Conditional and unconditional QTL analyses of seed hardness in vegetable soybean (Glycine max L. Merr.)

Abstract

The seed hardness of vegetable soybean (VSB) is generally regarded as an important quality characteristic that contributes largely to its processing and mouthfeel. However, the genetic control of it is still a gray area. To identify the dynamic quantitative trait loci (QTLs) and detect the genetic relationship between seed hardness and growth period traits at the QTL level, conditional and unconditional QTL analyses were performed using a population of 184 recombinant inbred lines in 2015, 2016 and 2017. For seed hardness at stage 1 to stage 4 (W1–W4), 12 and 8 QTLs were identified by unconditional and conditional mapping, respectively. The comparative analyses between unconditional and conditional mapping uncovered three types of dynamic QTLs underlying seed hardness in the development of VSB. These results demonstrated that genes underlying seed hardness were actively expressed in the interval between stage 2 and stage 3, which was in parallel with the mass filling period in the development of soybean seeds. For seed hardness at R6 stage (W), 11 unconditional QTLs were detected. When W was conditioned on the number of days after sowing to R6 stage (DAS), the number of days after flowering to R6 stage (DAF) and flower time (FT), 11, 2, and 2 conditional QTLs were identified, respectively. Four types of unique QTLs distinguished the contributions of DAS, DAF and FT to the genetic effects of W. Of these, uqW.D1b-1 and uqW.A1-2 control W with independent of DAS or FT. Hence, they would be valuable for the selection softer seed lines, without the simultaneous depression of growth period traits even though there exist significant positive correlation between them. The loci identified by conditional and unconditional QTL analyses may be useful for the improvements of decreased seed hardness with the best balance of growth period through marker assisted selection (MAS).