Phenotypic Evaluation for Water Deficit Stress Tolerance and the Study of Targeted Re-Sequencing Approach in Peanut

The segregating F2:4 and F2:5 generations from the cross between COC270 and TX071304 were screened for physiological traits SPAD reading, flower count, canopy temperature and leaf closure over two years 2015 and 2016 respectively, under water deficit conditions over different time periods. Significant differences were observed among the genotypes for SPAD, canopy temperature and leaf closure across years. There were significant differences among the genotypes for SPAD and leaf closure readings within years. The use of a stepwise regression model gave a significant correlation (r = 0.38) between the predicted yield and observed yield. The predicted yield based on this model was consistent with actual yield for most of the top ranks. An integrated approach of improved bioinformatics and targeted resequencing was used to identify and select homeologous SNPs in tetraploid peanuts for mapping studies. A SNP identification pipeline was developed using GATK software to identify SNPs. SNPs were identified using four different approaches, GATK pipeline, SWEEP filter, alignment against OLin transcriptome and few SNPs were selected from the peanut SNP chip. Forty-eight targets of around 400 bp length were selected for validation on a Fluidigm Access Array as a proof of concept, followed by mass sequencing on an Illumina MiSeq. Eighty –one percent of the SNP calls derived from the Fluidigm – MiSeq were validated for diploids, and 72% of the SNP calls were validated for tetraploids. This approach will benefit tetraploid breeding programs by reducing the cost of genotyping of QTL mapping populations and used in QTL studies on water deficit stress tolerance populations.