Validation of SNP markers associated with late leaf spot resistance in groundnut

Late leaf spot (LLS) disease causes over 70% yield loss to groundnut by reducing plant area available for photosynthesis. The objective of this research was to validate four SNP markers for the identification of LLS-resistant plants. A total of 188 F-2 plants derived from a cross between LLS-resistant CS16 and LLS-susceptible Shitouqi were genotyped with four SNP markers proposed to be linked to LLS resistance in groundnut. Phenotypic data (LLS severity score) was taken on F-2:3 families derived through selfing F-2 lines. Polymorphism test revealed that marker GKAMA02GL779 could not distinguish between the two divergent parents, hence it was excluded from further analysis. Single marker analysis using Kruskal-Wallis analysis of variance and linear regression, both established strong association between three SNP markers (GKAMA02GL582, GKAMA02GL829 and GKAMA02GL975) and LLS resistance with adjusted R-2 values of 0.758, 0.73 and 0.613, respectively. Three out of the four proposed markers for LLS resistance breeding have been validated and can be used in future breeding programmes to identify LLS-resistant groundnut lines.