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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
2013 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:

This project was renumbered from 3655-21000-048-24R to 3655-21000-062-08R. This is the final report, project terminated 07/31/2013. Population development. As a co-PI in this three year project, we developed three mapping populations that were used for linkage mapping of quantitative trait loci (QTL) for fruit sizes (fruit length and diameter). These include 150 recombinant inbred line (RILs) from the cross between Gy14 (US pickle cucumber) and 9930 (China fresh market type), 175 F3 families from a cross between a Chinese landrace (WI 7167) and a plant introduction line from Thailand (WI 7200A), and 500 F2 plants from Gy14 and a wild plant introduction line from India (WI 7221). This work fulfills Objectives 1 and 2.

Phenotypic data collection. Replicated trials were conducted at Hancock Experimental Station in 2011, 2012, and 2013 for the Gy14 × 9930 RIL populations. In the 2013 field season, all three populations are growing in the field for data collection. In 2011, the RIL population was also grown in East Lansing, Michigan and Raleigh, North Carolina. The multi-year and multi-location data of the RIL population are being used for QTL mapping with molecular marker data single nucleotide polymorphisms (SNPs) to identify major QTLs that determine fruit length and diameter in cucumber. Data collected from the other two populations are also being used for identifying fruit size QTLs in different genetic backgrounds and validation of QTL identified from the RIL population. This work fulfills objectives 1, 2, and 3 by developing SNP arrays for whole genome scan, developing and characterizing cucumber and melon populations, and combining genomic tools and phenotypic characterization to identify loci associated with fruit size.


Last Modified: 11/24/2014
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