@article{perkins-veazie_ma_schwickerath_meyer_chen_2023, title={The Absence of Malvidin-3-Glucoside in Petiole Tissue Predicts Rare Red-Type Flower of Eastern Redbud (Cercis canadensis L.)}, volume={13}, ISSN={["2077-0472"]}, DOI={10.3390/agriculture13030598}, abstractNote={Eastern redbud, Cercis canadensis L., is a popular ornamental tree in the U.S. and has flower colors of purple-type, red-type, and white-type. Most redbuds cultivars have purple-type flowers. Red-types and white-types are much less common. These unusual flower colors have become an important trait for incorporation into novel redbud cultivars. Eastern redbud seedlings require 3–5 years before blooming, making flower color selection a slow and expensive process. The ability to select seedlings for flower color type would significantly increase the efficiency of the breeding process. Redbud flower color is dominated by anthocyanin content; leaf petioles often show visible pink to purple color, indicating the potential presence of anthocyanin. In this study, anthocyanin profiles of 14 cultivars and 25 progenies of ‘Appalachian Red’ (red-type) × ‘Oklahoma’ (purple-type) were determined using HPLC. The petiole anthocyanin profiles were strongly indicative of plant flower-color types. Both peonidin-3-glucoside and malvidin-3-glucoside were dominant in petioles from all purple-type plants. In contrast, malvidin-3-glucoside was absent from petioles of red-type plants, and neither peonidin-3-glucoside nor malvidin-3-glucoside was detected among white-type cultivars. These results indicate that the presence or absence of peonidin-3-glucoside and malvidin-3-glucoside in petioles can be a physiological marker for identifying redbud flower color types.}, number={3}, journal={AGRICULTURE-BASEL}, author={Perkins-Veazie, Penelope and Ma, Guoying and Schwickerath, Jack and Meyer, Elisabeth and Chen, Hsuan}, year={2023}, month={Mar} }
 @article{chen_contreras_2022, title={Near-Hexaploid and Near-Tetraploid Aneuploid Progenies Derived from Backcrossing Tetraploid Parents Hibiscus syriacus x (H. syriacus x H. paramutabilis)}, volume={13}, ISSN={["2073-4425"]}, DOI={10.3390/genes13061022}, abstractNote={Hibiscus syriacus, azalea, is an important woody ornamental shrub planted throughout many temperate and subtropical regions of the world. However, flower size is smaller in this species than some of its relatives. To increase flower size, interspecific hybridization has been used, and such hybrid cultivars are usually characterized by larger flowers, increased vigor, diverse leaf shapes, and reduced fertility. Our earlier studies have shown that these hybrid cultivars could backcross with H. syriacus when used as male parents. To understand the breeding potential of these hybrid cultivars, two popular tetraploid hybrid cultivars, ‘Lohengrin’ and ‘Resi’, were used as pollen parents to backcross several tetraploid H. syriacus cultivars. As a result, 28.76% and 64.4% of ‘Lohengrin’ and ‘Resi’ progenies exhibited larger flowers than both of their parents. Interestingly, 14 of 18 progenies of ‘Resi’ were putative hexaploids, whereas 19 tested ‘Lohengrin’ progenies were tetraploid. Because putative hexaploid progenies were only observed among progenies of ‘Resi’, this hybrid cultivar appears to produce unreduced gametes. In addition, among the 14 putative hexaploids derived from ‘Resi’, 11 had larger flowers than both of their parents and their tetraploid siblings (p < 0.05). The 45S rDNA and 5S rDNA locus segregation among those BC1F1 progenies was tested by fluorescent in situ hybridization (FISH), and the wide range of 45S rDNA signal numbers among siblings indicated that these aneuploids resulted from unequal segregation or chromosome rearrangement. Chromosome counting confirmed aneuploidy among BC1F1 progenies. Ploidy diversity and aneuploidy have been known to contribute to various elements of morphological diversity, such as larger flower size and reduced fertility, which are important in ornamental plant breeding. The present study demonstrated the breeding potential of interspecific Hibiscus cultivars for increasing ploidy level and flower size.}, number={6}, journal={GENES}, author={Chen, Hsuan and Contreras, Ryan N.}, year={2022}, month={Jun} }
 @article{crawford_rojas_crawford_otten_schoenenberger_garfinkel_chen_2021, title={Characteristics of the Diploid, Triploid, and Tetraploid Versions of a Cannabigerol-Dominant F-1 Hybrid Industrial Hemp Cultivar, Cannabis sativa 'Stem Cell CBG'}, volume={12}, ISSN={["2073-4425"]}, DOI={10.3390/genes12060923}, abstractNote={Hemp (Cannabis sativa L.) has recently become an important crop due to the growing market demands for products containing cannabinoids. Unintended cross-pollination of C. sativa crops is one of the most important threats to cannabinoid production and has been shown to reduce cannabinoid yield. Ploidy manipulation has been used in other crops to improve agronomic traits and reduce fertility; however, little is known about the performance of C. sativa polyploids. In this study, colchicine was applied to two proprietary, inbred diploid C. sativa inbred lines, ‘TS1-3’ and ‘P163’, to produce the tetraploids ‘TS1-3 (4x)’ and ‘P163 (4x)’. The diploid, triploid, and tetraploid F1 hybrids from ‘TS1-3’ × ‘P163’, ‘TS1-3 (4x)’ × ‘P163’, and ‘TS1-3 (4x)’ × ‘P163 (4x)’ were produced to test their fertilities, crossing compatibilities, and yields. The results indicated a reduction in fertility in the triploids and the tetraploids, relative to their diploid counterparts. When triploids were used as females, seed yields were less than 2% compared to when diploids were used as females; thus, triploids were determined to be female infertile. The triploids resulting from the crosses made herein displayed increases in biomass and inflorescence weight compared to the diploids created from the same parents in a field setting. Statistical increases in cannabinoid concentrations were not observed. Lastly, asymmetric crossing compatibility was observed between the diploids and the tetraploids of the genotypes tested. The results demonstrate the potential benefits of triploid C. sativa cultivars in commercial agriculture.}, number={6}, journal={GENES}, author={Crawford, Seth and Rojas, Brendan M. and Crawford, Eric and Otten, Matthew and Schoenenberger, Thecla A. and Garfinkel, Andrea R. and Chen, Hsuan}, year={2021}, month={Jun} }
 @article{chen_werner_2021, title={Inheritance of Compact Growth Habit, and Investigation of Linkage to Weeping Architecture and Purple Leaf Color in Eastern Redbud (Cercis canadensis L.)}, volume={56}, ISSN={["2327-9834"]}, url={http://dx.doi.org/10.21273/hortsci16031-21}, DOI={10.21273/hortsci16031-21}, abstractNote={Eastern redbud ( Cercis canadensis L.) is a commonly used small landscape tree. Compact growth, purple leaf color, and weeping architecture are three popular ornamental phenotypes. Inheritances of weeping architecture and purple leaves have been reported previously. Inheritance of compact growth habit and its genetic linkage with the weeping and purple leaf genes have not been reported. In the present research, the inheritance of compact growth derived from ‘Ace of Hearts’ was explored in the F 1 , F 2 , and reciprocal backcross families resulting from the controlled hybridization of ‘Ruby Falls’ (normal growth/weeping architecture/purple leaf) × ‘Ace of Hearts’ (compact growth/nonweeping architecture/green leaf). All 27 F 1 individuals were nonweeping, green-leaved, and noncompact. A total of 572 F 2 progeny were obtained, and subsequent analysis of segregation revealed a single recessive gene controlled compact growth habit. Analysis of reciprocal backcross families confirmed this result as well. Weeping architecture and purple leaf color were also controlled by single recessive genes, confirming findings presented in previous studies in another redbud family. No linkage between the three genes was detected. This research is the first to report the inheritance of compact growth in eastern redbud and confirms independent assortment between the compact, purple leaf, and weeping genes.}, number={12}, journal={HORTSCIENCE}, publisher={American Society for Horticultural Science}, author={Chen, Hsuan and Werner, Dennis J.}, year={2021}, month={Dec}, pages={1513–1515} }
 @article{neill_contreras_stockwell_chen_2021, title={Screening Cotoneaster sp. for Resistance to Fire Blight Using Foliar Inoculation with Two Strains of Erwinia amylovora}, volume={56}, ISSN={["2327-9834"]}, DOI={10.21273/HORTSCI15872-21}, abstractNote={The genus Cotoneaster is composed of ≈400 species with a wide variety of growth habits and forms. These hardy landscape shrubs used to be commonplace because of their low maintenance and landscape functionality. However, the interest in and sales of cotoneaster have decreased for a variety of reasons, with the greatest being its susceptibility to a bacterial disease fire blight caused by Erwinia amylovora . The resistances of 15 different genotypes of Cotoneaster to a wild-type strain of Erwinia amylovora (Ea153) and a strain LA635 that has a natural mutation in avrRpt2 that encodes for a type III secretion effector were tested separately by inoculating leaves. Fire blight resistance was assessed by calculating the percent shoot necrosis (PSN) [PSN = 100 × (lesion length ÷ total branch length)] at 6 to 8 weeks after inoculation. Across all experiments, Cotoneaster genotypes H2011-01-002 and C. × suecicus ‘Emerald Sprite’ consistently had the lowest PSN values when inoculated with either strain. Cotoneaster × suecicus ‘Emerald Beauty’ was significantly more resistant to Ea153 than to LA635, whereas C. splendens was significantly more susceptible to Ea153 than to LA635.}, number={7}, journal={HORTSCIENCE}, author={Neill, Kristin E. and Contreras, Ryan N. and Stockwell, Virginia O. and Chen, Hsuan}, year={2021}, month={Jul}, pages={824–830} }
 @article{chen_lattier_vining_contreras_2020, title={Two SNP Markers Identified Using Genotyping-by-Sequencing Are Associated with Remontancy in a Segregating F1 Population of Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang®}, volume={145}, url={http://dx.doi.org/10.21273/jashs04847-20}, DOI={10.21273/jashs04847-20}, abstractNote={Lilacs ( Syringa sp.) have been used as ornamental plants since the mid-16th century and remain important in modern gardens due to their attractive and fragrant flowers. However, a short flowering season is a critical drawback for their ornamental value. Breeders have identified remontancy (reblooming) in dwarf lilac ( Syringa pubescens ), and have tried to introgress this trait into related species by interspecific hybridization. Molecular tools for lilac breeding are limited because of the shortage of genome sequence knowledge and currently no molecular markers are available to use in breeding for remontancy. In this study, an F 1 population from crossing Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang ® Purple was created and subjected to genotyping-by-sequencing (GBS) analysis and phenotyped for remontancy. Plants were categorized as remontant, semi-remontant, and nonremontant based on the relative quantity of inflorescences during the second flush of flowers. A total of 20,730 single-nucleotide polymorphism (SNP) markers from GBS were used in marker-trait association to find remontant-specific marker(s) without marker position information. Two SNP markers, TP70580 (A locus) and TP82604 (B locus), were correlated with remontancy. The two loci showed a partial epistasis and additive interaction effects on the level of remontancy. Accumulation of recessive alleles at the two loci was positively correlated with increased reblooming. For example, 87% of aabb plants were remontant, and only 9% were nonremontant. In contrast, 100% of AaBB plants were nonremontant. These two SNP markers associated with remontancy will be useful in developing markers for future breeding and demonstrate the feasibility of developing markers for breeding woody ornamental taxa that lack a reference genome or extensive DNA sequence information.}, number={2}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Chen, Hsuan and Lattier, Jason D. and Vining, Kelly and Contreras, Ryan N.}, year={2020}, month={Jan}, pages={104–109} }
 @article{vining_pandelova_hummer_bassil_contreras_neill_chen_parrish_lange_2019, title={Genetic diversity survey of Mentha aquatica L. and Mentha suaveolens Ehrh., mint crop ancestors}, volume={66}, url={http://dx.doi.org/10.1007/s10722-019-00750-4}, DOI={10.1007/s10722-019-00750-4}, number={4}, journal={Genetic Resources and Crop Evolution}, publisher={Springer Science and Business Media LLC}, author={Vining, Kelly J. and Pandelova, Iovanna and Hummer, Kim and Bassil, Nahla and Contreras, Ryan and Neill, Kristin and Chen, Hsuan and Parrish, Amber N. and Lange, Bernd Markus}, year={2019}, month={Apr}, pages={825–845} }
 @article{graebner_chen_contreras_haynes_sathuvalli_2019, title={Identification of the High Frequency of Triploid Potato Resulting from Tetraploid × Diploid Crosses}, volume={54}, url={http://dx.doi.org/10.21273/hortsci13797-18}, DOI={10.21273/hortsci13797-18}, abstractNote={Conventional wisdom regarding potato breeding indicates that a strong triploid block prevents the development of viable triploid seeds from crosses between tetraploid and diploid clones. However, in a recent set of crosses between elite tetraploid potatoes and an improved diploid hybrid population derived from group Stenotomum and group Phureja, 61.5% of the resulting clones were found to be triploid. If clones derived from one diploid parent suspected of producing a high frequency of unreduced gametes were excluded, then the frequency of triploid clones increased to 74.4%. Tubers of these triploids are generally intermediates of the two parental groups. Our findings indicate the possibility of using triploid potatoes in potato variety development programs and in genetic and genomic studies.}, number={7}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Graebner, Ryan C. and Chen, Hsuan and Contreras, Ryan N. and Haynes, Kathleen G. and Sathuvalli, Vidyasagar}, year={2019}, month={Jul}, pages={1159–1163} }
 @article{chen_xue_li_contreras_2019, title={Quantile Regression Facilitates Simultaneous Selection of Negatively Correlated Floral Traits among BC1F1 Progeny of Male-fertile Hybrid Hibiscus Cultivars Lohengrin and Resi (H. syriacus × H. paramutabilis)}, volume={144}, url={http://dx.doi.org/10.21273/jashs04569-18}, DOI={10.21273/jashs04569-18}, abstractNote={Hibiscus syriacus is a woody shrub in the Malvaceae family that is common in landscapes due to its broad adaptability and variable ornamental characteristics. Interspecific hybridization has been used to improve Hibiscus by building novel floral traits, hybrid vigor, and hybrid infertility. A few interspecific hybrid Hibiscus cultivars ( H. syriacus × H. paramutabilis ), such as Lohengrin and Resi, are notable because of their vigorous vegetative growth, female infertility, and large flowers. However, little is known about the male fertility and breeding potential of these hybrid cultivars, which could increase flower size by backcrossing to H. syriacus . In this study, we estimated male fertility of the two hybrid cultivars by acetocarmine staining and in vivo pollination and assessed selection methods for floral traits, specifically flower size and petal number. A BC 1 F 1 population of 294 individuals was developed by crossing hybrid cultivars Lohengrin or Resi with a variety of double-flowered H. syriacus cultivars. A negative correlation between petal number and petal area was detected by quantile regression, which is a method that circumvents the problem of simple linear regression, which violates statistical assumptions. Quantile regression was used to build simultaneous selection thresholds for different levels of required stringency. As expected, the female fertility of hybrid cultivars was extremely low or zero; however, the male fertility of hybrid cultivars was not reduced compared with H. syriacus cultivars. A negative linear correlation between the petal number and petal area of the BC 1 F 1 individuals was observed. In addition, quantile regression was recommended to set a single selection threshold to be applied to the selection of two negatively correlated traits, which was more effective than independent selection of petal numbers and petal areas among progeny.}, number={1}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Chen, Hsuan and Xue, Lan and Li, Tong and Contreras, Ryan N.}, year={2019}, month={Jan}, pages={70–76} }
 @article{lattier_chen_contreras_2019, title={Variation in Genome Size, Ploidy, Stomata, and rDNA Signals in Althea}, volume={144}, url={http://dx.doi.org/10.21273/jashs04618-18}, DOI={10.21273/jashs04618-18}, abstractNote={Althea ( Hibiscus syriacus ) is a shrub prized for its winterhardiness and colorful summer flowers. Altheas are tetraploids (2 n = 4 x = 80); however, breeders have developed hexaploids and octoploids. Previous studies report anatomical variation among polyploids, including stomata size. The purpose of this study was 4-fold. First, identify genome size and ploidy variation in cultivars via flow cytometry and chromosome counts. Second, create a ploidy series consisting of 4 x , 5 x , 6 x , and 8 x cytotypes. Third, investigate the ploidy series for variation in stomatal guard cell lengths, stomatal density, and copy number of fluorescent ribosomal DNA (rDNA) signals. Fourth, investigate segregation patterns of rDNA signals in a subset of pentaploid seedlings. Flow cytometry revealed most cultivars to be tetraploid with holoploid 2C genome sizes from 4.55 ± 0.02 to 4.78 ± 0.06 pg. Five taxa (‘Aphrodite’, ‘Pink Giant’, ‘Minerva’, Azurri Satin ® , and Raspberry Smoothie™) were hexaploids (6.68 ± 0.13 to 7.05 ± 0.18 pg). Peppermint Smoothie™ was a cytochimera with tetraploid cells (4.61 ± 0.06 pg) and octoploid cells (8.98 ± 0.13 pg). To create pentaploids, reciprocal combinations were made between hexaploid ‘Pink Giant’ and tetraploid cultivars. To create octoploids, seedlings were treated with agar solutions containing 0.2% colchicine or 125 μM oryzalin. Guard cell lengths were significantly different among the four cytotypes: 4 x (27.36 ± 0.04 μm), 5 x (30.35 ± 1.28 μm), 6 x (35.59 ± 0.63 μm), and 8 x (40.48 ± 1.05 μm). Measurements of stomatal density revealed a precipitous decline in average density from the 4 x cytotype (398.22 ± 15.43 stomata/mm 2 ) to 5 x cytotype (194.06 ± 38.69 stomata/mm 2 ) but no significant difference among 5 x , 6 x , and 8 x cytotypes. Fluorescent in situ hybridization (FISH) revealed an increase in 5S and 45S rDNA signals that scaled with ploidy: 4 x (two 5S + four 45S), 6 x (three 5S + six 45S), and 8 x (four 5S + eight 45S). However, pentaploid (5 x ) seedlings exhibited random segregation of rDNA signals between the 4 x and 6 x cytotypes, including all six possible combinations (two 5S, three 5S) × (four 45S, five 45S, six 45S).}, number={2}, journal={Journal of the American Society for Horticultural Science}, publisher={American Society for Horticultural Science}, author={Lattier, Jason D. and Chen, Hsuan and Contreras, Ryan N.}, year={2019}, month={Mar}, pages={130–140} }
 @article{lattier_chen_contreras_2017, title={Improved Method of Enzyme Digestion for Root Tip Cytology}, volume={52}, url={http://dx.doi.org/10.21273/hortsci12024-17}, DOI={10.21273/hortsci12024-17}, abstractNote={Chromosome numbers are an important botanical character for multiple fields of plant sciences, from plant breeding and genetics to systematics and taxonomy. Accurate chromosome counts in root tips of woody plants are often limited by their small, friable roots with numerous, small chromosomes. Current hydrolysis and enzyme digestion techniques require handling of roots before the root squash. However, optimum chromosome spread occurs when the cell walls have degraded past the point of easy handling. Here, we present a new enzyme digestion protocol that is fast, efficient, and flexible. This protocol reduces handling of the roots allowing for long-duration enzyme digestion. Digestions are performed on a microscope slide, eliminating the need for handling digested cells with forceps or pipettes. To illustrate the flexibility of this method across woody plant taxa, we performed chromosome counts on five angiosperms and one gymnosperm. Ploidy levels included diploids, triploids, and tetraploids with chromosome numbers ranging from 2 n = 16 to 2 n = 80. The range of holoploid 2C genome sizes spanned 1.54–24.71 pg. This protocol will provide a useful technique for plant cytologists working with taxa that exhibit a wide range of genome size and ploidy levels.}, number={7}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Lattier, Jason D. and Chen, Hsuan and Contreras, Ryan N.}, year={2017}, month={Jul}, pages={1029–1032} }
 @article{chen_chung_tsai_wei_hsieh_hsing_2015, title={Distribution of new satellites and simple sequence repeats in annual and perennial Glycine species}, volume={56}, url={http://dx.doi.org/10.1186/s40529-015-0103-9}, DOI={10.1186/s40529-015-0103-9}, abstractNote={The repeat sequences occupied more than 50 % of soybean genome. In order to understand where these repeat sequences distributed in soybean genome and its related Glycine species, we examined three new repeat sequences—soybean repeat sequence (SBRS1, SBRS2 and SBRS3), some nonspecific repeat sequences and 45S rDNA on several Glycine species, including annual and perennial accessions in this study. In the annual species, G. soja, signals for SBRS1 and ATT repeat can be found on each chromosome in GG genome, but those for SBRS2 and SBRS3 were located at three specific loci. In perennial Glycine species, these three SBR repeat frequently co-localized with 45S rDNA, two major 45S rDNA loci were found in all tetraploid species. However, an extra minor locus was found in one accession of the G. pescadrensis (Tab074), but not in another accession (Tab004). We demonstrate that some repetitive sequences are present in all Glycine species used in the study, but the abundancy is different in annual or perennial species. We suggest this study may provide additional information in investigations of the phylogeny in the Glycine species.}, number={1}, journal={Botanical Studies}, publisher={Springer Science and Business Media LLC}, author={Chen, Hsuan and Chung, Mei-Chu and Tsai, Yuan-Ching and Wei, Fu-Jin and Hsieh, Jaw-Shu and Hsing, Yue-Ie C.}, year={2015}, month={Dec} }