Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects.  Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height.  Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping.  This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP).  The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers.  Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome.  Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18).  Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance.  They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively.  Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.

The cultivated soybean (Glycine max (L.) Merr.) was distinguished from its wild progenitor Glycine soja Sieb. & Zucc. in growth period structure, by a shorter vegetative phase (V), a prolonged reproductive phase (R) and hence a larger R/V ratio. However, the genetic basis of the domestication of soybean from wild materials is unclear. Here, a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants (PAVs) while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different latitudes. The major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine spp. The genotyping was largely consistent with the taxonomic status, although a few accessions were intermediate between the two major clades identified. Allelic diversity was much higher in the wild germplasm than in the cultivated materials. A significant domestication signal was detected at 11 of the PAVs at 0.01 level. In particular, this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean. A significant marker-trait association with R/V ratio was detected at 14 of the PAVs, but stripping out population structure reduced this to three. These results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.