GWAS, QTL Analysis, and Transcriptome Profiling Reveal Candidate Genes for Symbiotic Nitrogen Fixation in Common Bean (Phaseolus vulgaris).

Effective utilization of existing variability for symbiotic nitrogen fixation (SNF) in common bean (Phaseolus vulgaris) for crop improvement requires an understanding of underlying genes and molecular mechanisms. To develop an understanding of the molecular genetic basis of SNF in common bean, we used complementary studies: genome-wide association analysis (GWAS), QTL analysis and transcriptome profiling. GWAS identified genomic regions and candidate genes on Pv03 and Pv09 for SNF. In the second study, we were able to confirm specific genomic regions that controlled SNF traits using QTL analysis of recombinant inbred line (RIL) population. We explored the utility of transcriptome profiling using RNA-sequencing to understand the molecular genetic basis of contrasting SNF phenotypes, SA36 and SA118 from the RIL population. Genes encoding receptor kinases, transmembrane transporters, and transcription factors were among differentially expressed genes between SA36 and SA118. The data and information generated in these two studies could support development of gene-based markers to accelerate genetic improvement of common beans for SNF.