Association Analysis of Agronomic Trait QTLs with SSR Markers in Released Soybean Cultivars

Abstract

The genotyping data of 85 simple-sequence repeat (SSR) markers on released cultivar population (RCP) (a representa-tive sample with 190 accessions) were obtained and analyzed for LD of pairwise loci and population structure, and then for asso-ciation between SSR loci and 11 soybean agronomic traits under TASSEL GLM (general linear model) program. The results showed that: (1) LD was detected extensively not only among syntenic markers but also among nonsyntenic ones, while the loci pairs with D′0.5 accounted for only 1.71% of the total ones. The syntenic D′ value attenuated fastly along with the increase of genetic distance. (2) Genetic structure analysis showed that RCP was composed of seven subpopulations. The 45 SSR loci with a total of 136 loci (time) were found to be associated with 11 agronomic traits in the RCP. Among those, 22 loci (times) were con-sistent with mapped QTLs from family-based linkage mapping procedure and 43 loci (times) were consistently detected in two experiment years. (3) There also found a certain number of loci associated simultaneously with two or more traits, which might be the genetic reason of correlation among traits as well as the pleiotropic effects of gene(s). (4) There found only a few association loci in released cultivar population coincided with those in landrace and wild populations, indicating the large difference of ge-netic structure between the populations. (5) The elite alleles of the agronomic traits along with their carriers were detected, such as the allele Satt347-300 for largest positive yield effect (+932 kg ha-1 for Zhongdou 26), Satt365-294 for biomass(+3 123 kg ha-1 for Huangmaodou), Be475343-198 for protein content (+0.41% for Huaidou 4), Satt150-273 for oil content (+2.32% for Kefeng 15), and were used to illustrate their potential in breeding programs.