cgSSR marker based trait associations for Sitotroga cerealella (Olivier) resistance in stored paddy rice

Rice is stored for a longer time and many primary and secondary insect pests attack grains, causing both quantitative and qualitative losses. Physicochemical characteristics of grain influence stored grain insect susceptibility and resistance. Identification of gene/Quantitative Trait Loci (QTLs) and introgression in the cultivars would provide the desired solution for varietal resistance against S. cerealella. A group of 80 rice varieties was used for genetic analysis for the identification of candidate genes responsible for Sitotroga cerealella resistance. Heat maps derived from values in the kinship matrix were used to group the varieties into three subpopulations. The largest subpopulation has 34 varieties, while the lowest had 19. The first three principal components (PCs) explained 16, 9, and 6 percent of total variation, respectively, as indicated by the Principal Component Analysis (PCA). The PCA results complemented the heat map results in defining population structure. Genome-wide association mapping can detect marker-trait associations/QTLs in a heterogeneous population of breeding lines, despite population structure and unequal family relatedness. As shown by the Genomic Association and Prediction Integrated Tool (GAPIT) heat map, there are three subpopulations in the association mapping panel. Two cgSSR markers, related to gene SDG725 and FLO2, were linked to the attributes and responsible for conferring resistance against S. cerealella infestation. This is the first report of association and that would help in the development of cultivar with S. cerealella resistance.