QTL mapping of domestication-related traits in soybean (Glycine max)

Abstract

Background and aims: Understanding the genetic basis underlying domestication-related traits (DRTs) is important in order to use wild germplasm efficiently for improving yield, stress tolerance and quality of crops. This study was conducted to characterize the genetic basis of DRTs in soybean (Glycine max) using quantitative trait locus (QTL) mapping.

Methods: A population of 96 recombinant inbred lines derived from a cultivated (ssp. max) x wild (ssp. soja) cross was used for mapping and QTL analysis. Nine DRTs were examined in 2004 and 2005. A linkage map was constructed with 282 markers by the Kosambi function, and the QTL was detected by composite interval mapping.

Key results: The early flowering and determinate habit derived from the max parent were each controlled by one major QTL, corresponding to the major genes for maturity (e1) and determinate habit (dt1), respectively. There were only one or two significant QTLs for twinning habit, pod dehiscence, seed weight and hard seededness, which each accounted for approx. 20-50 % of the total variance. A comparison with the QTLs detected previously indicated that in pod dehiscence and hard seededness, at least one major QTL was common across different crosses, whereas no such consistent QTL existed for seed weight.

Conclusions: Most of the DRTs in soybeans were conditioned by one or two major QTLs and a number of genotype-dependent minor QTLs. The common major QTLs identified in pod dehiscence and hard seededness may have been key loci in the domestication of soybean. The evolutionary changes toward larger seed may have occurred through the accumulation of minor changes at many QTLs. Since the major QTLs for DRTs were scattered across only six of the 20 linkage groups, and since the QTLs were not clustered, introgression of useful genes from wild to cultivated soybeans can be carried out without large obstacles.

Fig. 1.

Frequency distributions of phenotypes for nine domestication-related traits in a RIL population derived from a cross between G. max ssp. max and ssp. soja. Black bars indicate RILs which significantly exceeded the parental values at 0·001 probability. PVER (the proportion of the phenotypic variation explained by RILs) was calculated based on a Model II ANOVA (Sokal and Rohlf, 1981). FT, flowering time; DH, determinate habit; PH, plant height; NN, number of nodes; MIL, maximum internode length; TH, twinning habit; PD, pod dehiscence; SW, 100 seed weight; HS, hard seededness.

Fig. 2.

Six linkage groups harbouring significant QTLs for domestication-related traits in a RIL population derived from a cross between G. max ssp. max and ssp. soja. QTL analyses were conducted for each of the 2004 and 2005 tests (04 and 05) and the average of the two years (-C). The box delineates the one-LOD support interval, and the whiskers of each box delineate the two-LOD support interval. FT, flowering time; DH, determinate habit; PH, plant height; NN, number of nodes; MIL, maximum internode length; TH, twinning habit; PD, pod dehiscence; SW, 100 seed weight; HS, hard seededness.