Research Project: Trait Discovery, Genetics, and Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research

2020 Annual Report

Objectives
Objective 1: Phenotype, map, and identify traits of critical importance for vegetable growers, seed companies, and consumers in elite populations and in diverse genetic resources of Allium, Cucumis, and Daucus. Objective 2: Develop and release enhanced germplasm of Allium, Cucumis, and Daucus with superior traits. Objective 3: Determine the genetic bases and molecular processes for biotic and abiotic resistance, growth and productivity, nutritional value, and flavor characteristics in Allium, Cucumis, and Daucus. Objective 4: Develop informational resources and tools to evaluate phenotypic and genotypic data from Allium, Cucumis, and Daucus breeding and genetic research.

Approach
The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1: Identify unique phenotypic variation in carrot, onion, and cucumber germplasm collections and breeding stocks and genetically map key traits to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Objective 2: Incorporate valuable traits and release elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. Dense genetic maps are useful to improve the efficiency of crop improvement. We will identify unique phenotypes in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Objective 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation and develop molecular markers for traits in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information on trait genetics from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4: Summarize and catalog phenotypic, genotypic, and molecular data collected and develop accessible and searchable databases.

Progress Report
Onion: Ninety-two families segregating for resistance to Fusarium basal rot (FBR) were evaluated in replicated disease evaluations, and major FBR resistance loci mapped. Manuscript was submitted for publication in a scientific journal. Additional families were developed for mapping of unique foliar wax profiles that show resistance to thrips, the main insect pest of onion, phenotypes were scored, and DNA isolated for genotyping, which is underway. Genetic mapping of chartreuse bulb color was completed and published. An experimental hybrid onion with semi-glossy foliage associated with thrips resistance was evaluated in New York by collaborators and showed the least thrips damage from all evaluated germplasm. This hybrid is presently under USDA review for release to stakeholders. Seed was produced from new populations of red and yellow onions that show high levels of resistance to pink root, FBR, and/or thrips, and these populations are presently under USDA review for release to stakeholders. Cucumber: Multiple new cucumber mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size and shape, hypocotyl length, flowering time, parthenocarpy fruit setting, abiotic stress tolerance (low temperature germination) quantitative trait loci (QTL), and disease resistances (downy mildew, powdery mildew, angular leaf spot, and anthracnose). A panel of 300 cucumber lines were selected for genome-wide association study (GWAS). Inbred lines were under development for these lines for further seed increase. Phenotyping in both segregating and natural populations was conducted in a controlled growth chamber, greenhouses, or field trials for these traits. Genome wide or localized linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers with emphasis on use of high throughput whole genome re-sequencing tools. The genetic diversity and population structure of the USDA cucumber collection (1234 accessions) was also evaluated through genotyping-by-sequencing. Tolerance to sudden cold spells in an heirloom cucumber cultivar (‘Chipper’) was associated with a single nucleotide polymorphism (SNP) in the chloroplast DNA. This SNP conditions an amino acid change that causes changes in protein polarity that may explain cold tolerance. Carrot: A diverse collection of approximately 300 wild and cultivated carrot germplasm accessions was screened for heat and salinity tolerance during plant growth. A wide range of tolerance was observed with a higher incidence of tolerance in cultivated germplasm than in wild. Genomic data for this germplasm is being collected to undertake GWAS analysis and mapping populations are being prepared. The relationship between abiotic stress tolerance and nutritional quality as reflected in beta-carotene content was evaluated and no significant correlation was observed. A major gene controlling carotene accumulation was shown to be important for carrot domestication, and likely timelines and geographic locations for the origins of these genes are being evaluated.

Accomplishments
1. Thrips resistance in onions. Thrips are the main insect pest of onion, causing serious losses to both the seed and bulb crops. Heavy use of insecticides as the sole control measure has resulted in pesticide-resistant thrips populations that limit control options for growers. ARS scientists at Madison, Wisconsin, identified onions with unique profiles of waxes on foliage that suffer significantly less feeding damage by thrips. These unique profiles have been introduced into onion inbreds that produce a thrips-resistant, elite hybrid. New onion inbreds and a hybrid are under review for formal release to stakeholders in public institutions and seed companies.

2. Development of cucumber germplasm with enhanced disease resistances. Both downy mildew (DM) is and powdery mildew (PM) are very important diseases in U.S. cucumber production. Two plant Introduction (PI) lines show high resistance to these pathogens. Molecular markers associated with DM and PM resistance in the two lines were developed by ARS scientists at Madison, Wisconsin, and brought into an elite pickle cucumber line through marker-assisted selection. The performance of disease resistances and horticultural traits were evaluated. The resulting lines have high resistances in field trials as well as good horticultural traits. One such line is being prepared for public release for use by seed companies and public plant breeders.

3. Disease resistance in cucumber W2757. The legendary cucumber inbred line WI2757 released in 1982 by ARS researchers at Madison, Wisconsin, possesses a rare combination of resistances against nine pathogens. WI2757 has been an important source of disease resistance for cucumber breeding worldwide. However, WI2757 has some drawbacks such as later flowering, and poor growth under field conditions. The genetic basis for these traits is not known. ARS researchers at Madison, Wisconsin, conducted molecular mapping using populations involving WI2757, and uncovered a chromosome aberration called a paracentric inversion on chromosome 1 of WI2757, which harbors genes or traits for fruit length, diameter, fruit shape, fruit number, and flowering time. This finding may help more efficient use of WI2757 by plant breeders in industry and public institutions.

4. Discovery of several major genes controlling carrot root color. The first colors of carrot 1100 years ago were purple and yellow, and while purple pigments are not common in carrots today, purple carrots are of new interest by carrot growers, breeders and consumers. In three studies, ARS researchers at Madison, Wisconsin, with collaborators from the North Carolina State University and the National University of Cuyo in Argentina, used a diverse collection of modern and historic cultivated varieties and identified three major genes controlling anthocyanin pigment content and chemical structure influencing nutritional quality. This study provides support that genes for purple carrot color were important in the early stages of carrot domestication and improvement and it is of interest to plant geneticists, molecular biologists, breeders, nutritionists, vegetable growers, and agricultural historians as it provide additional insights into the fundamental mechanisms of anthocyanin accumulation that shape carrot breeding strategies to improve color and nutritional impact.

Review Publications
Colcol Marzu, J., Straley, E., Havey, M.J. 2019. Genetic analyses and mapping of pink-root resistance in onion. Journal of the American Society for Horticultural Science. 143(6):503-507. https://doi.org/10.21273/JASHS04509-18.
Pan, Y., Wang, Y., McGregor, C., Liu, S., Luan, F., Meiling, G., Weng, Y. 2019. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. Theoretical and Applied Genetics. 133:1-21. https://doi.org/10.1007/s00122-019-03481-3.
Wang, Y., Bo, K., Gu, X., Pan, J., Li, Y., Chen, J., Wen, C., Ren, Z., Ren, H., Chen, X., Grumet, R., Weng, Y. 2020. Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. Horticulture Research. 7:3. https://doi.org/10.1038/s41438-019-0226-3.
Che, G., Gu, R., Zhao, J., Liu, X., Cheng, Z., Wang, Z., Liu, R., Yan, L., Weng, Y., Zhang, X., Zi, H., Song, X., Shen, J. 2020. Gene regulatory network of carpel number variation in cucumber. Development. 147(7). https://doi.org/10.1242/dev.184788.
Myers, J.R., Wallace, L.T., Moghaddam, S.M., Kleintop, A.E., Echeverria, D., Thompson, H.J., Brick, M.A., Lee, R., McClean, P.E. 2019. Improving the health benefits of snap bean: Genome- wide association studies of total phenolic content. Nutrients. 11(10):2509. https://doi.org/10.3390/nu11102509.
Rett-Cadman, S., Colle, M., Mansfeld, B.N., Barry, C., Wang, Y., Weng, Y., Gao, L., Fei, Z., Grumet, R. 2019. QTL and transcriptomic analyses implicate cuticle transcription factor SHINE as a source of natural variation for epidermal traits in cucumber fruit. Frontiers in Plant Science. 10:1536. https://doi.org/10.3389/fpls.2019.01536.
Munaiz, E.D., Groves, R.L., Havey, M.J. 2019. Amounts and types of epicuticular leaf waxes among onion accessions selected for reduced damage by onion thrips. Journal of the American Society for Horticultural Science. 145(1):30-35. https://doi.org/10.21273/JASHS04773-19.
Munaiz, E.D., Havey, M.J. 2019. Genetic analyses of epicuticular waxes associated with the glossy foliage of ‘White Persian’ onion. Journal of the American Society for Horticultural Science. 145(1):67-72. https://doi.org/10.21273/JASHS04840-19.
Havey, M.J. 2020. Genetic mapping of chartreuse bulb color in onion. Journal of the American Society for Horticultural Science. 145(2):110-119. https://doi.org/10.21273/JASHS04861-20.
Lee, H., Havey, M.J. 2020. Variable penetrance among different sources of the male fertility restoration allele of onion. HortScience. 55(4):543-546. https://doi.org/10.21273/HORTSCI14709-19.
Li, Z., Han, Y., Niu, H., Wang, Y., Jiang, B., Weng, Y. 2020. Gynoecy instability in cucumber (Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent femaleness (F) locus. Horticulture Research. 7:32. https://doi.org/10.1038/s41438-020-0251-2.
Pan, Y., Wen, C., Han, Y., Wang, Y., Li, Y., Li, S., Cheng, X., Weng, Y. 2020. QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber. Journal of Theoretical and Applied Genetics. 133:2271-2290. https://doi.org/10.1007/s00122-020-03596-y.
Titcomb, T.J., Kaeppler, M.S., Sandoval Cates, S.B., Shannon, J.M., Simon, P.W., Tanumihardjo, S.A. 2019. Carrot leaves maintain liver vitamin A concentrations in male mongolian gerbils regardless of the ratio of alpha- to beta-carotene when beta-carotene equivalents are equalized. Journal of Nutrition. 149(6):951-958. https://doi.org/10.1093/jn/nxz036.
Iorizzo, M., Cavagnaro, P.F., Bostan, H., Zhao, Y., Zhang, J., Simon, P.W. 2019. A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole. Frontiers in Plant Science. 9:1927. https://doi.org/10.3389/fpls.2018.01927.
Corak, K.E., Ellison, S.L., Simon, P.W., Spooner, D.M., Dawson, J.C. 2019. Comparison of representative and custom methods of generating core subsets of a carrot germplasm collection. Crop Science. 59(3):1107-1121. https://doi.org/10.2135/cropsci2018.09.0602.
Simon, P.W., Iorizzo, M., Grzebelus, D., Baranski, R. 2019. The carrot genome. Cham, Switzerland:Springer Nature Switzerland AG. 372 p. https://doi.org/10.1007/978-3-030-03389-7.
Bannoud, F., Ellison, S., Paolinelli, M., Horejsi, T.F., Senalik, D.A., Fanzone, M., Iorizzo, M., Simon, P.W., Cavagnaro, P. 2019. Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.). Theoretical and Applied Genetics. 132:2485–2507. https://doi.org/10.1007/s00122-019-03366-5.
Bolton, A., Nijabat, A., Mahmood-Ur-Rehman, M., Naveed, N., Mannan, A., Ali, A., Rahim, M., Simon, P.W. 2019. Variation for heat tolerance during seed germination in diverse carrot [Daucus carota (L.)] germplasm. HortScience. 54(9):1470–1476. https://doi.org/10.21273/HORTSCI14144-19.
Curaba, J., Bostan, H., Cavagnaro, P., Senalik, D.A., Mengist, M., Zhao, Y., Simon, P.W., Iorizzo, M. 2020. Identification of an SCPL gene controlling anthocyanin acylation in carrot (Daucus carota L.) root. Frontiers in Plant Science. 10(1770):1-17. https://doi.org/10.3389/fpls.2019.01770.