Location: Vegetable Crops Research Unit
2013 Annual Report
2. 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.
Phenotypic data collection. In the 2011 field season, replicated trials were conducted in three locations (Hancock, Wisconsin; Raleigh, North Carolina; and East Lansing, Michigan) to collect data for fruit size (length and diameter) from the Gy14 x 9930 RIL populations. In the 2012 and 2013 field season, two more trials were conducted in Hancock, Wisconsin on this RIL population. Fruit size data have been, or will be used in QTL mapping to identify fruit size QTL in cucumber with molecular marker data. We also grew 175 F3 families and 432 F2 plants of XSBN x PI 249561 cross, as well RIL and F2 plants of GY14 x hardwickii cross at the Hancock Research Station. We have collected data for the following traits in these populations: flowering time, fruit length and diameter, fruit number and weight, and flesh color.
We sequenced the Gy14 cucumber genome at 20x genome coverage. We also re-sequenced the 9930 cucumber genome with the Illumina HiSeq 2000 platform (30x genome coverage). These sequences were sent to our collaborators in Israel for single nucleotide polymorphism (SNP) discovery and SNP array development. In total, 97,015 high quality SNPs were identified, and nearly 50% were spotted into a customized SNP array, which were used for hybridization with deoxyribonucleic acid (DNA) samples of 119 Gy14 x 9930 RILs for QTL mapping of fruit sizes in cucumber. Data analysis is underway, and we expect at least two manuscripts from the above-mentioned work.
QTL mapping and fruit size QTL validation in other mapping populations. We are developing microsatellite or simple sequence repeat (SSR)-based linkage maps using the XSBN x PI 249561 and Gy14 x HARD populations, which will be used in QTL mapping of fruit size and other traits. At this time, ~200 SSR marker loci have been placed on each map. With average marker interval of ~3 cM, phenotypic data are being collected from the field trials which will be used to identify major QTLs for fruit length and diameter, flowering time, and fruit number in cucumber. We anticipate two manuscripts from this part of research.
This research relates to objectives 1 and 2 through the development of populations for fruit size QTL mapping in cucumber, phenotypic data collection, genotyping, and the development of linkage maps.