Identification of QTL associated with pod number in soybean

Pod number is an important factor influencing soybean yield. In this study, a recombinant inbred line population derived from the cross between improved cultivar (Glycine max) and wild soybean (Glycine soja) was subjected to multi-environment phenotypic evaluation for pod number. Quantitative trait locus (QTL) mapping associated with pod number was performed utilizing both linkage analysis (LA) and genome-wide association study (GWAS) by integrating the phenotypic and genotypic data. The results showed that a total of 16 QTLs associated with pod number, notably, overlapping genomic intervals were observed between qPN10-1 (by linkage analysis) and qPN10-3 (by EMMAX), as well as between qPN11-2 (by LA) and qPN11-3 (by EMMAX), and these intervals were regarded as major-effect Quantitative trait locus regions. Furthermore, two candidate genes (Glyma.10G206300, and Glyma.10G207500) encode a basic Helix-Loop-Helix (bHLH) transcription factor and an armadillo (ARM)-repeat protein respectively, as determined through linkage disequilibrium analysis, SNP variant analysis, haplotype analysis, and gene functional annotation. These two candidates are possibly involved in the regulation of flower number, flowering time, and pod number (siliques number in Arabidopsis thaliana). These findings pave the way for gene cloning related to pod number, and provide novel insights into the genetic architecture underlying pod number variation in soybean.