Understanding the genetic basis of symbiotic nitrogen fixation in common bean (Phaseolus vulgaris L.) using genomic and transcriptomic analyses

Common bean (Phaseolus vulgaris L.) is able to fix atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF). SNF is a genetically complex trait controlled by several genes. Effective utilization of existing SNF variability in common bean for genetic improvement requires an understanding of its genetic architecture, which is poorly understood. To understand the molecular genetic architecture of SNF variability three studies were conducted: (i) genome-wide association study (GWAS), (ii) Quantitative Trait Loci (QTL) mapping study, and (iii) transcriptome profiling study. GWAS was conducted using an Andean Diversity Panel (ADP) comprised of 259 genotypes. The ADP was evaluated for SNF in both greenhouse and field experiments, and genotyped using an Illumina BARCBean6K_3 BeadChip with 5398 single nucleotide polymorphism (SNP) markers. A mixed linear model was used to identify marker-trait associations. The QTL mapping study was conducted using 188 F4:5 recombinant inbred lines (RILs) derived from cross of Solwezi and AO-1012-29-3-3A. These 188 F4:5 RILs were evaluated for SNF in greenhouse experiments, and genotyped using the same BARCBean6K_3 BeadChip. Transcriptome profiling was conducted on RILs SA36 and SA118 contrasting for SNF that were selected from the Solwezi x AO-1012-29-3-3A population used in the QTL mapping study. RNA samples were collected from leaves, nodules and roots of SA36 and SA118 grown under N fixing and non-fixing condition, and sequenced using Illumina technology. Using GWAS, significant associations for nitrogen derived from atmosphere (Ndfa) were identified on chromosomes Pv03, Pv07 and Pv09. QTL mapping identified QTL for Ndfa on Pv02, Pv04, Pv06, Pv07, Pv09, Pv10, and Pv11. The GWAS peak identified on Pv09 for Ndfa overlapped with the QTL on Pv09 for Ndfa identified in QTL mapping study. Previous studies have reported QTL for Ndfa on Pv04 and Pv10. Genes encoding receptor kinases, transmembrane transporters, and transcription factors (TFs) were among differentially expressed genes (DEGs) between SA36 and SA118 under N-fixing condition, but not under non-fixing condition. Out of the 51 genes that were in 400 kb region surrounding the GWAS peak on Pv07, only four including Phvul.007G048000 encoding a MADS BOX transcription factor (TF) were identified as expression candidates for SNF in the transcriptome profiling study. In the 400 kb region surrounding the GWAS peak on Pv09 there were 44 genes, but only Phvul.009G137500 encoding a WRKY TF was identified as an expression candidate gene in the RNA-seq study. Using GWAS, QTL mapping and transcriptome profiling, genomic regions and expression candidate genes for SNF have been identified. Once validated, these QTL and genes have potential to be used in marker-assisted breeding to circumvent challenges of phenotypic selection for SNF, and accelerate genetic improvement of common bean for symbiotic nitrogen fixation.