Characterization of Population Structure and Linkage Disequilibrium of Chinese Soybean Landerace Population and QTL Association Analysis of Traits Related to Breeding for Soybeans
|Keywords||Soybean (Glycine max L) landraces Genetic Diversity SSR marker LD Association Analysis QTL|
Soybean （Glycine max （L） Merr.） is one of the major crops originated in China, and more than 23000 accessions mainly containing landraces have been collected and conserved in Chinese gene bank. However, only a few accessions were utilized in breeding programs because of insufficient genetic information of the germplasm. To reveal the genetic diversity and genetic bases of landraces is crucial for the discovery and utilization of new genes in soybean. In this study, total 134 SSR markers evenly distributed in 20 chromosomes, were assayed for polymorphism among 371 commonly used Chinese soybean landraces, and the genetic structure of the populations were analyzed by using the STRUCTURE 2.2 program, and the relationship of subpopulations were also inferred. Furthermore, Association analyses were conducted to identify QTLs for thirteen important agronomic and quality traits by using TASSEL software. The main results were as follows:1. There were 1217 alleles of 134 pairs of SSR loci in 371 tested landraces, the average allele number per loci was 9.08, and the maximum and minimum value were 44 （Sat219 locus located on LGⅠ） and 2 （GMES4571 locus located on LG Al among other loci）, respectively. The average diversity index was 0.556, and the Sat372 locus on LG G had the maximum value （0.815）, and GMES4149 locus on LG M had the minimum value （0.083）.2. According to the FST values among six ecological populations of Chinese landraces, there appeared a decreasing trends from southern to north regions. The Middle and Lower Changjiang Valley Double Cropping, Spring and Summer Planting Cultivating Region （PopulationⅢ） had the highest allele number （945）, Central South Multiple Cropping, Spring, Summer, and Autumn Planting Cultivating Region （PopulationⅣ） had the most number of population-specific alleles （81） and the largest genetic diversity index （0.55）, Southwest Plateau Double Cropping （PopulationⅤ） possessed the largest number of special alleles per accession （0.78）, and South China Tropical Multiple Cropping （Population VI） had the richest alleles per accession.The tested accessions were divided into nine distinct clusters （Q1-Q9） with similar geographical origins and another mixture cluster （Q10） by using the STRUCTURE2.2 ADMIXTURE model. Among them, the accessions of Q3 and Q6 clusters were mainly from Northern China and Huang-Huai-Hai region, and other clusters were composed of soybean landrace from Southern China. The FST value between Q3 and Q6 cluster （0.2208） was distinctly lower than those among other clusters （except Q8）. Q2 cluster had the highest allele number （805）, the most number of population-specific alleles （27） and the largest genetic diversity index （0.54）, Q4 cluster possessed the largest number of special alleles per accession （1.00）. It indicated that the genetic diversity of landrace population from southern China was higher than those of Huang-Huai and North China.3. Among the total 8911 loci pairs of 134 SSR loci, only 7.05% performed linkage disequilibrium （LD） at the significant level of P<0.01. The LD decay was 0.49cM according to the D’values of syntenic SSR loci, and lower than those of Chinese landrace （1.02cM） and wild soybean （12.26cM） detected by 60 SSR loci （Wen,2008）. It showed that:（1） With the increase of marker density, the distance of LD decay was significantly reduced in Chinese soybean landraces, but the strength of linkage disequilibrium would be increased; （2） The distance of LD decay Chinese soybean landraces was smaller than that of wild soybean, but the strength of linkage disequilibrium rapidly decreased.4. Association analyses between thirteen breeding-related traits and SSR markers were conducted with the standard of r2>0.05 and P＜0.01. It showed that:（1） Total 60 SSR loci （time） were found to be associated with agronomic traits, and 36 loci（time） were associated with quality traits; （2） The number of detected SSR loci for one trait varied from 4 （flooding tolerance） to 15 （dry Tofu output）, and the average value was 7.23; （3） Forty-four associated loci were detected for the 13 traits, and 22 loci associated with two or more traits; （4） Twenty markers, accounting for 20.8% of 96 associated SSR loci （time）, were in agreement with mapped QTLs from family-based linkage mapping.5. The phenotypic allele effect was estimated through comparison between the average phenotypic value over accessions with the specific allele and that of accessions with "null allele", and then the average positive （negative） allele effect （AAE） of a locus was calculated over the estimated phenotypic effects of all positive （negative） alleles, and a set of elite alleles, loci and their carrier materials were screened out, including the BE475343-196 for largest positive for 100-seed weight effect （+12.7 g, N21175 as carrier）, Satt665-A338 for leaf length （+4.3 cm, N6141）, Satt489-291 for output of dry toufu, Sat312-351 （+17.69%, N24610）, Satt489-291 for output of dry soy milk （+10.44%, N22798.1）, Sat385-335 for protein content （+7.18%, N23590）, Satt239-221 for content of oleic acid（+16.30%, N23546）, and the allele Sat293-323 for largest negative days to maturity effect（-23.1 days, N04569） and Sat312-346 for days to flowering（-18.4 days, N24600） among other alleles.6. The difference of elite carriers were illustrated by analyzing the distribution of alleles for target traits in about 30 represent materials, and some carrier materials with most elite alleles as well as largest allele effects were identified, such as landrace N23628 carrying six larger positive alleles and N24598 with five negative alleles of seven SSR loci for plant height, N6141 possessing four positive alleles of seven SSR loci for 100-seed weight, accession N04569 carrying three negative alleles of five SSR loci for days to maturity, N23629 carrying three negative alleles of five SSR loci for days to maturity, and for quality traits, N23533 carrying four positive alleles of five SSR loci for content of oleic acid, N23583 carrying three positive alleles of five SSR loci for output of wet toufu. Furthermore, a number of materials with at least one complementary positive （negative） allele were screened out, and some strategies for pyramiding elite alleles and combining two types of elite materials were illustrate as an example of breeding by design in soybean.