Identification of transposable element markers associated with yield and quality traits from an association panel of independent mutants in peanut (Arachis hypogaea L.)

To identify marker–trait associations (MTAs) for yield and quality traits in peanut, genic and nongenic Arachis hypogaea transposable element (AhTE) markers were employed in a population consisting of independent mutants from several parents. The population was field-evaluated during the rainy seasons of 2014 and 2015, and genotyped with 110 AhTE markers to check the polymorphisms for AhMITE1 transposition. The gene diversity index ranged from 0.00 to 0.50 with average of 0.35, indicating low to moderate genetic diversity in the population. Diversity analysis indicated the grouping of mutants derived from each parent in respective subgroups. Marker–trait association analysis for 110 markers and 40 traits resulted in 132 highly significant MTAs, represented by 58 AhTE markers for 39 traits. Nutritional traits recorded the highest number of MTAs (38), followed by agronomic traits (35), productivity traits (31), foliar disease resistance (23), and taxonomic traits (5). Seventeen MTAs with phenotypic variance explained (PVE) value above 50 % were observed for resistance to late leaf spot (LLS) and rust, plant height, and pod width. The genic and nongenic AhTE markers associated with the above traits were analyzed for their genomic location and functional annotation so that the significance of these loci can be analyzed in the future.