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

Location: Vegetable Crops Research

2021 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
Cucumber. Multiple new cucumber mapping populations were developed for framework or fine genetic mapping of genes or quantitative trait loci (QTL) for fruit size/shape, fruit taste quality, and disease resistances (downy mildew, powdery mildew, angular leaf spot, and anthracnose). A panel of 399 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 controlled environments, 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 GWAS population was evaluated. Carrot. A diverse collection of USDA carrot breeding stocks and approximately 700 wild and cultivated carrot germplasm accessions was screened for tolerance to abiotic stress (heat, drought and salinity), root-knot nematodes, Alternaria leaf blight, seedling vigor, early flowering, flavor, and nutritional values. A wide range of stress and disease tolerance, vigor, and consumer quality was observed. Genomic data for this diverse genetic collection is being used to advance genetic analysis of these diverse traits. In a subset of these genetic stocks, variation in the interaction between carrots and native beneficial soil microbes was observed, suggesting that these plant-microbe interactions influence plant growth and resistance to Alternaria leaf blight, a major foliar disease of carrots. Comparisons were made for these interactions with carrots grown under conventional farming practices and under organic farming practices, and these contrasting production practices revealed additional differences in plant-microbe interactions. The significance of these differences is being investigated in ongoing research. Onion. An analysis of the genetic control of onion leaf epicuticular wax composition was completed and genes controlling this trait were identified with one major gene imparting significant control of this trait. This gene alters wax profiles and with it, attractiveness to the thrips insect which causes leaf damage and carries viral disease. Unique epicuticular wax profiles will be important germplasm for the development of onion cultivars that suffer less feeding damage from onion thrips compared with waxy onion.

Accomplishments
1. Identification and characterization of a new source of disease resistance to target leaf spot in cucumber. Target leaf spot (TLS) is among the most damaging foliar diseases in both open field and greenhouse cucumber productions. The name target spot derives from the ringed, or bull’s eye, appearance on leaves infected by the fungal pathogen by C. cassiicola. TLS is also becoming an increasing threat and causing significant economic losses in many other crops like cotton, and soybean. Surprisingly, no resistance genes have been cloned for this pathogen in any crops or model plants. ARS researchers in Madison, Wisconsin, identified and characterized a new source of resistance to the cucumber disease target leaf spot (TLS). We found that resistance is controlled by a single dominant gene, Cca-4. The resistance is due to the deletion of a single DNA base in the gene, which results in a truncated protein, rendering it inactive. In susceptible plants, expression of this gene is positively associated with pathogen growth and disease symptom development. This novel resistance gene variant for target leaf spot should be of interest to scientists interested in the molecular mechanisms of resistance. Cucumber breeders and growers will also benefit from this new disease resistance source and molecular tool for developing new cucumber varieties with resistance to leaf spot.

2. New sources of genes in diverse carrots to improve abiotic stress tolerance and nutritional value. Sustained carrot production will require the development of new carrot breeding stocks with improved tolerance to abiotic stress - heat, drought, and saline irrigation water. ARS researchers in Madison, Wisconsin, in collaboration with researchers in Bangladesh and Pakistan evaluated a diverse collection of wild and cultivated carrots and identified new sources of genes conferring abiotic stress tolerance. In addition to their high market value for growers, carrots provide consumers with orange pigments that are rich sources of vitamin A and purple pigments which are potent dietary antioxidants. Several of these new gene sources for abiotic stress also contain high levels of nutritional pigments, based on ARS research performed with collaborators in the U.S. and Polish universities. The combination of enhanced nutritional value in carrots better adapted to abiotic stress due to climatic factors provides vegetable breeders with breeding stocks to sustain and expand carrot production to better meet production challenges and growing consumer dietary needs.

Review Publications
Weng, Y., Garcia-Mas, J., Levi, A., Luan, F. 2020. Editorial: translational research for cucurbit molecular breeding: traits, markers, and genes. Frontiers in Plant Science. 11. Article 615346. https://doi.org/10.3389/fpls.2020.615346.
Havey, M.J., Hunsaker, D.J., Munaiz, E.D. 2021. Genetic analysis of the unique epicuticular-wax profile of ‘Odourless Greenleaf’ onion. Journal of the American Society for Horticultural Science. 146(2):118-124. https://doi.org/10.21273/JASHS05024-20.
Iglesias, L., Havey, M.J., Nault, B.A. 2021. Potential for managing onion thrips (Thrips tabaci) in organic onion production using multiple IPM tactics. Insects. 12(3). Article 207. https://doi.org/10.3390/insects12030207.
Amanullah, S., Gao, P., Agyei, B., Osaeab, A., Yang, T., Liu, S., Weng, Y., Luan, F. 2021. Genetic linkage mapping and QTL identification for morphology and fruit quality related traits of melon by SNP based CAPS markers. Scientia Horticulturae. 278(27 February 2021). Article 109849. https://doi.org/10.1016/j.scienta.2020.109849.
Palmieri Rocha, L., Ellison, S.L., Senalik, D.A., Simon, P.W., Brunet, J. 2020. Genetic markers to detect introgression of cultivar genes in wild carrot populations. Acta Horticulturae. 1264:165-174. https://doi.org/https://doi.org/10.17660/ActaHortic.2019.1264.20.
Abdelrazek, S., Simon, P.W., Colley, M., Aime, C., Mengiste, T., Hoagland, L. 2020. Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci. PLoS ONE. 15(6). Article e0233783. https://doi.org/10.1371/journal.pone.0233783.
Abdelrazek, S., Choudhari, S., Thimmapuram, J., Simon, P.W., Colley, M., Mengiste, T., Hoagland, L. 2020. Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype. Scientific Reports. 10. Article 13685. https://doi.org/10.1038/s41598-020-70683-x.
Iorizzo, M., Curaba, J., Pottorff, M., Ferruzzi, M., Simon, P.W., Cavagnaro, P. 2020. Carrot anthocyanins genetics and genomics: Status and perspectives to optimize its application for the food colorant industry. Genes. 11(8). Article 906. https://doi.org/10.3390/genes11080906.
Macko-Podgórni, A., Stelmach, K., Kwolek, K., Machaj, G., Ellison, S., Senalik, D.A., Simon, P.W., Grzebelus, D. 2020. Mining for candidate genes controlling secondary growth of the carrot storage root. International Journal of Molecular Sciences. 21(12). Article 4263. https://doi.org/10.3390/ijms21124263.
Sowa, M., Mourao, L., Sheftel, J., Kaeppler, M., Simons, G., Davis, C.R., Simon, P.W., Pixley, K.V., Tanumihardjo, S.A. 2020. Overlapping vitamin A interventions with provitamin A carotenoids and preformed vitamin A fortificant cause high liver retinol stores in male mongolian gerbils. Journal of Nutrition. 150(11):2912-2923. https://doi.org/10.1093/jn/nxaa142.
Nijabat, A., Bolton, A., Mahmood-Ur-Rehman, M., Ijaz Shah, A., Hussain, R., Naveed, N., Ali, A., Simon, P.W. 2020. Cell membrane stability and relative cell injury in response to heat stress during early and late seedling stages of diverse carrot (Daucus carota L.) germplasm. Hortscience Proceedings. 55(9):1446-1452. https://doi.org/10.21273/HORTSCI15058-20.
Simon, P.W., Rolling, W.R., Senalik, D.A., Bolton, A., Rahim, M.A., Mannan, M., Islam, F., Ali, A., Nijabat, A., Naveed, N.H., Hussain, R., Ijaz, A. 2021. Tapping into wild carrot diversity for new sources of abiotic stress tolerance to strengthen carrot pre-breeding in Bangladesh and Pakistan. Crop Science. 61(1):163-176. https://doi.org/10.1002/csc2.20333.
Geoffriau, E., Simon, P.W. (editors). 2021. Carrots and related Apiaceae crops, 2nd edition. Boston: CAB International. 346 p.
Li, S., Ji, F., Hou, F., Shi, Q., Xing, G., Chen, H., Weng, Y., Kang, X. 2021. Molecular, morphological and palynological assessment of hemerocallis core collection. Scientia Horticulturae. 285. Article 110181. https://doi.org/10.1016/j.scienta.2021.110181.
Weng, Y. 2021. Cucumis sativus: Chromosome evolution, domestication, and genetic diversity: Implications for cucumber breeding. In: Goldman, I., editor. Plant Breeding Reviews, Volume 44. Wiley Online Library. p. 79-111. https://doi.org/10.1002/9781119717003.ch4.
Yang, S., Zhang, K., Zhu, H., Zhang, X., Yan, W., Liu, D., Hu, J., Wu, Y., Weng, Y., Yang, L. 2020. Melon short internode (CmSi) encodes an erecta-like receptor kinase regulating stem elongation through auxin signaling. Horticulture Research. 7. Article 202. https://doi.org/10.1038/s41438-020-00426-6.
Liangliang, H., Zhuoshuai, J., Peng, L., Jing, S., Weng, Y., Peng, C., Shenli, D., Aiming, W., Yuhong, L. 2021. A mutation in CsHY2 encoding a phytochromobilin (PFB) synthase leads to a deficiency in phytochrome system and elongated hypocotyl 1(elh1) phenotype in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 134:2639-2652. https://doi.org/10.1007/s00122-021-03849-4.
Li, X., Sun, Y., Yang, Y., Yang, X., Xue, W., Wu, M., Chen, P., Weng, Y., Chen, S. 2021. Transcriptomic and histological analyses of the response of susceptible and resistant cucumbers to root-knot nematode infection reveal complex resistance via multiple signalling pathways. Frontiers in Plant Science. 12. Article 675429. https://doi.org/10.3389/fpls.2021.675429.
Hul, W., Jing, S., Fang, Y., Weng, Y., Peng, C., Shenli, D., Aiming, W., Yuhong, L. 2021. CsKTN1 for a katanin p60 subunit is associated with the regulation of fruit elongation in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 134:2429-2441. https://doi.org/10.1007/s00122-021-03833-y.