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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY

Location: Vegetable Crops Research Unit

2010 Annual Report


1a.Objectives (from AD-416)
Objective 1: Determine the genetic basis of and initiate selection for carrot, onion, cucumber, and melon quality attributes influencing human nutrition and health, disease resistances, and yield and quality components, and stress tolerance in cucurbits, and perform field performance and quality trials.

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.


1b.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 targets evaluation and genetic characterization of carrot, onion, cucumber, and melon germplasm for traits important to growers and consumers.

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.


3.Progress Report
Wild carrot germplasm was collected in Tunisia and initial evaluations made. Flowering behavior and plant morphology demonstrated wide diversity. Field evaluations of carrot, onion and cucumber breeding stocks and experimental hybrids developed by this program were carried out in California, Michigan, Oregon and Wisconsin. Antioxidant activity was associated with carrot pigments and bioavailability was found to vary with chemical structure and plant tissue structure. Genetic variation was evaluated at the molecular level in a carrot genomic library and found to be associated with the expression of genes for the accumulation of carotenoid pigments.

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.


4.Accomplishments
1. Development of cucumber genomic resources. Although cucumber is an important vegetable crop in the U.S., available genetic and genomics resources are very limited which impede progress in cucumber breeding. In collaboration with Roche/454, the cucumber inbred line Gy14 was sequenced and assembled. The genome was characterized for microsatellite sequences and 83,000 genomic SSR primer pairs were designed which are publicly accessible. Development of a high-resolution genetic map is underway. Three hundred markers have been placed on this map. This research is an important contribution to the cucurbit research community worldwide, which will facilitate studies in genetic mapping, gene cloning, and marker-assisted plant breeding.

2. Little leaf and determinate growth habit are two important traits of cucumber with potentials to develop new cucumber lines with improved yield. We developed an extended genetic map of cucumber placing 176 molecular markers across seven chromosomes. The numbers of markers mapped in chromosomes 1 through 7 were 11, 6, 35, 18, 46, 45, and 15, respectively. Molecular markers for little leaf and determinate growth habit were identified, which should be useful for marker-assisted selection in cucumber breeding. This map also provides a good starting point for map-based cloning of these genes.

3. Carrot antioxidant activity is associated with pigment type, amount and tissue structure. Carrots vary widely among diverse genetic stocks for color including not only orange color but also purple, yellow, red and white. Experiments with this range of colored carrots demonstrated that higher orange, red, yellow or purple pigment concentration had higher antioxidant activity. Purple carrots from Asia, Middle East and Europe varied in pigment content, chemical structure of anthocyanin pigments and site of pigment accumulations within the root. This variation influences the amount of pigment uptake during digestion or bioavailability. This information will inform nutritionists about use of carrots in the diet to improve consumer health.

4. Genetic control of orange carrot pigments. Modern carrots accumulate orange carotene pigments, but wild carrots are white. Genetic analysis demonstrated that two genes account for much of the difference between wild and modern carrots. This information provides insight into the genetic origins of modern carrots and assists breeders in developing more nutritious carrots with implications for plant breeding to improve other crops.

5. Development of a new haploid mapping family of onion. Gynogenic haploids were extracted from hybrids from a cross of a doubled-haploid line crossed with an inbred. These haploids were asexually propagated off of the basal plate and bulbils produced. These bulbils will be planted in replicated trials and measured for health-enhancing fructans and flavonoids. Genetic mapping of SNPs will be done using this population and genetic analyses completed without heterozygosity. A major quantitative trait locus controlling mitochondrial sorting was mapped to a specific region on chromosome 3 of cucumber. Studies will continue to identify candidate genes for this unique trait.


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.


Review Publications
Peloquin, S.J., Simon, P.W., Jansky, S.H. 2009. The Concept of Horizontal Linkage and Its Application to Genetics and Breeding. In: Mohan, R.H., editor. Research Advances in Heredity. 1st edition. Kerala, India:Global Research Network. p. 1-7.

Havey, M.J., Raines, S., Henson, C.A. 2009. Genetic Analyses of Carbohydrate Accumulation in Onion. Journal of the American Society for Horticultural Science. 134:618-623.

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.

Last Modified: 8/27/2014
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