Identification of genomic differences and the candidate genes for drought tolerance in peanut

The peanut minicore accessions and seven check varieties were evaluated for the growth, productivity and physiological traits under well-watered and water stressed conditions during the summer seasons of 2018 and 2019 in a split plot design. Main plot factor (moisture regimes) sub plot factor (genotypes) and their interactions showed significant differences for most of the traits. Yield traits followed by growth and physiological traits showed high variability. Relative water content (RWC) and SPAD chlorophyll meter reading (SCMR) were significantly positively correlated with the yield. Based on the drought tolerance index (DTI), drought tolerant (DT) and drought susceptible (DS) genotypes were identified. Single nucleotide polymorphisms (SNPs) from the whole genome re-sequencing (WGRS) data of DT (ICG-11855, ICG-14475, ICG-11219 and C76-16) and DS (ICG-5662, ICG-4911, ICG-3673 and A72) genotypes were compared to identify the genomic difference. Of the 2902001 SNPs observed between the two groups, 203 loci had contrasting alleles between DT and DS genotypes. They corresponded to seven genes on chromosomes A05, A07, A08, B03 and B09, and these genes were metabolically active in drought tolerance. These genes also carried one or more transposable elements in their gene body or promoter regions or both, indicating yet another layer of functional regulation. The gene Arahy.824BKL, coding for zinc knuckle family protein, was previously also shown to be significantly upregulated in the leaves during senescence. Overall, the SNPs and the genes identified from this study could be useful in deciphering the gene function and genomics-assisted breeding for drought tolerance in peanut.