi, Alessandra and Colantuoni, Vittorio and Aversano, Riccardo}, year={2014}, month={Jan}, pages={506–513} }
 @article{grzebelus_iorizzo_senalik_ellison_cavagnaro_macko-podgorni_heller-uszynska_kilian_nothnagel_allender_et al._2013, title={Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers}, volume={33}, ISSN={1380-3743 1572-9788}, url={http://dx.doi.org/10.1007/S11032-013-9979-9}, DOI={10.1007/S11032-013-9979-9}, abstractNote={Carrot is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94 cultivated and 65 wild carrot accessions. The accessions were attributed to three separate groups: wild, Eastern cultivated and Western cultivated. Twenty-seven markers showing signatures for selection were identified. They showed a directional shift in frequency from the wild to the cultivated, likely reflecting diversifying selection imposed in the course of domestication. A genetic linkage map constructed using 188 F2 plants comprised 431 markers with an average distance of 1.1 cM, divided into nine linkage groups. Using previously anchored single nucleotide polymorphisms, the linkage groups were physically attributed to the nine carrot chromosomes. A cluster of markers mapping to chromosome 8 showed significant segregation distortion. Two of the 27 DArT markers with signatures for selection were segregating in the mapping population and were localized on chromosomes 2 and 6. Chromosome 2 was previously shown to carry the Vrn1 gene governing the biennial growth habit essential for cultivated carrot. The results reported here provide background for further research on the history of carrot domestication and identify genomic regions potentially important for modern carrot breeding.}, number={3}, journal={Molecular Breeding}, publisher={Springer Science and Business Media LLC}, author={Grzebelus, Dariusz and Iorizzo, Massimo and Senalik, Douglas and Ellison, Shelby and Cavagnaro, Pablo and Macko-Podgorni, Alicja and Heller-Uszynska, Kasia and Kilian, Andrzej and Nothnagel, Thomas and Allender, Charlotte and et al.}, year={2013}, month={Oct}, pages={625–637} }
 @article{yildiz_willis_cavagnaro_iorizzo_abak_simon_2013, title={Expression and mapping of anthocyanin biosynthesis genes in carrot}, volume={126}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/S00122-013-2084-Y}, DOI={10.1007/S00122-013-2084-Y}, abstractNote={Anthocyanin gene expression has been extensively studied in leaves, fruits and flowers of numerous plants. Little, however, is known about anthocyanin accumulation in roots of carrots or other species. We quantified expression of six anthocyanin biosynthetic genes [phenylalanine ammonia-lyase (PAL3), chalcone synthase (CHS1), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR1), leucoanthocyanidin dioxygenase (LDOX2), and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT)] in three carrot inbreds with contrasting root color: solid purple (phloem and xylem); purple outer phloem/orange xylem; and orange phloem and xylem. Transcripts for five of these genes (CHS1, DFR1, F3H, LDOX2, PAL3) accumulated at high levels in solid purple carrots, less in purple-orange carrot, and low or no transcript in orange carrots. Gene expression coincided with anthocyanin accumulation. In contrast, UFGT expression was comparable in purple and orange carrots and relatively unchanged during root development. In addition, five anthocyanin biosynthesis genes [FLS1 (flavonol synthase), F3H, LDOX2, PAL3, and UFGT] and three anthocyanin transcription factors (DcEFR1, DcMYB3 and DcMYB5) were mapped in a population segregating for the P 1 locus that conditions purple root color. P 1 mapped to chromosome 3 and of the eight anthocyanin biosynthesis genes, only F3H and FLS1 were linked to P 1. The gene expression and mapping data suggest a coordinated regulatory control of anthocyanin expression in carrot root and establish a framework for studying the anthocyanin pathway in carrots, and they also suggest that none of the genes evaluated is a candidate for P 1.}, number={7}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Yildiz, Mehtap and Willis, David K. and Cavagnaro, Pablo F. and Iorizzo, Massimo and Abak, Kazim and Simon, Philipp W.}, year={2013}, month={Mar}, pages={1689–1702} }
 @article{adamo_zampella_quétel_aversano_dal piaz_de tommasi_frusciante_iorizzo_lepore_carputo_2012, title={Biological and geochemical markers of the geographical origin and genetic identity of potatoes}, volume={121}, ISSN={0375-6742}, url={http://dx.doi.org/10.1016/j.gexplo.2012.07.006}, DOI={10.1016/j.gexplo.2012.07.006}, abstractNote={Abstract There is a growing interest in agriculture productions combining safety and quality attributes with clear regional identity. In the last few years several methods have been employed for food authentication and traceability. In this study we tested geochemical data for elemental concentrations of Mn, Cu, Zn, Rb, Sr and Cd and strontium isotope ratio in combination with biological data of 11 secondary metabolites and DNA as markers for the authentication of the origin of early potatoes at small geographical scale levels in Italy. DNA fingerprints through 12 SSR (simple sequence repeat) primer pairs allowed cultivar identification, confirming the discrimination power of molecular markers. Element concentrations, strontium isotope ratio and secondary metabolite data, through multivariate statistics (partial least squares discriminant analysis, PLS-DA), made it possible to clearly assign all the potato samples to the respective administrative regions of cultivation. The validation of the models was successful. It included external prediction tests on 20% of the data randomly selected from each administrative province and a study on the robustness of these multivariate data treatments to uncertainties on measurement results.}, journal={Journal of Geochemical Exploration}, publisher={Elsevier BV}, author={Adamo, Paola and Zampella, Mariavittoria and Quétel, Christophe R. and Aversano, Riccardo and Dal Piaz, Fabrizio and De Tommasi, Nunziatina and Frusciante, Luigi and Iorizzo, Massimo and Lepore, Laura and Carputo, Domenico}, year={2012}, month={Oct}, pages={62–68} }
 @article{alessandro_galmarini_iorizzo_simon_2012, title={Molecular mapping of vernalization requirement and fertility restoration genes in carrot}, volume={126}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/S00122-012-1989-1}, DOI={10.1007/S00122-012-1989-1}, abstractNote={Carrot (Daucus carota L.) is a cool-season vegetable normally classified as a biennial species, requiring vernalization to induce flowering. Nevertheless, some cultivars adapted to warmer climates require less vernalization and can be classified as annual. Most modern carrot cultivars are hybrids which rely upon cytoplasmic male-sterility for commercial production. One major gene controlling floral initiation and several genes restoring male fertility have been reported but none have been mapped. The objective of the present work was to develop the first linkage map of carrot locating the genomic regions that control vernalization response and fertility restoration. Using an F2 progeny, derived from the intercross between the annual cultivar 'Criolla INTA' and a petaloid male sterile biennial carrot evaluated over 2 years, both early flowering habit, which we name Vrn1, and restoration of petaloid cytoplasmic male sterility, which we name Rf1, were found to be dominant traits conditioned by single genes. On a map of 355 markers covering all 9 chromosomes with a total map length of 669 cM and an average marker-to-marker distance of 1.88 cM, Vrn1 mapped to chromosome 2 with flanking markers at 0.70 and 0.46 cM, and Rf1 mapped to chromosome 9 with flanking markers at 4.38 and 1.12 cM. These are the first two reproductive traits mapped in the carrot genome, and their map location and flanking markers provide valuable tools for studying traits important for carrot domestication and reproductive biology, as well as facilitating carrot breeding.}, number={2}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Alessandro, María S. and Galmarini, Claudio R. and Iorizzo, Massimo and Simon, Philipp W.}, year={2012}, month={Sep}, pages={415–423} }
 @article{iorizzo_mollov_carputo_bradeen_2011, title={Disease resistance gene transcription in transgenic potato is unaltered by temperature extremes and plant physiological age}, volume={130}, ISSN={0929-1873 1573-8469}, url={http://dx.doi.org/10.1007/S10658-011-9765-7}, DOI={10.1007/S10658-011-9765-7}, number={4}, journal={European Journal of Plant Pathology}, publisher={Springer Science and Business Media LLC}, author={Iorizzo, Massimo and Mollov, Dimitre S. and Carputo, Domenico and Bradeen, James M.}, year={2011}, month={Mar}, pages={469–476} }
 @article{iorizzo_aversano_bradeen_frusciante_carputo_2012, title={Fertilization fitness and offspring ploidy in 3x × 2x matings in potato}, volume={146}, ISSN={1126-3504 1724-5575}, url={http://dx.doi.org/10.1080/11263504.2011.620640}, DOI={10.1080/11263504.2011.620640}, abstractNote={Abstract The main objective of the current research was to study the reproductive behaviour of artificial triploid potato hybrids between wild Solanum commersonii and the cultivated potato Solanum tuberosum. When used in 3x × 2x crosses, triploids gave aneuploid progenies with somatic chromosome number ranging from 29 to 36. Fertilization fitness data suggested that the survival rate of gametes produced by the triploid parents may be related to their chromosome number. In addition, consistent with molecular data, our results indicated that fitness of gametes and chromosome number of progenies are influenced by the genome dosage of interspecific triploids. Since a main route to polyploidy formation is via 2n gametes and triploids, our study may contribute to a better understanding of polyploid plant reproduction, evolution and breeding.}, number={2}, journal={Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology}, publisher={Informa UK Limited}, author={Iorizzo, M. and Aversano, R. and Bradeen, J. M. and Frusciante, L. and Carputo, D.}, year={2012}, month={Jun}, pages={317–321} }
 @article{carputo_aversano_barone_di matteo_iorizzo_sigillo_zoina_frusciante_2009, title={Resistance to Ralstonia solanacearum of Sexual Hybrids Between Solanum commersonii and S. tuberosum}, volume={86}, ISSN={1099-209X 1874-9380}, url={http://dx.doi.org/10.1007/S12230-009-9072-4}, DOI={10.1007/S12230-009-9072-4}, number={3}, journal={American Journal of Potato Research}, publisher={Springer Science and Business Media LLC}, author={Carputo, Domenico and Aversano, Riccardo and Barone, Amalia and Di Matteo, Antonio and Iorizzo, Massimo and Sigillo, Loredana and Zoina, Astolfo and Frusciante, Luigi}, year={2009}, month={Feb}, pages={196–202} }