Chromosome segment detection for seed size and shape traits using an improved population of wild soybean chromosome segment substitution lines

Size and shape of soybean seeds are closely related to seed yield and market value. Annual wild soybeans have the potential to improve cultivated soybeans, but their inferior seed characteristics should be excluded. To detect quantitative trait loci (QTLs)/segments of seed size and shape traits in annual wild soybean, its chromosome segment substitution lines (CSSLs) derived from NN1138-2 (recurrent parent, Glycine max) and N24852 (donor parent, Glycine soja) and then modified 2 iterations (coded SojaCSSLP3) were improved further to contain more lines (diagonal segments) and less heterozygous and missing portions. The new population (SojaCSSLP4) composed of 195 CSSLs was evaluated under four environments, and 11, 13, 7, 15 and 14 QTLs/segments were detected for seed length (SL), seed width (SW), seed roundness (SR), seed perimeter (SP) and seed cross section area (SA), respectively, with all 60 wild allele effects negative. Among them, 16 QTLs/segments were shared by 2–5 traits, respectively, but 0–3 segments for each of the 5 traits were independent. The non-shared Satt274 and shared Satt305, Satt540 and Satt239 were major segments, along with other segments composed of two different but related sets of genetic systems for SR and the other 4 traits, respectively. Compared with the literature, 7 SL, 5 SW and 2 SR QTLs/segments were also detected in cultivated soybeans; allele distinction took place between cultivated and wild soybeans, and also among cultivated parents. The present mapping is understood as macro-segment mapping, the segments may be further dissected into smaller segments as well as corresponding QTLs/genes.