Abstract
Annual wild soybean (Glycine soja Sieb. and Zucc.), the wild progenitor of the cultivated soybean [Glycine max (L.) Merr.], is valuable for improving the later. The construction of a linkage map is crucial for studying the genetic differentiation between these species, but marker density is the main factor limiting the accuracy of such a map. Recent advances in next-generation sequencing technologies allow for the generation of high-density linkage maps. Here, two sets of inter-specific recombinant inbred line populations, named NJIRNP and NJIR4P, composed of 284 and 161 lines, respectively, were generated from the same wild male parent, PI 342618B, and genotyped by restriction-site-associated DNA sequencing. Two linkage maps containing 5,728 and 4,354 bins were constructed based on 89,680 and 80,995 single nucleotide polymorphisms, spanning a total genetic distance of 2204.6 and 2136.7 cM, with an average distance of 0.4 and 0.5 cM between neighboring bins in NJRINP and NJRI4P, respectively. With the two maps, seven well-studied loci, B1 for seed bloom; G and I for seed coat color; E2, E3, qDTF16.1 and two linked FLOWERING LOCUS T for days to flowering, were detected. In addition, two SB and two DTF loci were newly identified in wild soybean. Using two high-density maps, the mapping resolution was enhanced, e.g., G was narrowed to a region of 0.4 Mb on chromosome 1, encompassing 54 gene models, among which only Glyma01g40590 was predicted to be involved in anthocyanin accumulation, and its interaction with I was verified in both populations. In addition, five genes, Glyma16g03030, orthologous to Arabidopsis Phytochrome A (PHYA); Glyma13g28810, Glyma13g29920, and Glyma13g30710 predicted to encode the APETALA 2 (AP2) domain; and Glyma02g00300, involved in response to red or far red light, might be candidate DTF genes. Our results demonstrate that RAD-seq is a cost-effective approach for constructing high-density and high-quality bin maps that can be used to map QTLs/genes into such small enough regions that their candidate genes can be predicted.
Highlights
Soybean [Glycine max (L.) Merr.], is one of the most economically important leguminous seed crops
Using an recombinant inbred lines (RILs) population from a cross between two soybean cultivars, an initial genetic map defining 1550 cM of the soybean genome comprising 31 linkage groups consisting of 132 RFLPs, isozymes, and morphological and biochemical markers was reported in Lark et al (1993)
Nannong86-4 and Nannong493-1, two cultivars in maturity group (MG) VI with days to maturity between 166 and 180 descripted by Gai et al (2001), characterized by shiny seed bloom (SB), yellow seed coat color (SCC), later flowering, high yield, and high oil content were used as female parents, while PI 342618B, an annual wild soybean in MG I characterized by SB, black SCC, early flowering, high protein content, low 100-seed weight (1.1 g), and tolerance to flooding was used as a shared male parent
Summary
Soybean [Glycine max (L.) Merr.], is one of the most economically important leguminous seed crops. In the past two decades, there have been a number of reports on the construction of soybean genetic maps. Using an RIL population from a cross between two soybean cultivars, an initial genetic map defining 1550 cM of the soybean genome comprising 31 linkage groups consisting of 132 RFLPs, isozymes, and morphological and biochemical markers was reported in Lark et al (1993). Since this initial linkage map, researchers have developed more than 40 linkage maps. The above genetic maps have provided tools for understanding the genetic bases of soybean quantitative traits but have mainly focused on cultivated soybeans, while only few studies have investigated inter-specific crosses, which facilitate the detection and use of favorable exotic genes to broaden the cultivar’s genetic bases
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