本研究在前期已发掘短片段InDels和SNPs基础上，基于全基因组重测序分析在一个重组自交系群体的两个亲本中品03-5373（ZP）和中黄13（ZH）之间检测到不均匀分布在大豆20条染色体上的13573个长片段InDels，其中，Chr11上最少，有321个，Chr18上最多，有1246个。长片段InDels在染色体两臂的平均密度显著高于着丝粒区，与大豆基因组注释基因的分布模式一致。位于基因区的长片段InDels有2704个，占总数目的19.9%，其中319个为可导致蛋白质序列截短或延长的大效应InDels。重点对前期鉴定的株高相关QTL（qPH16）进行分析，共鉴定到35个长片段InDels，并将其开发成InDel标记，其中26个InDel标记（74.3%）在ZP和ZH之间表现出明显的多态性。利用开发的标记结合已有的4个SNPs标记对由ZP和ZH衍生的242个重组自交系进行基因型鉴定和QTL定位，将qPH16的定位区间从原来的960 kb缩小到477.55 kb，包含65个注释基因。在SNPs和短片段InDels开发基础上，进一步开发长片段InDels，可为大豆重要农艺性状的遗传分析和分子辅助选择育种提供更加全面的遗传变异信息。

大豆株高是由主效或微效基因控制的重要农艺性状。在已报道的株高QTL中，绝大部分定位区间较大，限制了大豆株高分子调控机制的解析。增加遗传图谱的标记密度会显著地提高QTL定位的效率和准确性。本研究利用双亲中黄13和中品03-5373及其衍生的241个重组自交系（RILs）全基因组重测序数据，构建一个包含4011个重组bin标记、总遗传距离为3139.15 cM的高密度遗传图谱，相邻bin标记间的平均距离为0.78 cM。比较基因组分析表明，所构建的遗传图谱与大豆参考基因组具有较高的共线性。基于此图谱，在6个环境中共检测到9个株高QTL，包括3个新位点（qPH-b_11，qPH-b_17和qPH-b_18）。其中，两个环境稳定主效QTL qPH-b_13和qPH-b_19-1可解释10.56%～32.7%的表型变异。qPH-b_13和qPH-b_19-1被精细定位到440.12 kb和237.06 kb的基因组区间，分别包含54和28个注释基因。进一步的拟南芥同源基因功能和候选基因表达分析表明，基因Glyma.13G292600和Glyma.19G194100分别为qPH-b_13和qPH-b_19-1的候选功能基因。

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.