In order to integrate genomics in breeding and development of drought-tolerant groundnut\ngenotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential.\nWe used 3249 diversity array technology sequencing (DArTSeq) markers for a genetic analysis of 125\nICRISAT groundnut mini core collection evaluated in 2015 and 2017 for genome-wide marker-trait\nassociation for some physiological traits and to determine the magnitude of linkage disequilibrium\n(LD). Marker-trait association (MTA) analysis, probability values, and percent variation modelled by\nthe markers were calculated using the GAPIT package via the KDCompute interface. The LD analysis\nshowed that about 36% of loci pairs were in significant LD (p < 0.05 and r2 > 0.2) and 3.14% of the pairs\nwere in complete LD. The MTAs studies revealed 20 significant MTAs (p < 0.001) with 11 markers.\nFour MTAs were identified for leaf area index, 13 for canopy temperature, one for chlorophyll content\nand two for normalized difference vegetation index. The markers explained 20.8% to 6.6% of the\nphenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified\non the respective homeologous chromosome on the B subgenome. This could be due to a common\nancestor of the A and B genome which explains the linkage detected between markers lying on\ndifferent chromosomes. The markers identified in this study can serve as useful genomic resources\nto initiate marker-assisted selection and trait introgression of groundnut for drought tolerance after\nfurther validation.
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