Progress 03/12/18 to 03/11/23
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. This is the final report for this project which terminated in March 2023. See the report for the replacement project, 5090-21000-073-000D, ⿿Trait Discovery, Genetics, Genomics, and Enhancement of Cucumis, Daucus, and Allium Germplasm for additional information. (Objective 1) Many cucumber lines were phenotyped in greenhouse, growth chamber and field trials to identify various horticulturally important traits including fruit size and shape, hypocotyl length, flowering time, parthenocarpy fruit setting, abiotic stress tolerance (low temperature germination), and disease resistances (downy mildew, powdery mildew, angular leaf spot, and anthracnose). A panel of 399 cucumber lines were established genome-wide association study (GWAS). Inbred lines for lines in the GWAS panel were developed by continuous self-pollination. This panel was subjected for multiple-year, multiple environment phenotyping focusing on downy and powdery mildew resistances, and plant architecture and yield-related traits. 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. Insects and microbial diseases can significantly reduce the commercial value of the onion crop, but in a diverse collection of onion varieties held in the USDA germplasm collection, some varieties exhibit minimal damage due to these insects and diseases. Seed was produced from onions selected over years for less damage under natural pressure from the insect referred to as thrips, which not only damages the leaves of onion plants, but also vectors viral diseases that significantly reduce the productivity of the onion crop. Variation in the amounts and types of epicuticular waxes on the surface of onion leaves was found to significantly influence the damage caused by thrips and in an analysis of onion breeding stocks, a single gene was demonstrated to control much of the variation in wax composition. Beyond the insect damage to the onion crop due to thrips, two microbial diseases called pink root and Fusarium basal rot also significantly reduce onion productivity and postharvest storage quality. Carrot provides 12-13% of the dietary vitamin A for U.S. consumers and new breeding populations with higher nutritional value. Novel colors were identified and advanced to increase seed production and expand testing. Experimental hybrid carrots from the USDA program performed very well in trial comparisons with commercial cultivars and seed released by the USDA program to the U.S. seed industry is used by them to develop the majority of the current U.S. crop. USDA carrot breeding selections with very good flavor and nematode resistance were among those with superior field performance, and unique, superior nematode resistance derived from USDA carrot germplasm contributes to reduced use of pesticides for production of the U.S. crop. Carrot populations selected for the expanding U.S. organic carrot industry were advanced in the breeding program. (Objective 2) The abovementioned cucumber work resulted in many inbred lines, introgression lines, near-isogenic lines which may be of value to plant breeders or cucurbit researchers. These germplasm lines include the GWAS panel of 399 inbred lines from the core collection will be made publicly available. Given the significant damage that thrips inflict on onion due to their feeding and to the viruses they carry, the development of DNA markers were developed to track this gene to develop thrips resistant onion cultivars. Onion selections with high levels of resistance to pink root and Fusarium basal rot were used to track the incorporation of genetic resistance to these two diseases and a single gene was found to confer significant resistance to pink root, and three genes were found to control resistance to Fusarium. Carrot genetic mapping populations and diverse germplasm were phenotyped for nematode and Alternaria leaf blight resistance, top size, flavor, and root pigment content, and molecular genetic markers were developed to incorporate these traits into new breeding stocks. 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 carrot genome sequence was completed in a collaborative project led by ARS researchers in Madison, Wisconsin, along with collaborators at the University of California-Davis. The carrot genome has been used to provide molecular genetic markers to better understand angiosperm evolution, the genetic and molecular basis of orange and purple carrot color, and the identity of genes associated with the domestication of 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. A wide range of stress and disease tolerance, vigor, and consumer quality was also observed in this germplasm collection. (Objective 3) The whole genomes of the cucumber GWAS panel were genotyped with genotyping-by-sequencing (GBS) as well as whole genome resequencing. The genetic diversity and population structure of the GWAS population was evaluated. Many segregating populations (F2, F2:3 and recombinant inbred lines) were developed for target traits, and linkage maps were developed using genotyping-by-sequencing, and the DArTagging SNP genotyping technologies. QTL analysis, linkage analysis and association analysis were performed in these populations. Genes and QTLs for many traits were identified to understand the genetic basis of these traits. Several genes or disease resistance QTK were fine mapped or cloned, which helped elucidating the underlying molecular mechanisms regulating those traits New red and yellow onion breeding stocks were developed with resistance to both pink root and Fusarium basal rot. In addition to these breeding stocks, one onion hybrid and seven other onion breeding populations with novel bulb color, mild flavor, and very long storage ability, were released to vegetable breeders and researchers. Carrot inbred breeding stocks and breeding pools incorporating newly characterized genes for improved productivity, nematode and Alternaria leaf blight resistance, flavor, color and nutritional value was initiated and advanced to release for use by carrot breeding programs and evaluation by researchers. (Objective 4) This project also generate wealthy information on cucumber genome sequences for the core collection, molecular markers, gene sequences for target traits, phenotypic data for the GWAS panel genetic maps, information for genes and QTL. All these resources are being made available to the public through publications and publicly accessible databases Plant germplasm evaluation and plant breeding and genetics programs for crops including carrot generate large datasets to characterize crop traits and their genetic makeup. These datasets are often grouped into databases by the crop, or family of related crops, that have been characterized. In this project a database called CarrotOmics was developed to provide a resource for collecting and organizing genetic and agricultural data for carrot and related crops. The images and genomic data collected constitutes a database that is of vital importance and interest to plant researchers, crop breeders in public and private sector, crop production and processing industries, and consumers. The carrot breeding stocks, genetic information, and CarrotOmics database provide a valuable foundation for ongoing research. ACCOMPLISHMENTS 01 Map-based cloning of a new gene for downy mildew resistance in cucumber. The gene dm5.3 confers high-level resistance against downy mildew (DM), which is a severe disease in cucumber production, but the underlying resistance mechanism is unknown. ARS scientists in Madison, Wisconsin, conducted fine genetic mapping of dm5.3 to identify the gene and obtain clues to the mechanism. Extensive phenotyping and fine mapping narrowed dm5.3 into a 144 kilobase region. Multiple lines of evidence identified the ⿿sigma factor binding protein 1⿿ (CsSIB1), a member of the VQ motif- containing protein family as the gene responsible. A single base pair mutation in CsSIB1 was likely the cause of dm5.3-conferred DM resistance. In response to DM pathogen inoculation, CsSIB1 exhibited higher expression in the resistant than in the susceptible plants. Identification of the gene will lead to an improved understanding of the molecular mechanisms of DM resistance in cucumber and other crop plants. This work also provides molecular markers that could be used for marker-assisted breeding of DM resistance in cucumber breeding. 02 Development of a database for carrots and related crops. In crop improvement programs large datasets to characterize crop traits and their genetic makeup are generated. These datasets, known as databases, are often grouped by the crop, or family of related crops, that have been characterized. With recent sequencing of the carrot genome, large datasets are rapidly being generated, so ARS researchers in Madison, Wisconsin, developed a database called CarrotOmics to provide a resource for collecting and organizing agricultural and genetic data for carrot and related crops. The images and genomic data collected constitutes a database that is of great interest to plant researchers, crop breeders in public and private sector, crop production and processing industries, and consumers since the carrot breeding stocks and genetic information in the CarrotOmics database provides a valuable foundation for ongoing research.
Impacts
(N/A)
Publications
- Trivino, N., Rodriguez-Sanchez, A., Filley, T., Camberato, J., Colley, M., Simon, P.W., Hoagland, L. 2023. Carrot genotypes differentially alter soil microbial communities and scavenge nitrogen from organic materials in soil. Frontiers in Plant Science. Article (the author) 2023. https://doi.org/10. 1007/s11104-023-05892-0.
- Che, G., Pan, Y., Liu, X., Li, M., Zhao, J., Yan, S., Yuting, H., Wang, Z., Cheng, Z., Song, W., Zhou, Z., Wu, T., Weng, Y., Zhang, X. 2022. Natural Variation in CRABS CLAW contributes to fruit length divergence in cucumber. The Plant Cell. 35(2). https://doi.org/10.1093/plcell/koac335.
- Nijabat, A., Manzoor, S., Faiz, S., Naveed, N., Bolton, A., Khan, B., Ali, A., Simon, P.W. 2023. Variation in seed germination and amylase activity of diverse carrot [daucus carota (L.)] germplasm under simulated drought stress. HortScience. 58(2):205-214. https://doi.org/10.21273/HORTSCI16806- 22.
- Rolling, W.R., Senalik, D.A., Iorizzo, M., Ellison, S., Van Deynze, A., Simon, P.W. 2022. CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). Horticulture Research. 2022, 1-8. https://doi.org/10.1093/database/baac079.
- Chintha, P., Sarkar, D., Pecota, K., Dogramaci, M., Shetty, K. 2021. Improving phenolic bioactive-linked functional qualities of sweet potatoes using beneficial lactic acid bacteria-based biotransformation strategy. Horticulturae. 7(10). Article e367. https://doi.org/10.3390/ horticulturae7100367.
- Brainard, S., Ellison, S., Simon, P.W., Dawson, J., Goldman, I. 2021. Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values.. Theoretical and Applied Genetics. 135:605⿿622. https://doi.org/10.1007/s00122-021- 03988-8.
- Zhai, X., Wu, H., Wang, Y., Zhang, Z., Shan, L., Zhao, X., Wang, R., Liu, C., Weng, Y., Wang, Y., Liu, X., Ren, H. 2022. The fruit glossiness locus, dull fruit (D) encodes a C2H2 type zinc finger transcription factor CsDULL in cucumber (Cucumis sativus L.). Horticulture Research. 2022, 9: uhac146. https://doi.org/10.1093/hr/uhac146.
- 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.K., Ando, K., Mccreight, J.D., Schaffer, A., Burger, J., Tadmor, Y., Katzir, N. , Tang, Z., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, P.W., 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. (2019): Vol. 4747(D1):D1128-D1136.. https://doi.org/10.1093/nar/gky944.
- Tan, J., Wang, Y., Dymerski, R.D., Wu, Z., Weng, Y. 2022. Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus). Theoretical and Applied Genetics. 135:4197⿿4215. https://doi.org/10.1007/ s00122-022-04212-x.
- Chen, F., Yong, J., Zhang, G., Liu, M., Wang, Q., Zhong, H., Pan, Y., Chen, P., Weng, Y., Li, Y. 2023. LTR retrotransposon insertion inside CsERECTA for a LRR receptor-like Serine/threonine-protein kinase results in compact (cp) plant architecture in cucumber. Journal of Theoretical and Applied Genetics. Article number 31. https://doi.org/10.1007/s00122-023-04273-6.
- Feng, Z., Sun, L., Dong, M., Fan, S., Xi, K., Wang, W., Song, L., Weng, Y., Liu, X., Ren, H. 2023. Novel players in organogenesis of and flavonoid biosynthesis in cucumber glandular trichomes. Plant Physiology. 192 (4), 2723-2736. https://doi.org/10.1093/plphys/kiad236.
- Liu, H., Zhao, J., Chen, F., Wu, Z., Tan, J., Nguyen, N., Cheng, Z., Weng, Y. 2023. Improving Agrobacterium tumefaciens-mediated genetic transformation for gene function studies and mutagenesis in cucumber (Cucumis sativus). Genes. 14(3), 601. https://doi.org/10.3390/ genes14030601.
- Zhao, J., Bo, K., Pan, Y., Li, Y., Yu, D., Li, C., Chang, J., Wu, S., Wang, Z., Zhang, X., Gu, X., Weng, Y. 2022. Phytochrome-interacting factor PIF3 integrates phytochrome B and UVB signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls. Journal of Experimental Botany. 74(15):4520-4539. https://doi.org/10.1093/plcell/ koac335.
- Perez, M.B., Carvajal, S., Beretta, V., Bannoud, F., Fangio, F., Berli, F., Fontana, A., Salomon, V.M., Gozalez, R., Valerga, L., Altamirano, J., Yildiz, M., Iorizzo, M., Simon, P.W., Cavagnaro, P., Churio, S. 2023. Characterization of purple carrot germplasm for antioxidant capacity and root concentration of anthocyanins, phenolics, and carotenoids. Plants. 12(9) Article 1796. https://doi.org/10.3390/plants12091796.
|
Progress 10/01/21 to 09/30/22
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. 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. ACCOMPLISHMENTS 01 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. 02 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.
Impacts
(N/A)
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. https://doi.org/10.1007/s00122-021-03901- 3.
- 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. https://doi.org/10.3390/genes12101464.
- 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. https:// doi.org/10.3389/fnut.2021.787351.
- 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. https://doi. org/10.3390/plants10091972.
- 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. https://doi.org/10.1007/s00122-021-04026- 3.
- 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. https://doi.org/10.1016/j.scienta.2022.111059.
- 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. https://doi.org/10.1021/acsfoodscitech.1c00433.
- 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. https://doi.org/10.1021/acsfoodscitech.1c00453.
- 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. https://doi.org/10.21273/ JASHS05075-21.
- 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. https://doi.org/10.3390/ horticulturae7120538.
- 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. https://doi.org/10.1007/s00122-022-04100-4.
|
Progress 10/01/20 to 09/30/21
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. 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. Record of Any Impact of Maximized Teleworking Requirement: The size of the cucumber field program in 2021 was reduced due to restrictions by the University of Wisconsin and USDA limiting field workers. The size of the carrot seed production trial and breeding stock evaluation in field programs was reduced due to restrictions prohibiting project personnel to travel to the major winter nursery trial to harvest the crop. The initiation of new projects and activities was reduced for both programs given limited access to laboratories. ACCOMPLISHMENTS 01 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. 02 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.
Impacts
(N/A)
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.
|
Progress 10/01/19 to 09/30/20
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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 01 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. 02 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. 03 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. 04 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.
Impacts
(N/A)
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.
- 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.
- 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.
- Che, G., Gu, R., Zhao, J., Liu, X., Song, X., Zi, H., Cheng, Z., Shen, J., Wang, Z., Song, X., Liu, R., Yan, L., Weng, Y., Zhang, X. 2020. Gene regulatory network controlling carpel number variation in cucumber. Development. 147 (7).
- 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.
- 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.
- 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.
- 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.
- Havey, M.J. 2020. Genetic mapping of chartreuse bulb color in onion. Journal of the American Society for Horticultural Science. 145(2):110-119.
- Lee, H., Havey, M.J. 2020. Variable penetrance among different sources of the male fertility restoration allele of onion. HortScience. 55(4):543-546.
- 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.
- 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.
- 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.
- 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.
- 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.
- Simon, P.W., Iorizzo, M., Grzebelus, D., Baranski, R. 2019. The carrot genome. Cham, Switzerland:Springer Nature Switzerland AG. 372 p.
- 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.
- 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.
- 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.
|
Progress 10/01/18 to 09/30/19
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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. Accomplishments 01 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. 02 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. 03 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.
Impacts
(N/A)
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.
|
Progress 10/01/17 to 09/30/18
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. Research has been initiated for all milestones including planning for development of new breeding populations, planting germplasm for evaluation in field sites and controlled environments, initiation of disease screening, field phenotyping, laboratory evaluations, and genetic marker analysis. Database development is underway and new data collected has been entered.
Impacts
(N/A)
Publications
- Byrne, P.F., Volk, G.M., Gardner, C.A., Gore, M.A., Simon, P.W., Smith, S. 2018. Sustaining the future of plant breeding: The critical role of the USDA-ARS National Plant Germplasm System. Crop Science. 58(2):451-468.
|
|