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United States Department of Agriculture

Agricultural Research Service


Location: Vegetable Crops Research

2013 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. BSL-1; Recertified through August 5, 2012. Certificate #SC09-161R.

3. Progress Report:
New wild carrot germplasm was collected in Tunisia, California, and Morocco. USDA experimental carrot breeding entries were evaluated for field productivity and consumer quality traits, as well as resistance to nematodes, and Alternaria leaf blight was evaluated in California and Wisconsin, respectively. New USDA hybrids performed very well in the trial, as did USDA germplasm. Flavor evaluation was also performed for all entries. Nine flavonoid and four carotenoid pathway genes and three additional nematode resistance genes were identified as candidate genes and genetically mapped. Families were developed to determine the genetic basis of carrot cytoplasmic male sterility restoration, alternaria resistance, and additional nematode resistance. The carrot transcriptome was analyzed and characterized and simple sequence repeat (SSR) markers were developed. Carrot transposable element variation was evaluated but not observed in a wild relative of carrot from North Africa. Carrot breeding is more efficient with genetic information about important traits and molecular tools to facilitate the breeding progress. Onion germplasm were screened for resistance to pink root and Fusarium, foliage variation evaluated, and traits genetically analyzed including fructans, male-fertility restoration, leaf waxiness, and bulb colors. Completed sequencing of onion complementary deoxyribonucleic acid (cDNAs) and presently identifying large numbers of single nucleotide polymorphisms in onion. Gynogenic haploids were previously extracted from hybrids from a cross of a doubled-haploid line with an inbred to map deoxyribonucleic acid (DNA) polymorphisms. This will shorten time for hybrid development to reduce development costs and increase grower competitiveness. New cucumber mapping populations were developed for framework or fine genetic mapping of genes controlling fruit skin and spine color, little leaf, parthenocarpy fruit setting, anthracnose resistance, and powdery mildew resistance quantitative trait loci (QTL)S. Phenotyping was conducted in both the greenhouse and field for fruit number, size and flowering dates, parthenocarpy fruit setting, as well as disease resistances. Linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers. Molecular and cytological tools were used to reveal the evolutionary history of chromosomes in Cucumis species. Machine trials were conducted in commercial fields. These results will accelerate genetic selection in cucumber breeding programs. This research relates to Objective 1 by elucidating the genetic basis of carrot, onion, and cucumber disease resistance, consumer quality, and seed productions, and to Objective 2 to develop genetic and breeding stocks, by developing genetic maps, transposon mobility patterns, and marker-assisted selection populations of carrot, onion, and cucumber.

4. Accomplishments

Review Publications
Lu, J., Qi, J.J., Shi, Q.X., Shen, D., Zhang, S.P., Shao, G.I., Li, H., Sun, Z.Y., Weng, Y., Shang, Y., Van Treuren, R., Van Dooijeweert, W., Zhang, Z.H., Huang, S.W. 2012. Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS One. Available:

Alessandro, M.S., Galamarini, C.R., Iorizzo, M., Simon, P.W. 2013. Molecular mapping of vernalization requirement and fertility restoration genes in carrot. Theoretical and Applied Genetics. 126(2):415-423.

Simon, P.W., Iorizzo, M., Senalik, D.A., Szklarczyk, M., Grzebelus, D., Spooner, D.M. 2012. De novo assembly and characterization of the carrot mitochondrial genome using next generation sequencing data from whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. Biomed Central (BMC) Plant Biology. 12:1-17.

McManus, M.T., Joshi, S., Leung, S., Albert, N., Pither-Joyce, M., Shaw, M., Mccallum, J., Searle, B., Shigyo, M., Jakse, J., Havey, M.J. 2012. Genotypic variation in sulfur assimilation and metabolism of onion (Allium cepa L.) III. Characterization of sulfite reductase. Phytochemistry. 83:34-42.

Iorizzo, M., Grzebelus, D., Senalik, D.A., Szklarczyk, M., Spooner, D.M., Simon, P.W. 2012. Against the traffic: The first evidence for mitochondrial DNA transfer into the plastid genome. Mobile Genetic Elements. 2(6):261-266.

Iorizzo, M., Senalik, D.A., Ellison, S., Grzebelus, D., Cavagnaro, P., Allender, C., Brunet, J., Spooner, D.M., Van Deynze, A., Simon, P.W. 2013. Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). American Journal of Botany. 100(5):930-938.

Azhaguvel, P., Rudd, J.C., Ma, Y., Luo, M., Weng, Y. 2011. Fine genetic mapping of greenbug aphid resistance gene Gb3 in Aegilops tauschii. Theoretical and Applied Genetics. 124(3):555-564.

Weng, Y., Yang, L., Koo, D., Li, Y., Xuejiao, Z., Luan, F., Havey, M.J., Jiang, J. 2012. Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly . Plant Journal. 71:895-906.

Garcia-Mas, J., Benjak, A., Sanserverino, W., Bourgeois, M., Mir, G., Gonzalez, V.M., Henaff, E., Camara, L., Cozzuto, L., Lowy, E., Alioto, T., Capella-Gutierrez, S., Blanca, J., Canizares, J., Ziarsolo, P., Gonzalez-Ibeas, D., Rodriguez-Moreno, L., Droege, M., Du, L., Alvarez-Tejado, M., Lorente-Galos, B., Mele, M., Yang, L., Weng, Y., Navarro, A., Marques-Bonet, T., Aranda, M.A., Nuez, F., Pico, B., Gabaldon, T., Roma, G., Guigo, R., Casacuberta, J.M., Arus, P., Puigdomenech, P. 2012. The genome of melon (Cucumis melo L.). Genome amplification in the absence of recent duplication in an old widely cultivated species. Proceedings of the National Academy of Sciences. 109(29):11872-11877.

Yang, L., Li, D., Li, Y., Gu, X., Huang, S., Garcia-Mas, J., Weng, Y. 2013. A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. Biomed Central (BMC) Plant Biology. 13(53):1-14.

Bowman, M.J., Simon, P.W. 2013. Quantification of the relative abundance of plastome to nuclear genome in leaf and root tissues of carrot (Daucus carota L.) using quantitative PCR. Plant Molecular Biology Reporter. 31(4):1040-1047.

Duangjit, J., Bohanec, B., Chan, A.P., Town, C.T., Havey, M.J. 2013. Transcriptome sequencing to produce SNP-based genetic maps of onion. Theoretical and Applied Genetics. 126(8)2093:2101.

He, X., Li, Y., Pandey, S., Yandell, B.S., Pathak, M., Weng, Y. 2013. QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L). Theoretical and Applied Genetics. 126(8):2149-2161.

Li, Y., Wen, C., Weng, Y. 2013. Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor. Theoretical and Applied Genetics. 126(8):2187-2196.

Yildiz, M., Willis, D.K., Cavagnaro, P.F., Iorizzo, M., Abak, K., Simon, P.W. 2013. Expression and mapping of anthocyanin biosynthesis genes in carrot. Theoretical and Applied Genetics. 126(7):1689-1702.

Last Modified: 10/18/2017
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