Stem growth habit dictates plant architecture and influences flowering and podding (seed setting), making it an essential morphological and breeding agronomic trait of soybean (Glycine max). Stem growth habit in soybean is affected by photoperiod and environment and is determined by genetic variation at major genes. Classical genetic analysis identified two critical loci, designated Determinacy 1 (Dt1) and Determinacy 2 (Dt2). Dt1 is an ortholog of Arabidopsis thaliana TERMINAL FLOWER1 (TFL1) and specifies an indeterminate stem growth habit, whereas Dt2 specifies a semi-determinate growth habit. MADS-box proteins, including Dt2, SUPPRESSOR OF OVEREXPRESSION OF CO1 (GmSOC1) and MADS-box genes downregulated by E1 (GmMDE), repress Dt1 expression. Photoreceptors encoded by the E3 and E4 loci regulate the expression of soybean FLOWERING LOCUS T (GmFT) orthologs via circadian clock genes and E1, and GmFTs compete with Dt1 to regulate stem growth habit. Study of the molecular mechanism underlying the regulation of stem growth habit in soybean has focused on the repression of Dt1 expression. Here we provide an overview of progress made in elucidating the genetic and molecular bases of stem growth habit in soybean, with emphasis on the molecular components responsible for integrating photoperiodic flowering and stem growth habit.

Soybean [Glycine max (L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative InDel markers. First, we identified 17,613 InDel sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups (LG). The total genetic distance was 2347.3cM and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3cM and 0.1cM, respectively. Finally, we validated the genetic map constructed by newly developed InDel markers by QTL analysis of days to flowering (DTF) under different environments. One major QTL (qDTF4) and four minor QTL (qDTF20, qDTF13, qDTF12, and qDTF11) on 5 LGs were detected. These results demonstrate the utility of the InDel markers developed in this work for map-based cloning and molecular breeding in soybean.