Genome-wide Association Analysis Of Quality Traits Based On Snp In Alfalfa

The quality of alfalfa(Medicago L.)is a quantitative traits which was controlled by polygenes.GWAS(Genome-wide association)analysis was an effective method for quantitative trait analysis.In this study,119 alfalfa varieties(lines)were used as experimental materials,and six quality traits such as crude protein,crude ash,neutral detergent fiber,acid detergent fiber,dry matter and relative feeding value were used as the evaluation indexes.Genome-wide association analysis of quality related traits based on 53,028 SNP molecular markers was performed in alfalfa.The main results of the study were as follows:1.Phenotype analysis of quality traitsPhenotypic variation analysis of six quality traits of 119 alfalfa varieties(lines)were performed.The result showed that,each quality traits had different degree of variation in different varieties.The minimum coefficient of variation was dry matter and the maximum coefficient of variation was relative feeding value.The correlation analysis showed that,crude protein was significantly positive correlated with relative feeding value.Neutral detergent fiber was significantly positive correlated with acid detergent fiber.Crude protein was significantly negative correlated with neutral detergent fiber,acid detergent fiber.Principal component analysis results showed that the comprehensive scores of 15 alfalfa varieties(lines)such as Rambler alfalfa,Sitel,Aible,Yuxian alfalfa,Juneng801,Eureka,Hexi alfalfa,K4,Victoria,Apollo II,Golden Empress,Diamond T,WL343,Xianfeng555 and Angus were greater than 1.Cluster analysis results showed that 119 alfalfa were divided into3 groups.Group I was composed with 18 varieties(lines),Group II was composed with 78varieties(lines),and Group III was composed with 23 varieties(lines).The comprehensive evaluation results showed that the 15 varieties(lines)whose comprehensive score was greater than 1 were classed in Group I except Golden Empress,WL343,Xianfeng555 and Angus.Those varieties(lines)had high nutritional value and good palatability,could be used as good quality alfalfa varieties(lines).2.GWAS analysisGenome-wide association analysis showed that,a total of 484 SNP loci related to quality traits were detected at the level of P<0.0001.The range of explanatory phenotype variation(R2)was 7.47%-55.85%.Among them,86 SNP loci were related to crude protein,76 SNP loci were related to crude ash,117 SNP loci were related to neutral detergent fiber,70 SNP loci were related to acid detergent fiber,32 SNP loci were related to dry matter and 103 SNP loci were related to relative feeding value.Eighty-two stable association sites were detected.Among them,12 stable association sites were related to crude protein,one stable association sites were related to crude ash,25 stable association sites were related to neutral detergent fiber,15 stable association sites were related to neutral detergent fiber,23 stable association sites were related to dry matter and 6stable association site were related to relative feeding value.Thirty-nine pleiotropy SNPs were detected,R2 ranged from 7.47%-48.27%,with an average of 19.28%.Among them,SNP152416_c2_g3_i5 was significantly correlated with crude protein,neutral detergent fiber,acid detergent fiber,dry matter and relative feeding value.8 pleiotropy SNPs were significantly correlated with 4 traits and 30 pleiotropy SNPs were significantly correlated with three traits.