Marker-trait association analysis for grain shape traits in rice (Oryza sativa L.)

Marker-trait association study was undertaken to identify genomic regions linked to SSR markers with grain shape traits in rice. The association analysis identified 20 and 8 marker-trait association by GLM and MLM approaches, respectively at P values ≤ 0.005. GLM approach identified association for three traits on chromosome 1, 2, 4, 5, 6, 8, 9, 11 and 12 explaining 16.07% to 38.66% phenotypic variance whereas MLM approach detected association for four traits on chromosome 1, 4, 7, 8 and 11 explaining 15.51% to 27.24%. In GLM approach, the marker loci RM430_200 located on chromosome 5 showed highly significant association with test weight explained maximum phenotypic variance of 38.66%. While in MLM, marker RM320_250 located on chromosome 7 showed highly significant association with grain breadth accounted for 27.24% of phenotypic variance. The significant marker-trait association was lower in MLM compared to those in GLM. MLM method was proven to be useful in controlling false associations. The marker-trait association identified from the present study would be validated and utilized in marker assisted breeding programs of grain shape traits in rice.