Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.)

Summary

In order to integrate genomics in breeding and the development of drought-tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used 3,249 diversity array technology sequencing (DArTSeq) markers for a genetic analysis of 125 ICRISAT groundnut mini core collections evaluated in 2015 and 2017 for genome-wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD). Marker-trait association (MTA) analysis, probability values, and percent variation modelled by the markers were calculated using the GAPIT package via the KDCompute interface. The LD analysis showed that about 36% of loci pairs were in significant LD (p < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. The MTA studies revealed 20 significant MTAs (p < 0.001) with 11 markers. Four MTAs were identified for leaf area index, 13 for canopy temperature, 1 for chlorophyll content and 2 for normalized difference vegetation index. The markers explained 20.8% to 6.6% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. This could be due to a common ancestor of the A and B genome, which explains the linkage detected between markers lying on different chromosomes. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance after further validation.