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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Research Project #434439

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

Location: Vegetable Crops Research

2019 Annual Report

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.

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: A large family was created for mapping of resistance to Fusarium basal rot, and disease evaluations are underway. Additional families were developed for mapping of unique foliar types that show resistance to thrips, the main insect pest of onion, as well as unique bulb colors that may be of interest to consumers. These families have been planted in the field for phenotypic characterization. A hybrid onion was developed with semi-glossy foliage associated with thrips resistance and provided to collaborators in New York to assess resistance in replicated field plots. New populations of red and yellow onion were developed that show high levels of resistance to pink root, Fusarium basal rot (FBR), and/or thrips. Seed of these populations is being increased for eventual release to stakeholders. Cucumber: Multiple new cucumber mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size and shape, 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 GWAS panel members for seed increase. Phenotyping in both segregating and natural populations was conducted in a controlled growth chamber, greenhouses, or field locations 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. Carrot: A diverse collection of ~300 wild and cultivated carrot germplasm accessions was screened for heat and salinity tolerance during seed germination. 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 and another controlling anthocyanin accumulation was discovered, and likely timelines and geographic locations for the origins of these genes are being evaluated. Advances in phenotyping carrot plant morphology were made with the development of a machine phenotyping pipeline, and diverse germplasm is being phenotyped.

1. Accelerated cucumber breeding for disease resistances through marker-assisted selection. Downy mildew (DM) is at present the most important disease in U.S. cucumber production, and it has been especially devastating since 2004 when a new strain of the disease appeared, defeating the old resistance source. Powdery mildew (PM) is another important cucumber disease pathogen. High resistance to the new DM strain, and to PM, has been identified in some wild cucumber lines, such as PI (Plant Introduction) 197088 and PI 330628, but their direct use in cucumber breeding is difficult due to the complex genetics of resistance and unacceptable fruit quality. ARS scientists at Madison, Wisconsin, with collaborators at North Carolina State University (Raleigh), Nunhems Vegetable Seeds in the Netherlands, and Harris Moran Clause Seeds, Inc., conducted multi-location, multi-year field trials to investigate responses to natural infection of both pathogens in plants derived from crosses with the two PI lines. Genetic analysis identified important genetic factors for the high resistance to the mildew pathogens. Molecular markers associated with the most important contributors of genes for resistance were developed, and they were successfully utilized as a selection tool (marker-assisted selection) during breeding for cucumbers with high DM and PM resistance. With this tool, we were able to bring multiple genes (each of which only contributes partial resistance) to elite pickling cucumber breeding lines. The resulting lines were shown to have high resistance in field trials; they also have good horticultural traits for field production, and they are of much interest to seed companies developing new cucumber varieties, and growers struggling with these diseases.

2. Sources of genetic diversity for heat and salinity tolerance were identified. Abiotic stress has been considered to be very challenging for carrot growers. Since carrot is categorized as a cool-season crop, heat tolerance has been anticipated to be minimal. Furthermore, in past research evaluating a few cultivars, a high level of salinity sensitivity, was observed. Since salinity is a common problem for crops grown under irrigation, like carrot, the sensitivity to salinity was considered to be a significant long-term challenge for sustainable carrot production. To determine if diverse carrot germplasm might contain genetic variation for heat and salinity tolerance, approximately 300 diverse carrot cultivars and wild carrot seed stocks were evaluated by USDA, ARS researchers in Madison, Wisconsin, with collaborators at the University of Wisconsin – Madison and universities in Bangladesh (Bangladesh Agricultural University) and Pakistan (Sargodha University and University of Agriculture – Faisalabad), for heat and salinity tolerance during seed germination, a particularly vulnerable stage in the carrot life cycle where abiotic stress can take a devastating toll on crop production. Interestingly, a wide range in seed germination tolerance was observed among this diverse germplasm. Overall a higher incidence of tolerance was observed in cultivated carrot, but there were examples of tolerance in both wild and cultivated carrot germplasm. From the diverse sources of abiotic stress tolerance, a few cultivated carrots exhibited both heat and salinity tolerance, and these stocks are sources of newly identified genetic variations of particular interest to carrot growers, breeders, and researchers, to better understand the fundamental bases of abiotic stress tolerance, and to develop carrot cultivars with better abiotic stress tolerance. Breeders and other researchers are evaluating germplasm and initiating crosses to study these traits in more detail and to develop new breeding stocks.

3. Discovery of a major gene controlling orange carotenoid pigment accumulation in carrot roots. The first colors of carrot 1100 years ago were purple and yellow, but orange carrots are grown globally today. Furthermore, carrots accumulate more orange carotenoids than any other crop, and when they are consumed, the carotenoids of orange carrots are metabolized to vitamin A. In this study, USDA, ARS researchers in Madison, Wisconsin, with collaborators from the University of Wisconsin – Madison, used a diverse collection of modern and historic cultivated varieties and wild carrot accessions, and they associated a region of the carrot genome that contains the Or gene with the presence of carotenoids. This gene has been demonstrated to control carotenoid accumulation in other crop families but has not previously been described in carrot. This study provides support that Or was 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 provides additional insights into the fundamental mechanisms of carotenoid accumulation that shape carrot breeding strategies to improve color and nutritional impact.

Review Publications
Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., Reddy, U., Ando, K., McCreight, J.D., Schaffer, A.A., Burger, J., Tadmor, Y., Katzir, N., Tang, X., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, W.P., Levi, A., Garcia-Mas, J., Grumet, R., Fei, Z. 2018. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):1128-1136.
Wu, S., Zhang, B., Keyhaninejad, N., Rodriguez, G.R., Kim, H.J., Chakrabarti, M., Illa-Berenguer, E., Taitano, N.K., Gonzalo, M.J., Diaz, A., Pan, Y., Leisner, C.P., Halterman, D.A., Buell, C. Robin, Weng, Y., Jansky, S.H., van Eck, H., Willemsen, J., Monforte, A.J., Meulia, T., van der Knaap, E. 2018. Tomato reveals a common mechanism underlying morphological diversification in domesticated plants. Nature Communications. 9:4734.
Wang, X., Bao, K., Reddy, U.K., Bai, Y., Hammar, S.A., Jiao, C., Wehner, T.C., Madera, A.R., Weng, Y., Grumet, R., Fei, Z.J. 2018. The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development. Horticulture Research. 5(64):1-13.
Yang, L., Liu, H., Zhao, J., Pan, Y., Cheng, S., Lietzow, C.D., Wen, C., Zhang, X., Weng, Y. 2018. LITTLELEAF (LL) encodes a WD40 repeat domain-containing protein associated with organ size variation in cucumber. Plant Journal. 95:834-847.
Pan, J., Tan, J., Wang, Y., Zheng, X., Owens, K., Li, D., Li, Y., Weng, Y. 2018. STAYGREEN (CsSGR) is a candidate for the anthracnose (Colletotrichum orbiculare) resistance locus cla in Gy14 cucumber. Journal of Theoretical and Applied Genetics. 131(7):1577-1587.
Yagcioglu, M., Jiang, B., Wang, P., Wang, Y., Ellialtioglu, S.S., Weng, Y. 2019. QTL mapping of low temperature germination ability in cucumber. Euphytica. 215:84.
Rong, F., Chen, F., Hunag, L., Zhang, J., Cheng, Z., Hou, D., Weng, Y., Chen, P., Li, Y. 2018. A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cl) in cucumber (Cucumis sativus L.). Journal of Theoretical and Applied Genetics. 132:113-123.
Liu, X., Wang, T., Bartholomew, E., Black, K., Dong, M., Zhang, Y., Yang, S., Cai, Y., Weng, Y., Ren, H. 2018. Comprehensive analysis of NAC transcription factors and their expression during cucumber fruit spine development. Horticulture Research. 5, Article number:31.
Zhao, J., Jiang, L., Che, G., Li, Y., Pan, Y., Zhao, W., Zhong, Y., Ding, Y., Yan, S., Sun, C., Weng, Y., Zhang, X. 2019. A functional allele of CsFUL1 regulates fruit length through repressing CsSUP and inhibiting auxin transport in cucumber. The Plant Cell. 31:1289–1307.