QTL Mapping of Domestication-related Traits in Soybean (Glycine max)

Abstract

Background and AimsUnderstanding 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.MethodsA population of 96 recombinant inbred lines derived from a cultivated (ssp. max) × 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 ResultsThe 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.ConclusionsMost 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.

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

“…3d and Supplementary Fig. 11b), respectively 21 .We also detected a GWAS signal responsible for purple or white flower color at the W1 locus 22 and a GWAS signal corresponding to seed coat color variation at the I locus [23][24][25] . We found that these two signals underwent selection during domestication and improvement, respectively (Supplementary Fig.…”

“…In our analyses, selection signals were detected in almost all reported domestication-related QTL regions 21 ( Fig. 3 and Supplementary Table 10).…”

A Major Soybean QTL,qPDH1, Controls Pod Dehiscence without Marked Morphological Change

“…Therefore, the inverse correlation between the small sizes of these characters and the shattering resistance, which was found by Tiwari and Bhatia (1995), might reflect no more than the differences between the wild and cultivated species. Another plausible explanation is that other QTLs conditioning shattering resistance were involved in the genotypic differences found in the previous studies, although several shattering-resistant cultivars besides Hayahikarirelated ones are likely to harbor shattering-resistance alleles at qPDH1 as well (Bailey et al, 1997;Funatsuki et al, unpublished results) and this QTL seems to have played a role in the domestication process (Liu et al, 2007).…”

“…& Zucc., which scatters its seeds via pod dehiscence (Hymowitz and Singh, 1987). Although in general, soybean (G. max) is more resistant to pod dehiscence (shatteringresistant) than G. soya (Liu et al, 2007), significant genetic variation has been found among soybean cultivars (e.g. Tsuchiya, 1986;Romkaew and Umezaki, 2006).…”

Evaluation and QTL mapping of phosphorus concentration in soybean seed

“…In 2008, three suggestive QTL were detected on chromosomes 10, 18, and 20 (Table 3). Suggestive QTL were those QTL possessing peaks in LOD scores that did not exceed the genome wide threshold, but on the chromosome level were at or exceeded significant P \ 0.05 (Liu et al 2007;Tiwari et al 2009;Willems et al 2010). The LOD scores of these QTL ranged from 2.6 to 2.9 and the variation explained was 11.9-19.4 %.…”