Genetic structure and molecular markers-trait association for physiological traits related to seed vigour in rice

Abstract Good quality seed is an important factor for a good crop and harvest. Vigour is the key performing trait of quality seed. Many physiological traits influence seed vigour in rice. Association of molecular markers with eleven physiological traits were investigated in a representative population. A representative population was constituted by including genotypes from all the phenotypic groups of the 11 physiological traits from the shortlisted population of 120 genotypes. The genotypic accessions with rich in multiple physiological traits were identified from the representative population. STRUCTURE, GenAlEx and Darwin software were used to classify the population. Generalized Linear Model (GLM) and Mixed Linear Models (MLM) were used in the marker-trait association analysis using the TASSEL software. Wide variations among the genotypic accessions were observed for the physiological traits estimated from the panel population. Linkage disequilibrium was detected for the 11 physiological traits in the panel population. STRUCTURE software classified the population into two genetic structure groups. Higher values of gene diversity and polymorphic information content (PIC) were estimated from the population based on genotyping using 50 simple sequence repeat markers. Genotypes present within groups and sub-groups showed similarity for their physiological traits. Strong association of the markers with physiological parameters namely RM167 for seed vigour index-I; RM7364 and RM235 for seed vigour index-II; RM440, RM223 for seedling dry weight; RM 256,RM25181, RM6547, RM328, RM201 for rate of root growth; RM 20, RM13335, RM216 for rate of shoot growth while RM20A and RM201 for absolute growth rate were detected by both GLM and MLM analyses. Markers detected in this association analysis may be potential use for future seed vigour improvement in rice.