Linkage Analysis And Association Analysis For Yield And Yield-related Traits In Soybean

Soybean(Glycine max(L.)Merr.)is an important food and oil crop,which providing about 69%and 27%dietary protein and oil all of the world,respectively.However,the yield of unit area of soybean is very low,so it is very important to improve the ability of soybean production.While yield and related traits in crops,including soybean,belong to complex quantitative traits,which result from the interaction between genotype and environment.It is becoming more and more difficult to improve yield using traditional,phenotypic-based breeding methods.The development and application of molecular marker in plant provide new selections for us:marker-assisted selection(MAS)and molecular design breeding,which will help us get insight the molecular mechanism of yield and related traits.In order to explore the genetic mechanism of yield of soybean and MAS application in soybean,the QTL of yield and yield related traits were widely investigated using RIL-based linkage analysis and germplasm-based association mapping.In present study,the genetic diversity and relationship of cultivated and wild soybean were analysis using 74 SSR,covering whole genome,providing the basis for wild soybean germplasm application in soybean breeding.The main results of this study were as following:1.QTL analysis of yield-related traits were conducted using recombination inbred line(Kefeng1 ×Nannong1138-2)as materials,fifty one additive QTL were identified by complete interval method(CIM)with WinQTLcart2.5 software,29 main effect QTL and 43 pairwise epistasis QTL were identified with Network2.0.The results showed that there were significance differences among recombination inbred lines for each trait and between years;There out of 51 additive QTL identified by WinQTLcart2.5 for flowering time,mainly distributed on chromosome 2,6 and 8;one for mature on chromosome 2;6 for plant height on chromosome 2,6,17 and 18;3 for branch number on chromosome 5,6 and 18;4 for node number of main stem on chromosome 6,14 and 17;one for shoot diameter on chromosome 13;8 for yield per plant,mainly distributed on 1,4,7,10,13 and 18;two for pod number on chromosome 4 and 18;five for seed number per plant on chromosome 1,4,5,13 and 18;4 for seed length on chromosome 2,7,8 and 10;one for seed width on chromosome 2;two for seed height on chromosome 2 and 17;5 for ratio of seed length to seed width on 6,8,10,11 and 17;three for ratio seed length to seed height on chromosome 8 and 19;three for ratio of seed width to seed height on chromosome 10,13 and 16.Combined QTL mapping were conducted on two years data with Network2.0,most of the results were common with above,and some new QTL were identified.Forty two pairs epistasis QTL were detected for 16 yield and related traits with Network2.0,6 pairs out 42 for seed length,5 for seed width,6 for seed height,1 for RIL,4 for RLW,4 for RHW,1 for node number of main stem,1 for pod number,3 for shoot diameter,3 for maturity,3 for flowering time,3 for hundred seed weight.2.Genetic diversity of cultivated and wild soybean was analysis and compared using 74 SSR markers.The results showed wild soybean possessed higher genetic diversity than cultivated soybeans,and some new alleles have been created in cultivated soybeans.Model-based STRUCTURE analysis and Principal Coordinate Analysis(PCoA)showed a clear genetic structure.Phylogenetic analysis indicated that cultivated soybeans have more closed genetic distance than wild soybeans.We found 237 specific alleles for wild soybean population,and 89 for cultivated soybean population,these specific alleles accounted for 35.28%of all alleles of entire sample.AMOVA exhibited that 92.98%of the total variation was due to the differences within populations and the remaining 7.02%due to difference between cultivated soybean and wild soybean population.These results suggested that wild soybean should support introgression efforts and provide genetic diversity for future soybean breeding.3.Association mapping was conducted in soybean germplasm population to detect QTL for ten yield and related traits with 205 SSR markers.The results showed there were significant differences among individuals,and significant differences between experimental pots and years for most traits,respectively.LD analysis of 205 pairs of SSR markers showed there was extensive LD intra-chromosome or inter-chromosome,and that the LD decay rapidly in study population.In the whole population,9.98%of the SSR pairs were in LD(P?0.01);20.63%of the all SSR pairs were in LD(P?0.01)for synteny of SSR.Seventy SSR cover whole genome were selected to assess genetic structure,161 SSR-trait association were detected in present study with two models(Q+K,PCA+K),involving 65 SSR markers,with some associated only detected by one model,40 loci were co-associated with more than one traits,and many association in the confidence interval of previously report,or closed to the previously reports.The phenotypic allele effect of 35 association loci was estimated to discover increase allele that can be used in soybean molecular assist selection breeding.4.In order to investigate the genetic basis of seed size and shape,GWAS was conducted to detect SNP that associated with seed size and shape with 1142 SNP in 191 soybean accessions.Our results indicated that there was extensive phenotypic variation in 191 soybean accessions for seed size and seed shape traits.One hundred thirty six SNP-trait associations were detected with two models(Q+K,PCA+K),involving 79 SNP,19 out of 79 associated with hundred seed weight,27 for seed length,19 for seed width,32 for seed height,8 for RLW,19 for RLH,10 for RWH,and 34 SNP co-associate with two or more traits.It was very interesting that co-associated mainly with seed size or seed shape,respectively,maybe seed size and shape were controlled by different genetic factor.5.Wild soybean was used as material to conduct association mapping to detect SSR that associated with yield related traits.Four subpopulation structure were identified with STRUCTURE2.2,and twenty two SSR traits association were detected with MLM model(Q+K),three out of 22 for days to flowering,five for days to maturing,five for useless pod rate,four for pod number,seven for hundred seed weight and five for yield per plant.most of the marker-traits association only detected in one environment,especially for traits with low heritability,such as pod number per plant and useless pod per plant,and some association were consistent with previously report.