Identification and Fine Mapping of a Quantitative Trait Locus Controlling the Total Flower and Pod Numbers in Soybean

Total flower and pod numbers (TFPN) and effective pod numbers per plant (PNPP) are among the most important agronomic traits for soybean production. However, the underlying genetic mechanism remains unclear. In this study, we constructed a recombinant inbred line population derived from a cross between JY73 (high TFPN) and TJSLH (low TFPN) to map loci for the two traits. In total, six QTL for TFPN and five QTL for PNPP were identified, among which a QTL on chromosome 4, named qFPN4, explained 9.2% and 9.6% of the phenotypic variation of TFPN and PNPP, respectively. Analysis of residual heterozygous lines for qFPN4 indicated that TFPN or PNPP was controlled by a single dominant gene at this locus and delimited the QTL into a similar to 2.62 Mb interval which tightly linked to an Indel marker C1-5. This mapping result was further confirmed by bulked segregant analysis (BSA) of the near isogenic lines. The genome-sequencing-based BSA also identified eight candidate genes carrying nonsynonymous SNPs and/or Indels; two genes, Glyma.04G176600 and Glyma.04G178900, were nominated as the most promising genes for qFPN4 based on additional expression and function analysis. These results improve our understanding of the genetic mechanism of TFPN and PNPP and indicate the potential for soybean yield improvement.