@article{surzenko_bastidas_reid_curaba_zhang_bostan_wilson_dominique_roberson_ignacio_et al._2024, title={Functional recovery following traumatic brain injury in rats is enhanced by oral supplementation with bovine thymus extract}, volume={38}, ISSN={["1530-6860"]}, DOI={10.1096/fj.202301859R}, abstractNote={AbstractTraumatic brain injury (TBI) is one of the leading causes of death worldwide. There are currently no effective treatments for TBI, and trauma survivors suffer from a variety of long‐lasting health consequences. With nutritional support recently emerging as a vital step in improving TBI patients' outcomes, we sought to evaluate the potential therapeutic benefits of nutritional supplements derived from bovine thymus gland, which can deliver a variety of nutrients and bioactive molecules. In a rat model of controlled cortical impact (CCI), we determined that animals supplemented with a nuclear fraction of bovine thymus (TNF) display greatly improved performance on beam balance and spatial memory tests following CCI. Using RNA‐Seq, we identified an array of signaling pathways that are modulated by TNF supplementation in rat hippocampus, including those involved in the process of autophagy. We further show that bovine thymus‐derived extracts contain antigens found in neural tissues and that supplementation of rats with thymus extracts induces production of serum IgG antibodies against neuronal and glial antigens, which may explain the enhanced animal recovery following CCI through possible oral tolerance mechanism. Collectively, our data demonstrate, for the first time, the potency of a nutritional supplement containing nuclear fraction of bovine thymus in enhancing the functional recovery from TBI.}, number={3}, journal={FASEB JOURNAL}, author={Surzenko, Natalia and Bastidas, Johana and Reid, Robert W. and Curaba, Julien and Zhang, Wei and Bostan, Hamed and Wilson, Mickey and Dominique, Ashley and Roberson, Julia and Ignacio, Glicerio and et al.}, year={2024}, month={Feb} }
 @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{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{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{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{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{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{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{becchimanzi_avolio_bostan_colantuono_cozzolino_mancini_chiusano_pucci_caccia_pennacchio_2020, title={Venomics of the ectoparasitoid wasp Bracon nigricans}, volume={21}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-019-6396-4}, abstractNote={AbstractBackgroundVenom is one of the most important sources of regulation factors used by parasitic Hymenoptera to redirect host physiology in favour of the developing offspring. This has stimulated a number of studies, both at functional and “omics” level, which, however, are still quite limited for ectophagous parasitoids that permanently paralyze and suppress their victims (i.e., idiobiont parasitoids).ResultsHere we present a combined transcriptomic and proteomic study of the venom of the generalist idiobiont waspBracon nigricans, an ectophagous larval parasitoid of different lepidopteran species, for which we recently described the host regulation strategy and the functional role of the venom in the induction of physiological changes in parasitized hosts. The experimental approach used led to the identification of the main components ofB. nigricansvenom involved in host regulation. Enzymes degrading lipids, proteins and carbohydrates are likely involved in the mobilization of storage nutrients from the fat body and may concurrently be responsible for the release of neurotoxic fatty acids inducing paralysis, and for the modulation of host immune responses.ConclusionThe present work contributes to fill the gap of knowledge on venom composition in ectoparasitoid wasps, and, along with our previous physiological study on this species, provides the foundation on which to develop a functional model of host regulation, based both on physiological and molecular data. This paves the way towards a better understanding of parasitism evolution in the basal lineages of Hymenoptera and to the possible exploitation of venom as source of bioinsecticidal molecules.}, number={1}, journal={BMC GENOMICS}, author={Becchimanzi, Andrea and Avolio, Maddalena and Bostan, Hamed and Colantuono, Chiara and Cozzolino, Flora and Mancini, Donato and Chiusano, Maria Luisa and Pucci, Pietro and Caccia, Silvia and Pennacchio, Francesco}, 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{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{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} }