GmBRC1 is a Candidate Gene for Branching in Soybean (Glycine max (L.) Merrill)

Abstract

Branch number is one of the main factors affecting the yield of soybean (<i>Glycine max</i> (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait nucleotides (QTNs) were associated with branch numbers in a soybean core collection. Among these QTNs, a linkage disequilibrium (LD) block <i>qtnBR6-1</i> spanning 20 genes was found to overlap a previously identified major quantitative trait locus <i>qBR6-1</i>. To validate and narrow down <i>qtnBR6-1</i>, we developed a set of near-isogenic lines (NILs) harboring high-branching (HB) and low-branching (LB) alleles of <i>qBR6-1</i>, with 99.96% isogenicity and different branch numbers. A cluster of single nucleotide polymorphisms (SNPs) segregating between NIL-HB and NIL-LB was located within the <i>qtnBR6-1</i> LD block. Among the five genes showing differential expression between NIL-HB and NIL-LB, <i>BRANCHED1</i> (<i>BRC1</i>; Glyma.06G210600) was down-regulated in the shoot apex of NIL-HB, and one missense mutation and two SNPs upstream of <i>BRC1</i> were associated with branch numbers in 59 additional soybean accessions. <i>BRC1</i> encodes TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1 and 2 transcription factor and functions as a regulatory repressor of branching. On the basis of these results, we propose <i>BRC1</i> as a candidate gene for branching in soybean.