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United States Department of Agriculture

Agricultural Research Service

Research Project: Translational Genomics for Recessive Disease Resistance in Cucumber

Location: Vegetable Crops Research Unit

2013 Annual Report


1a.Objectives (from AD-416):
1) Develop a high-resolution cucumber inter-varietal linkage map placing at least 1,200 SSRs anchored with whole genome scaffolds..
2)Develop an efficient RNAi/transformation or VIGS..
3)Develop elite lines with DM and ZYMV resistance; identify molecular markers for the recessive DM and ZYMV resistance genes that can be used for MAS in breeding..
4)Identify candidate genes for downy-mildew and ZYMV resistance, and verify their functions.


1b.Approach (from AD-416):
SSR markers were explored from cucumber whole genome sequence, and selected for mapping in an F2:3 mapping populations. Expect to place 1,200 SSRs on the map. 2. SNP discovery, SNP array development and use for fine mapping SNPs will be identified through alignment of whole genome sequences of two sequenced cucumber genotypes (9930 and Gy14), validated. SNP microarray will be manufactured through contract service to a company. The array will be used for SNP linkage mapping to identify markers linked with downy mildew and ZYMV disease resistance gene. 3. Cloning of ZYMV disease resistance locus from cucumber. Will use map-based cloning strategy.


3.Progress Report:

This project was renumbered from 3655-21000-048-36R to 3655-21000-062-10A. Development of applied genomics tools. We are developing a recombinant inbred line (RIL) population from Gy14 x 9930 mating for high-density genetic mapping. Currently 150 F7/F8 RILs are available; over 400 more are under development. For linkage mapping, a consensus cucumber genetic with 1,362 marker loci, mainly simple sequence repeat (SSRs) has been developed and released. The resulting map was used to anchor the Gy14 draft genome scaffolds for more complete physical map. For single nucleotide polymorphisms (SNP) discovery, we have re-sequenced four cucumber lines. For developing the virus induced gene silencing (VIGS) functional genomics assay tool, we have obtained the necessary permission and biosafety permits and have received the Apple latent spherical virus (ALSV) cloning vectors from a lab in Japan.

Molecular mapping/cloning of downy mildew (DM) and zucchini yellow mosaic virus (ZYMV) resistances and understanding of molecular interactions between the downy mildew pathogen and cucumber host. For quantitative trait loci (QTL) mapping of DM resistance, we have developed several mapping populations including a RIL population from plant introduction line (PI) 197088 × Coolgreen and PI 197088 x Poinsett 76, as well as an F2:3 population from PI 330628 x 9930. Several F2 populations among old and new resistance sources are being developed for study of inheritance and allelism tests. For cloning of ZYMV resistance gene, SSR markers were scored across the genomic region carrying this resistance and linkage mapping was initiated. Crosses were also made between potyvirus resistant TMG1 cucumber with divergent susceptible cucumber germplasm for linkage mapping with SSRs across the genomic region carrying the zym locus. For DM-cucumber interactions, we compared infection stages and DM pathogen growth on susceptible and resistant cucumber lines. We also conducted transcriptome profiling in resistant and susceptible lines in response to DM pathogen inoculation.

Evaluate economic benefits. We have undertaken an extensive survey of slicing and pickling cucumber statistics through discussions with growers and processors. We have also developed an extensive discussion instrument for gathering information on regional value chains from grower to processor with the intent to understand relationships between growers and processors, the distribution of economic risks between growers and processors and quantitative values necessary to model the viable geographic scope of regional processing centers and the minimum feedstock necessary by size of processor.

Outreach. The research team members attended a number of stakeholders’ meetings or professional meetings, gave presentations and organized workshops aiming to enhance communication with various segments of the industry, and to educate the public on the need for sound scientific practices to resolve biological problems.

This research relates to objectives 1 and 2 through the development of applied genomics tools, molecular mapping/cloning of downy mildew and zucchini yellow mosaic virus resistances and understanding of molecular interactions between the downy mildew pathogen and cucumber host, evaluating economic benefits, and outreach.


Last Modified: 7/30/2014
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