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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

Location: Vegetable Crops Research Unit

Project Number: 3655-21000-062-08
Project Type: Reimbursable

Start Date: Aug 01, 2010
End Date: Jul 31, 2013

Objective:
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.

Approach:
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.

Last Modified: 9/21/2014
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