Using presence/absence variation markers to identify the QTL/allele system that confers the small seed trait in wild soybean (Glycine soja Sieb. & Zucc.)

Glycine soja has the potential to improve upon the cultivated soybean (G. max) in protein content, resistance/tolerance to stresses, and other traits, but its small 100-seed weight (100SW) is usually undesired. To explore the 100SW QTL-allele system of G. soja, the recombinant inbred line population NJRINY with 286 lines was developed from a cross between G. max (NN86-4, 17.9 g) and G. soja (PI342618B, 1.1 g) and was tested over 4 years. The genetic linkage map was constructed with 181 PAV (presence/absence variation) and 42 SSR markers. The quantitative trait locus (QTL) mapping results showed that the wild genetic system of 100SW was composed of three groups of QTLs, including (1) 15 additive QTLs, which accounted for 55.1 % of the phenotypic variation (PV), with each locus contributing 1.5-8.1 % of the PV and all of the wild alleles having negative effects (-0.1 to -0.5 g); (2) 17 epistatic QTL pairs, which accounted for 19.0 % of the PV, with epistatic effects positive for parental type (0.1-0.2 g) and negative for recombinants and all of the QTLs in epistatic pairs having simultaneously additive effects except one pair (SW16); (3) a collection of unmapped minor QTLs that accounted for 22.9 % of the PV. Among the detected total additive and/or epistatic QTLs, 12 QTLs have been reported in the literature, but five of the QTLs and all of the epistatic pairs have not been reported before. The results can be used for marker-assisted breeding for 100SW.