Physical mapping and candidate gene prediction of branch number on the main stem in soybean [Glycine max (L.) Merr.

Abstract

Branch number on the main stem (BNMS) is an important factor that affects crop plant architecture and yield in soybean [Glycine max (L.) Merr.]. With the aim of elucidating the genetic basis of BNMS, 10 consensus quantitative trait loci (QTLs) were identified, which were on 9 chromosomes and explained 0.3–33.3% of the phenotypic variance. One new QTL-qBN.N (R2 = 19.6%) was detected in two populations (F2:3-Taiyuan 2017 and F2:4-Taiyuan 2018), which occur only in Taiyuan. Thus, the interaction analysis of QTL × environment confirmed that QTL-qBN.N was greatly affected by the environment. Of these, QTL-qBN.C2 (R2 = 33.3%) was defined as a major QTL, and was also verified and fine-mapped in the recombinant inbred line population. The high-coverage re-sequencing of two parental lines and newly developed InDel PCR-based markers allowed the region of qBN.C2 to be narrowed down to 304.9 kb. According to the gene annotation of the QTL interval, a total of 24 genes were obtained. Three potential candidate genes were identified by quantitative real-time PCR, and only Glyma.06G188400 had the highest relative expression at the axillary meristem, and thus it may potentially participate in branching development. The successful and rapid fine-mapping and discovery of candidate genes for BNMS in soybean were achieved in this study.