2012 Annual Report
Objective 2: Utilize current biotechnology to discover and evaluate genetic variation and to map agriculturally important traits in Allium, Cucurbit, and Daucus germplasm, and to develop genetic and breeding stocks.
Sub-objective 2.A. Construct genetic maps of nuclear and organellar genomes using candidate genes, SCARs, SSRs, SNPs, transposon insertions, BACs, and cytogenetic stocks.
Sub-objective 2.B. Fine map pigment and carbohydrate genes in carrot and onion, resistance genes for nematode in carrot and viruses in cucurbits, and epistasis, yield and quality components in cucumber.
Sub-objective 2.C. Perform marker-assisted selection of carrot nematode resistance, onion male sterility, and cucurbit yield and quality.
Sub-objective 2.D. Evaluate transgene escape in cucurbits.
Sub-objective 2.E. Determine transposon mobility in carrot.
Discovery Goal 1 - Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucurbit, and Daucus vegetables, genetically characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasms.
Many biotechnological tools have been developed to improve the efficiency of crop improvement. Objective 2 evaluates and develops these tools of carrot, onion, cucumber, and melon improvement. Identify adequate DNA polymorphisms in elite onion, cucumber, melon, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits.
Discovery Goal 2.A – Identify adequate DNA polymorphisms in elite onion, cucumber, melon, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits.
Discovery Goal 2.B – Evaluate variation at candidate genes in pigment and carbohydrate biochemical pathways for mapping in onion, cucurbit, and carrot.
Discovery Goal 2.C – Identify and utilize markers to accurately identify desirable genotypes for male sterility restoration in onion, cucurbit yield, and carrot nematode resistance.
Discovery Goal 2.D – Appraise the potential benefit(s) that transgenes might confer on transgenic populations using the ELISA test to estimate the degree of viral infection in wild populations and to determine the potential risk of virus gene introgression from commercial transgenic cultivation.
Discovery Goal 2.E - Determine if native transposable elements in the carrot genome, such as DcMaster, and introduced ones, such as maize elements Ac and Ds transpose to new chromosomal regions.
Onion germplasm was screened for resistance to pink root and Fusarium basal rot. Evaluated crosses among different sources of semi-glossy foliage to determine if this phenotype is conditioned by multiple genes. Continued development of onion families segregating for health-enhancing fructans and anthocyanins, male-fertility restoration, leaf waxiness, & bulb colors. Sequencing identified large numbers of single nucleotide polymorphisms in onion. Gynogenic haploids were previously extracted from hybrids, asexually propagated, planted in trials and measured for health-enhancing fructans and flavonoids. Deoxyribonucleic acid (DNA) was isolated from over 180 haploids for genetic mapping. These markers will be used to more efficiently develop lines for commercial production. This will shorten time for hybrid development to reduce development costs & increase grower competitiveness. Crosses were completed to validate a major quantitative trait locus on chromosome 3 of cucumber that controls mitochondrial sorting. A major grant from the USDA-Specialty Crops Research Initiative (SCRI) program will support cloning of the Zucchini Yellow Mosaic Virus resistance in cucumber.
Three new cucumber mapping populations were developed for genetic mapping of fruit quality & yield-related genes and powdery mildew resistance quantitative trait loci (QTLs). Two populations were observed & data collected for fruit quality and yield related traits including fruit number, size and flowering dates, as well as powdery mildew resistance. Molecular markers were added for construction of a high-resolution genetic map. An integrated genetic-physical map for cucumber was developed. Molecular and cytological investigations are revealing the evolutionary history of chromosomes in several cucurbit species. Machine trials were conducted in commercial fields and cucumber genomic resources are being developed which include whole genome sequencing & characterization. NB-LRR type resistance gene homologs were identified and characterized from cucumber genome and were genetic mapped. Molecular mapping of genes for resistances against the anthracnose and powdery mildew pathogens are underway.
Havey, M.J., Kielkowska, A.Z. 2011. In vitro flowering and pollen viability of cucumber. Plant Cell Tissue And Organ Culture. 109:73-82.
Howard, N., De Leon, N., Havey, M.J., Martin, W. 2012. Diallel analysis of floral longevity in Impatiens walleriana. Journal of the American Society for Horticultural Science. 137(1):47-50.
Zhang, H., Wang, H., Guo, S., Ren, Y., Gong, G., Weng, Y., Xu, Y. 2011. Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai. Euphytica. 186:329-342.
Calderon, C.I., Yandell, B.S., Havey, M.J. 2012. Genetic mapping of paternal sorting of mitochondria in cucumber. Theoretical and Applied Genetics. 125:11-18.
Grzebelus, D., Baranski, R., Spalik, K., Allender, C., Simon, P.W. 2011. Daucus. In: Kole, C., editor, Wild Crop Relatives: Genomic and Breeding Resources. New York, NY:Springer. p. 91-113.
Li, D., Weng, Y., Cuevas, H., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J.E., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z. 2011. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. Biomed Central (BMC) Genomics. 12:396-409.
Bo, K., Song, H., Shen, J., Qian, C., Staub, J.E., Simon, P.W., Lou, Q., Chen, J. 2011. Inheritance and mapping of the ore gene controlling the quantity of ß-carotene in cucumber (Cucumis sativus L.) endocarp. Molecular Breeding. 30(1):335-344.
Cavagnaro, P.F., Chung, S., Manin, S., Yildiz, M., Ali, A., Alessandro, M.S., Iorizzo, M., Senalik, D.A., Simon, P.W. 2011. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. Biomed Central (BMC) Genomics. 12:386.
Staub, J.E., Simon, P.W., Cuevas, H.E. 2011. USDA, ARS EOM 402-10 high B-carotene cucumber. HortScience. 46:1426-1427.
Cavagnaro, P.F., Weng, Y., Senalik, D.A., Simon, P.W., Harkins, T.T., Huang, S. 2010. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). Biomed Central (BMC) Genomics. 11:569-588.
Baransi, R., Maksylewicz-Kaul, A., Nothnagel, T., Cavagnaro, P., Simon, P.W., Grzebelus, D. 2011. Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci. Genetic Resources and Crop Evolution. 59(2):163-170.
Iorizzo, M., Senalik, D.A., Grzebelus, D., Bowman, M., Cavagnaro, P.F., Matvienko, M., Ashrafi, H., Van Deynze, A., Simon, P.W. 2011. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. Biomed Central (BMC) Genomics. 12:389.