Screening of Groundnut Germplasm for Foliar Fungal Diseases and Population Structure Analysis Using Gene Based SSR Markers

Groundnut (Arachis hypogaea L.) is an excellent cash crop having multipurpose uses of each plant part i.e., direct consumption, cooking oil and a rich source of protein feed for animals. Rust and late leaf spot (LLS) are two major foliar fungal diseases of groundnut and can cause yield loss up to 70%. Use of fungicide is costly approach and it is not environment-friendly also, therefore breeding new cultivars with genetic resistance is sustainable, environment-friendly and cost effective approach. Screening and identification of resistant cultivar is one of the primary objective for groundnut improvement. Use of molecular markers, particularly gene based, are user friendly and cost effective approach to identify groundnut resistant genotypes. The present investigation aimed to screen groundnut germplasm using allele specific primers for foliar fungal diseases (LLS and rust). The study consisted 30 uncharacterized germplasm lines and 4 check varieties of Groundnut. A set of 4 gene based SSR markers were selected for screening of groundnut germplasms for foliar fungal diseases i.e., LLS and rust. A total of 14 alleles were identified with an average of 3.5 alleles per locus for polymorphic SSR markers. The gene diversity and Polymorphic Information Content (PIC) values varied between 0.3972-0.5778 with an average of 0.47 respectively. The genetic relationships among Groundnut genotypes are presented in SSR based UPGMA tree. Principle Co-ordinate analysis (PCA) based on origin formed 4 major population groups. The population structure of the 34 Groundnut genotypes was estimated using STRUCTURE v2.3.3 software based on SSR markers. The optimum K value was determined by using Structure Harvester, where the highest peak was observed at delta K = 2. The number of sub populations (K) was identified based on maximum likelihood and delta K (dK) values, with two core and pure groups and an admixture group. Current study identified four germplasms i.e., AH8054, CS21181, CS708, Akola White to be used as foliar disease resistant cultivar for groundnut hybridization and improvement.