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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

2022 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
Cucumber. Multiple cucumber mapping populations were developed for framework or fine genetic mapping of genes or quantitative trait loci (QTL) for fruit flavor (smell, taste and texture) quality, and disease resistances (downy mildew, and powdery mildew). A panel of 239 cucumber lines were used 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 controlled environments, greenhouses, or field trials for flowering time, number of lateral branches, leaf color, plant height, number of nodes, fruit parthenocarpy, immature and mature fruit color, and fruit flavor attributes. A genetic map was developed using genotyping-by-sequencing in an F2 population from the cross between 9930 and WI76633 inbred lines. Linkage analysis identified genes or QTL for fruit flavor attributes. The genetic diversity and population structure of the GWAS population was evaluated. Several quantitative trait loci (QTL) for downy mildew resistance (dm4.1, dm5.2 and dm5.3) were fine mapped. Carrot. Orange and purple carrots from a collection of approximately 700 wild and cultivated carrot germplasm accessions were evaluated for variation in the orange carotenoid and purple anthocyanin tap root pigments. Until recently, two genes, Y and Y2, had been identified that account for the dramatic shift from yellow to orange carrots. But within the last decade two more genes, Or and CH, were found to also account for the orange color typical of carrots. This year we evaluated the magnitude of the effects that the Or and CH genes have on carrot color and we determined that both of these genes have a significant, roughly similar, effect in influencing carotene content and intensity of orange color. Color variation in purple carrots was found to be controlled by a messenger RNA (ribonucleic acid) referred to as a transcription factor that controls the biosynthetic genes producing anthocyanin pigments. An evaluation of storage root shape was also evaluated in this collection of carrots and, using a method known as association analysis, the genetic map locations for several genes were identified for root length, width, curvature of the root shoulder and tip, and the length to diameter ratio. An evaluation of genetic variation for salinity and drought tolerance was expanded and new sources of tolerance for both abiotic stressors were identified in cultivated carrots originating in several different regions of the world. Carrot field trials were resumed to evaluate crop yield and quality under conventional farming practices and under organic farming practices and new breeding stocks with improved nematode resistance, flavor, and yield were identified for further study and release to carrot growers and vegetable seed companies. Onion. Epicuticular waxes on the surface of onion leaves vary widely in amount and composition, and a unique profile of waxes was discovered in the cultivar ‘Odorless Greenleaf’. This cultivar is relatively resistant to thrips insects and that resistance was found to be associated with leaf wax composition. A single gene was demonstrated to control much of the variation in wax composition. Given the significant damage that thrips inflict on onion due to their feeding and to the viruses they carry, the ability to track this gene with molecular markers will be important in the development of thrips-resistant onion cultivars. In related studies, variation in the epicuticular waxes among onion cultivars grown under organic production was found to associated with variation not only in thrips damage but also with variation in bulb rot caused by several bacteria. Resistance to Fusarium basal rot, an important fungal disease, was found to be controlled by three genes. In addition to these studies, seven onion inbreds and breeding populations, and one hybrid, were released to vegetable breeders and researchers.

1. Identified and characterized a new gene for fruit skin feature in cucumber. Cucumber fruit skin could be smooth or rough (or netted), which is an important fruit quality trait. For fresh market cumbers, consumers prefer smooth skin, but processing cucumber often needs thick and tough skin. Previously, the H gene for heavy fruit netting was found to control skin toughness in cucumber. ARS researchers in Madison, Wisconsin, identified and characterized a new gene for fruit netting in cucumber. We sequenced the Rs gene that encodes a protein called SHINE1 (CsSHN1)/Wax Inducer1 (CsWIN1), which is known to play important roles in shaping skin features in flesh fruit crops like cucumber. Fruit with netted skin have different structures from that with smooth skin supporting multiple functions of the CsSHN1 gene. The expression level of CsSHN1 gene was positively correlated with the degree of fruit skin netting in different cucumber lines. Comparative analysis of cucumber and melon uncovered conserved and divergent genetic mechanisms underlying fruit skin netting that may reflect the different selection histories in the two crops. This work provides insights into genetic control of fruit epidermal features in cucumber which is of importance in cucumber breeding for different market classes.

2. New insights into the accumulation of orange color in carrots. Carrots are orange because they accumulate alpha- and beta-carotene, which are converted to vitamin A when we eat orange carrots. Studies dating back to the 1960’s observed that the recessive allele of the Y2 gene, when introduced into yellow carrots which lack these carotenes, accounts for the accumulation of orange color. More recently, studies in the 2010’s observed that a second gene, OR has what was speculated to have a similar function to Y2 in the accumulation of both carotenes while the CH gene accounts for the accumulation of alpha-carotene only. To better understand the action and interactions of these genes, ARS researchers in Madison, Wisconsin, in collaboration with researchers at the University of Wisconsin evaluated variation in only the CH and OR genes in carrots that don’t vary for the Y2 gene. Results confirmed that the OR gene accumulates both carotenes. Interestingly, the CH gene also increased the accumulation of alpha-carotene and to a lesser extent beta-carotene. This study indicates that these genes interact positively to account for the uniquely dark orange color of modern carrots, and suggests that the role these genes may play in accounting for variation in color during carrot domestication is of significant interest in developing our understanding of crop history.

Review Publications
Coe, K., Ellison, S., Senalik, D.A., Dawson, J., Simon, P.W. 2021. The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]. Theoretical and Applied Genetics. 134:3351–3362.
Bannoud, F., Carvajal, S., Ellison, S., Senalik, D.A., Gomez Talquenca, S., Massimo, I., Simon, P.W., Cavagnaro, P. 2021. Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in the carrot root phloem. Genes. 12(10), 1464.
Riaz, N., Yousaf, Z., Yasmin, Z., Munawar, M., Younas, A., Rashid, M., Aftab, A., Shamsheer, H., Yasin, H., Najeebullah, M., Simon, P.W. 2022. Development of carrot nutraceutical products as an alternative supplement for the prevention of disease. Frontiers in Nutrition. 8:787351.
Acharya, B., Mackasmiel, L., Taheri, A., Ondzighi-Assoume, C.A., Weng, Y., Dumenyo, C.K. 2021. Identification of bacterial wilt (erwinia tracheiphila) resistances in USDA melon collection. Plants. 10(9), 1972.
Bo, K., Duan, Y., Qiu, X., Zhang, M., Shu, Q., Sun, Y., He, Y., Shi, Y., Weng, Y., Wang, C. 2022. Promoter variation in a homeobox gene, CpDll, is associated with deeply lobed leaf in Cucurbita pepo L. Theoretical and Applied Genetics. 135:1223–1234.
Das, A., Singh, S., Islam, Z., Munsh, A., Behera, T., Dutta, S., Weng, Y., Dey, S. 2022. Current progress in genetic and genomics-aided breeding for stress resistance in cucumber (Cucumis sativus L.). Scientia Horticulturae. 300, 111059.
Du, X., Davila, M., Williams, C., Weng, Y. 2022. Fresh cucumber fruit physicochemical properties, consumer acceptance, and impact of variety and harvest date. Journal of the Science of Food and Agriculture. 2, 616-629.
Williams, C., Weng, Y., Du, X. 2022. Sensory profiles of 10 cucumber varieties using a panel trained with chemical references. ACS Food Science and Technology. 2:815-824.
Wallace, L.T., Havey, M.J. 2021. Genetic analysis of mitochondrial sorting from the MSC3 mosaic mutant of cucumber. Journal of the American Society for Horticultural Science. 146(5):346-350.
Straley, E., Marzu, J., Havey, M.J. 2021. Genetic analyses and mapping of resistance to fusarium basal rot in onion. Journal of the American Society for Horticultural Science. 7,538.
Zhang, H., Wang, Y., Tan, J., Weng, Y. 2022. Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, cucumis sativus. Journal of Theoretical and Applied Genetics. 135, pages2101–2119.