Genetic and Genomic Study of Shoot Branching in Soybean

Abstract

The number of soybean branch directly affected yield components of pod and seed number per plant by generating more pod bearing sites on the branches. The number of branches in soybean is immensely affected by various environmental factors, numerous genetic factors and their interactions. For this reason, a little genetic factors associated with branch number has been identified. The causal genes controlling branch development has not been identified in soybean. QTLs associated with number of branches and promising candidate genes including BRANCHED1 (BRC1) and REVOLUTA (REV) for branch development were identified using bi-parental mapping population and high-resolution genetic map. <br/> To validate the major QTL, genetic association within a set of 430 soybean germplasms under three geographic replications was analyzed. Resultantly, a total of six out of 45 markers, which were located in the major QTL for branch number, were significantly associated with branch numbers that measured in at least two geographical replications. The six markers located in exon of BRANCHED1 (BRC1) gene, intron of gene encoding transcription factor TFIIE alpha subunit and intergenic regions. In the meantime, using a set of near-isogenic lines (NILs) derived from a F6 residual heterozygous line (RHL) for the major QTL, expression of two candidate genes between the NILs were compared. The result showed in that the BRC1 gene was significantly down-regulated in NIL that exhibited more branches (p-value < 0.001), and no significant expression difference was identified for the other gene encoding TFIIE alpha subunit. In addition, genetic association of missense and upstream SNP for BRC1 gene were identified in 59 accessions. <br/> RNA-seq analysis for the set of NILs was conducted to provide global view of comprehensive mechanism for branch development in soybean. As a result, a total 376 differentially expressed genes were identified by comparison of the set of NILs. These DEGs were mapped to biological pathways such as abiotic stress signaling, plant-hormonal, secondary metabolism and development. Hormonal pathways, including auxin, cytokinin, gibberellin and abscisic acid, which were associated with branch development, were observed. <br/> Through a series of study about soybean branch development, strong candidate gene (BRC1) controlling branch development in soybean was identified. This gene encodes TEOSINTE BRANCHED 1/CYCLODEA/PROLIFERATING CELL FACTORS (TCP) transcription factor 18. The TCP transcription factor (TF) family are involved in developmental growth, such as leaf development, flower symmetry and shoot branching. Based on bioinformatics analysis such as phylogenetic tree, gene structure, motif conservation, synteny and expression pattern analysis, we could construct the duplication network of soybean TCPs. Through the duplication network, it was revealed that soybean TCP family was duplicated by whole genome duplication (WGD) and tandem duplication. Thus, the retention and structural/transcriptional divergence which could be supported by gene balance hypothesis and sub-/neo-functionalization were observed. <br/> These results will be helpful for understanding of branch development, breeding high yield soybean by increased branches and evolution of TCP TF genes.<br/> <br/> Keywords: soybean, branch, QTL, association, BRC1, evolution<br/>