Whole Genome Approach for Genetic Analysis in Cucumber: Fruit Size As a Test Case
Vegetable Crops Research Unit
2011 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.
Development of populations for fruit size Quantitative Trait Loci (QTL) mapping in cucumber. We are in the process of developing a recombinant inbred line (RIL) mapping population for QTL mapping of fruit size in cucumber. Now 124 RILs from the cross between Gy14 and 9930 have been advanced at F6 and F7. Thirty more RILs are currently at F4 or F5. Within the next 12 months, we will have a minimum of 150 F7 RILs. Another RIL population is Gy14 × PI 183967. Sixty nine F8 RILs are currently available for use. Two additional mapping populations are being developed. One is from cucumber cultivar Rissen Schol × PI 183967, and the other from XSBN × PI 183967. The populations are currently at F2. We plan to develop 150 F2:3 families from each cross for use in this project.
Phenotypic data collection. In the 2011 field season, replicated trials were conducted in three locations with the Gy14 × 9930 RIL populations. Another RIL population segregating for fruit size is the Gy14 × PI 183967. Sixty nine RILs were planted in the 2010 field season (3 reps per RIL). Fruit size data were collected for each RIL.
Deoxyribonucleic acid (DNA) samples of cucumber line 9930 were prepared and sent for whole genome sequencing for single-nucleotide polymorphism (SNP) identification.
Leaf sample from the Gy14 x 9930 RILs have been collected for DNA extraction. Project monitoring is done through e-mail correspondence and conference calls. In January 2011 during the Plant and Animal Genome Meeting, all participants met to review the progress and plan the research.