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United States Department of Agriculture

Agricultural Research Service

Research Project: WHOLE GENOME APPROACH FOR GENETIC ANALYSIS IN CUCUMBER: FRUIT SIZE AS A TEST CASE
2012 Annual Report


1a.Objectives (from AD-416):
1. Develop cucumber and melon SNP arrays for whole genome scan. We will utilize internal genomic information and public databases to create two SNP arrays: one for cucumber and one for melon.

2. Develop and characterize cucumber and melon populations segregating for fruit size. A set of segregating populations from cucumber will be analyzed for fruit size phenotype, including detailed analyses of ovary and fruit development pre- and post-anthesis.

3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. Genetic analysis using the SNP arrays developed in this project and segregating populations for fruit size will identify QTL associated with fruit size.


1b.Approach (from AD-416):
1. SNP identification. Sequencing data will be analyzed using bioinformatics tools to identify SNPs. 2. Microarray printing and validation. The microarray will be self designed and printed using the Agilent eArray platform. 3. Phenotyping segregating populations for fruit size. Three mapping populations will be used for phenotyping of fruit size (RIL and F2:3 families). Phenotypic data will be collected from field trials in two years (2010 and 2011) at two locations. 4. Characterize ovary and fruit development in parental lines. Fruits of three cucumber types: pickling, Chinese Long and hardwickii (PI183967) will be examined for ovary and fruit development. Ovaries will be examined for length, diameter, and presence and number of ovules pre- and post-anthesis The identified key features will be used in combination with segregation analyses and studies of field performance to partition contributions of fruit size QTL identified by WGS experiments. 5. Whole genome scan of different population segregating for fruit size QTL analysis will be performed to establish marker-fruit size trait associations.


3.Progress Report:

Development of populations for fruit size quantitative trait loci (QTL) mapping in cucumber. We continued developing a recombinant inbred line (RILs) mapping population for QTL mapping of fruit size in cucumber. Now 145 RILs from the cross between Gy14 and 9930 have been advanced at F7 and F8. A new population was developed for fruit size QTL mapping from XSBN-3 and PI 249561. One hundred and forty five F2 plants were advanced to F3 for fruit size phenotyping.

Phenotypic data collection. Replicated trials were conducted in three locations with the Gy14 × 9930 RIL populations. Data for fruit size of F2 plants from XSBN-3 x PI 249561 has been collected. Leaf sample from the Gy14 x 9930 RILs will be collected for DNA extraction.

This research relates to 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.


Last Modified: 11/28/2014
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