Analysis of Loci and Alleles Associated with Hybrid Yield in Soybean

Abstract

Single marker regression analysis is an effective way to detect differences among genotypes associated with marker alleles in quantitative traits. Eight soybean parental materials, seven from Huang-Huai region in China and one from the USA with maturity groups II-IV, were used to develop a set of diallel crosses according to Griffing's Method II, including the eight parents and their 28 crosses. The molecular data of 300 SSR markers on eight parental materials were obtained and analyzed for association between SSR markers and hybrid yield using the single marker regression analysis. The hybrid crosses were dissected into their allele constitution and the effects of alleles and genotypic values of single locus were estimated. The results showed that 38 SSR loci located on 17 linkage groups were identified to associate with hybrid yield in the diallel crosses with more loci on linkage groups D1a and M. Eight of the 38 loci were located within a region of ±5 cM apart from a known QTL identified from family-based linkage (FBL) mapping. Each of the loci explained 11.95%-30.20% of the phenotypic variance of hybrid yield. The allele pairs of the hybrids were composed of four parts, i.e. positive dominant heterozygous loci, positive additive homozygous loci, negative additive homozygous loci and dominant heterozygous loci, with their relative importance in a descending order. Among the 38 loci associated with hybrid yield, nine elite (loci such as Satt449, Satt233, and Satt631) and nine elite alleles (such as Satt449-A311, Satt233-A217, and Satt631-A152) were identified. Nine heterozygous allele pairs such as Satt449-A291/311, Satt233-A202/207, and Satt631-A152/180 were detected. These results may provide some relevant information for understanding the genetic basis of heterosis and lay a foundation for hybrid soybean breeding by design.