2010 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.
New onion families were developed segregating for health-enhancing fructans, male-fertility restoration, leaf waxiness, and bulb colors. A new haploid mapping family was developed for mapping of molecular markers. Work continued on the identification of gene conditioning resistance to Zucchini Yellow Mosaic Virus.
These markers will be used to more efficiently develop lines for commercial production. This will shorten time for hybrid development to reduce development costs and increase grower competitiveness.
Three cucumber mapping populations were developed for genetic mapping of fruit quality- and yield-related genes. In 2009 field season, recombinant inbred line populations were phenotyped for fruit quality and yield related traits including fruit number, size and flowering dates. An extended microsatellite map was developed. Machine trials were conducted in commercial fields under standard practice. Cucumber genomic resources are being developed which include whole genome sequencing and characterization. Resistance gene analogs (RGAs) in the cucumber genome were bioinformatically identified, and primer pairs were designed within or near those RGA sequences. The markers were genetically mapped.
5.Significant Activities that Support Special Target Populations
A nomination was written for a Hispanic student for a UW Biotech Training and Advanced Opportunity Fellowship, which were awarded and provided 4 years funding as a graduate student in Plant Breeding & Plant Genetics at UW-Madison.
Weng, Y. 2010. Genetic diversity among cucumis metuliferus populations revealed by cucumber microsatellites. HortScience. 45(2):214-219.
Azhaguvel, P., Weng, Y., Babu, R., Manickavel, A., Saraswathi, D.V., Balyan, H.S. 2010. Fundamentals of Physical Mapping. In: Kole, C., Abbot, A. G., editors. Principles and Practices of Plant Genomics, Volume 3: Advanced Genomics. Boca Raton, FL:CRC Press. p. 24-62.
Jakse, M., Hirschegger, P., Bohanec, B., Havey, M.J. 2010. Evaluation of Gynogenic Responsiveness and Pollen Viability of Selfed Doubled Haploid Onion Lines and Chromosome Doubling via Somatic Regeneration. Journal of the American Society for Horticultural Science. 135(1):67-73.
Melgar, S., De Biologia, E., Havey, M.J. 2010. The Dominant Ms Allele in Onion Shows Reduced Penetrance. Journal of the American Society for Horticultural Science. 135:49-52.
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W., Wang, X., Xie, B., Ni, P., Ren, Y., Zhu, H., Li, J., Lin, K., Jin, W., Fei, Z., Li, G., Staub, J.E., Kilian, A., Van Der Vossen, E.A., Wu, Y., Guo, J., He, J., Jia, Z., Ren, Y., Tian, G., Lu, Y., Ruan, J., Qian, W., Wang, M., Huang, Q., Li, B., Xuan, Z., Cao, J., Wu, Z., Zhang, J., Cai, Q., Bai, Y., Zhao, B., Han, Y., Li, Y., Li, X., Wang, S., Shi, Q., Liu, S., Cho, W.K., Kim, J., Xu, Y., Heller-Uszynska, K., Miao, H., Cheng, Z., Zhang, S., Wu, J., Yang, Y., Kang, H., Li, M., Liang, H., Ren, X., Shi, Z., Wen, M., Jian, M., Yang, H., Zhang, G., Yang, Z., Chen, R., Liu, S., Li, J., Ma, L., Liu, H., Zhou, Y., Zhao, J., Fang, X., Li, G., Fang, L., Li, Y., Liu, D., Zheng, H., Zhang, Y., Qin, N., Li, Z., Yang, G., Yang, S., Bolund, L., Kristiansen, K., Zheng, H., Li, S., Zhang, X., Yang, H., Wang, J., Sun, R., Zhang, B., Jiang, S., Wang, J., Du, Y., Li, S. 2009. The Genome of the Cucumber, Cucumis Sativus L. Nature Genetics. 41(12):1275-1281.
Cuevas, H.E., Song, H., Staub, J.E., Simon, P.W. 2010. Inheritance of Beta-Carotene-Associated Flesh Color in Cucumber (Cucumis Sativus L.) Fruit. Euphytica. 171(3):301-311.
Cuevas, H.E., Staub, J.E., Simon, P.W., Zalapa, J.E. 2010. A Consensus Linkage Map that Identifies Genomic Regions Controlling Beta-Carotene Quantity and Fruit Maturity in Melon (Cucumis Melo L.). Theoretical and Applied Genetics. 119:741-756.
Just, B.J., Santos, C.F., Yandell, B.S., Simon, P.W. 2009. Major QTL for Carrot Color are Associated with Carotenoid Biosynthetic Genes and Interact Epistatically in a Domesticated x Wild Carrot Cross. Theoretical and Applied Genetics. 119(7):1155-1169.
Ortiz, R., Simon, P.W., Jansky, S.H., Stelly, D. 2009. Ploidy Manipulation of the Gametophyte, Endosperm, and Sporophyte in Nature and for Crop Improvement – A Tribute to Prof. Stanley J. Peloquin (1921-2008). Annals Of Botany. 104(5):795-807.
Simon, P.W., Cavagnaro, P.F., Senalik, D.A. 2009. SplinkBES - A Splinkerette-Based Method for Generating Long End Sequences From Large Insert DNA Libraries. Biotechniques. 47:681-690.
Sun, T., Simon, P.W., Tanumihardjo, S.A. 2009. Antioxidants and Antioxidant Capacity of Biofortified Carrots (Daucus Carota, L.) of Various Colors. Journal of Agricultural and Food Chemistry. 57(10):4142-4147.
Charron, C.S., Kurilich, A.C., Clevidence, B.A., Simon, P.W., Harrison, D.J., Britz, S.J., Baer, D.J., Novotny Dura, J. 2009. Bioavailability of Anthocyanins from Purple Carrot Juice: Effects of Acylation and Plant Matrix. Journal of Agricultural and Food Chemistry. 57(4):1226-1230.
Mills, J.P., Simon, P.W., Tanumihardjo, S.A. 2008. Biofortified Carrot Intake Enhances Liver Antioxidant Capacity and Vitamin A Status in Mongolian Gerbils. Journal of Nutrition. 138(9):1692-1698.
Ipek, M., Ipek, A., Simon, P.W. 2008. Genetic Characterization of Allium Tuncelianum: An Endemic Edible Allium Species With Garlic Odor. Scientia Horticultureae. 115(4):409-415.
Weng, Y., Staub, J.E., Johnson, S., Huang, S. 2010. An Extended Intervarietal Microsatellite Linkage Map of Cucumber, Cucumis Sativus L. HortScience. 45:882-886.
Vogel, J.P., Garvin, D.F., Gu, Y.Q., Lazo, G.R., Anderson, O.D., Bragg, J.N., Chingcuanco, D.L., Weng, Y., Belknap, W.R., Thomson, J.G., Dardick, C.D., Baxter, I.R. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.
Weng, Y., Lu, H., Rudd, J.C., Burd, J.D. 2009. Molecular mapping of greenbug resistance genes Gb2 and Gb6 in T1AL.1RS wheat-rye translocations. Plant Breeding. 129:472-476.