| Soybean(Glycine max L.Merr.)is widely used in agricultural production because it is important oil and forage crops in the world.It originated from China,but now its self-sufficiency rate is very low,the imports of soybean has more than 80 million tons in last year,therefore,high yield breeding become the super ordinate breeding goal.Seed size and shape traits are among the main factors influencing yield,and they are quantitative traits controlled by multiple genes,so it is quite necessary to research the genetic basis of these traits by the high-density linkage map.Previous studies have shown that lower markers density are limited to reveal the genetic basis in QTL mapping for seed size and shape traits.This study focusses on studying the genetic basis of these traits and to search for the stable QTL through the whole genome-level.Single nucleotide polymorphism(SNP)markers covering the whole genome were obtained by SLAF-seq of F2:10 lines from direct and reciprocal crosses between Lishuizhongzihuang and Nannong 493-1 using the software of HighMap.We aim at detecting QTLs for the seed size and shape traits(seed length,seed width,seed thickness,length-to-width,length-to-thickness,width-to-thickness and 100-seed weight)in F2:10(E1)and F2:11(E2)populations by the software of IciMapping 4.1 and to estimate the additive effects,environment-by-QTL interaction effects,additive-by-additive interaction effects and their interaction effects with environments.To discover the candidate gene according to the physical location of the QTLs markers in the genome,then screen these genes by homology analysis with Arabidopsis and observe the expression level in seed of soybean.The results are as follows:1.11846 SNP markers were mapped into 20 linkage groups,the total length of the linkage map was 3395.32 cM,with an average marker spacing of 0.43 cM.Among the 11846 markers,1373 markers showed the significantly segregation distortion(P<0.05),and 1846 markers showed the highly significantly segregation distortion(P<0.01),favoring either the marker alleles of female parent Lishuizhongzihuang(59.74%)or male parent Nannong 493-1(40.36%).2.In total,190 additive QTLs distributed in 20 chromosomes with the heritabilities ranged from 0.90-14.33%.Among these 190 QTLs,105 QTLs were detected in El and 85 QTLs were detected in E2,25 stable QTLs were detected both in El and E2.50 environment-by-QTL interactions were detected with the heritabilities of 0.43?14.93%,44 of these QTLs were consistent with 190 additive QTLs.A total of 393 epistatic QTLs were detected in the two environments,194 epistatic QTLs with the heritabilities ranged from 0.60?5.17%were detected in E1 and 199 epistatic QTLs with the heritabilities ranged from 0.60?3.67%were detected in E2.We detected 4 epistatic with environments QTLs with the heritabilities ranged from 0?0.68%distributed on the chromosomes 16-16,5-10,13-1 and 2-20.The results implied that the additive effects,environment-by-QTL interaction effects,epistatic effects and their interactions with environment are important genetic components of seed size and shape.The above seven traits were controlled mainly by additive QTL and QTL-by-QTL interaction,and modified by QTL-by-environment interaction.3.In total,3,813 candidate genes were found in the marker interval of 190 additive QTLs.Among these 3,813 genes,91 genes were homologous to Arabidopsis genes of seed size and shape traits,and 12 genes of these 91 genes were expressed highly in seed tissue.So these 12 genes may regulate seed size and shape traits in soybean as in Arabidopsis.The results of the study will lay a foundation for further research on the genetic basis and molecular mechanisms of soybean seed size and shape traits,which is expected to guide the high yield breeding of soybean. |
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