| The annual wild soybean(Glycine soja Sieb. et Zucc.), known as the ancestor of the cultivated soybean [Glycine max (L.)Merr.], is endemic to East Asia with most of its range in China. It is believed that the wild soybean holds a reservoir of genetic variation potentially useful for improvement of cultivated soybeans. In this study, total 204 SSR makers which distributed evenly on twenty molecular linkage groups of soybean, and 174 wild soybean accessions from four geographic eco-regions in China were utilized for association analysis by whole genome scan. Genetic diversity and analyzed structure of the population were analyzed. Moreover, based on linkage disequilibrium of pairwise loci and population structure analysis, the genotyping data of 204 simple sequence repeat (SSR) markers with phenotypic data of 19 agronomic and quality traits were used in association mapping. The main results were as follows:1. The present analysis detected relatively high level of variation in G. soja populations(A value was 1815,8.9 alleles per locus, and PIC was 0.63). In comparison, the genetic diversity of G. soja was much higher than that of G. max at nuclear genome level, which indicated the genetic diversity obviously decreased during the domestication processa. There existed evidences supporting that eco-geographic differentiation had its sound genetic basis for wild soybean populations. The results of AMOVA showed that significant portions of the variation existed among the populations of G. soja at DNA molecular level. There existed a plenty of geo-ecotype-specific-present alleles, geo-ecotype-specific-deficit alleles in different eco-regions of G. soja. Genetic structure analysis showed that 174 wild soybean accessions were composed of four subpopulations, which associated with their geographic eco-types, indicating existed genetic bases of the classification of geographic eco-types.2. We detected the linkage disequilibrium of pairwise loci based on the genotypic data of 204 SSR markers, and found that the LD occurred commonly, but the proportion was quite low when P<0.01. Further results indicated that the LD decay distance was 3.74cM in G.soja. The wild population had higher value and slower attenuation of LD than those of the cultivated soybean population.3. Total 96 SSR loci associated with the agronomic traits and quality traits respectively, were screened out from the wild soybean accessions. Among sixty loci associated with agronomic traits, seven of nineteen SSR loci associated with days of flowering, four of fifteen SSR loci associated with days of maturity and one of four loci associated with plant height were located in the regions of±5 cM where a target QTL was also identified by the family-based linkage mapping method. Among 36 loci associated with quality traits, one of two loci associated with content of seed protein was located in a region of±5 cM where a QTL was identified from family-based linkage mapping.4. Alleles for loci associated with several traits had different phenotypic effect in different traits. Satt168-A247 and Satt168-A239 had the first-rank value of positive phenotypic effect for fat and linoleic acid content, respectively. Satt168-A267 had the first-rank value of negative phenotypic effect associated with linolenic acid. The difference of size and direction of allele phenotypic effect value might explain the genetic base of the phenotypic correlation of some related traits.5. There was great difference of the genetic structure of the tested materials with extreme phenotypic value. The accession with extreme phenotypic value possessed the alleles with bigger positive phenotypic effect. For example, accession N24181, whose fat content was 17.5%, contained five alleles with bigger positive effect values, and N23283 with 7.7% fat content had four alleles with bigger negative phenotypic effect. The difference of allele distribution in the materials might be the genetic base of their phenotypic correlation. In summary, the results implied that association mapping could offer further genetic information complementary to the family-based linkage mapping for genetic and breeding studies in soybean. |
PDF Full Text Request