Marker-trait association of the major pyruvate pathway genes regulating yield related traits in rice (Oryza sativa L.)

Pyruvate is the primary respiratory substrate used to provide energy for growth and development in plants. The role of genetic variants of pyruvate pathway genes with yield and its attributing traits in rice is not properly understood. In this study, association of sixteen yield traits with SNPs and In/Dels of nine pyruvate metabolism pathway genes (Os01g0649100, Os01g0743500, Os04g0671700, Os05g0186300, Os06g0246500, Os07g0630800, Os10g0159800, Os11g0210300 and Os11g0216000) were analyzed using the mixed linear models with principal component analysis (MLM+PCA) based population correction approach. The majority of the traits were found to follow a normal distribution pattern. Besides, MLM+PCA analysis showed a significant association of five markers with six different yield-related traits and the proportion of phenotypic variation explained ranged from 3.56 to 4.56%. Furthermore, the pyruvate dehydrogenase E1 alpha subunit (Os06g0246500) gene (Chr06:7602782) showed the highest mean percent difference (19.36%) for plant height. Moreover, most of the IRRI elite lines possessed favorable alleles for plant height (74.55%) and flag leaf area (79.28%) and in contrast, popular varieties like Swarna have inferior alleles for the yield trait-associated SNPs. Thus, genetic variation in the pyruvate pathway genes associated with yield-related traits could be exploited in rice improvement programs.