| In this study,SRAP molecular markers were used to evaluate phenotypic variation and genetic diversity of 401 flax germplasms,build a connected group;Through resequencing technology studies,genetic diversity,population structure,linkage disequilibrium and association analysis were performed on 269 flax gerrmplasms.SNP loci and candidate genes associated with yield and quality-related traits were obtained,and gene function annotations were performed by NR,Swiss-port,KEGG,and GO databases.The main findings are as follows:1.The average coefficient of variation of 14 phenotypic traits of 401 flax germplasms was 17.87%,and the average genetic diversity index was 2.132.A total of 234 polymorphic bands were amplified by 26 pairs of SRAP primers.The polymorphism information content(PIC)averaged 0.60.In cluster analysis,the 401 flax resources were divided into 2 categories and 7 sub-categories,respectively,which were consistent with the sources from 7 different regions both at home and abroad.2.The sequence data of 1.3684Tb was obtained by Hi-seq sequencing of 269 flax varieties.The average ratio of mapping to the flax reference genome was 96.32%,and the average GC content was 38.57%.The average sequencing depth was 12.55.A total of 1,069,106 SNPs were obtained in 4037 Scaffolds.3.Sexteen significant SNP loci and 57 candidate genes were identified to be associated with yield-related traits.Five height-related SNPs were scaffold9:516785,scaffold977:291500,scaffold297:924133,scaffold345:220084,scaffold182:630023,and fourteen candidate genes were obtained;Four stem length related SNPs was scaffold123:1933585/1934089,scaffold2404:110872/111109,on which fifteen candidate genes were obtained;Two branchnumber relatedSNPs were scaffold31:1694349/13273,and fourteen candidate genes were obtained;The SNP scaffold462:594151was associated with balls per plant,on which 7 candidate genes were obtained;The SNPs associated with thousand seed weightwere scaffold261:57823,Scaffold373:565281,scaffold107:55172,and five candidate genes were obtained;Two SNPs scaffold1037:394952 and scaffold312:72968 were associated with seeds per ball,and8 candidate genes were found;Two SNPs scaffold31:960134/964139 were related to seed weightper plant,and only lcandidate gene was obtained;two other SNPs scaffold376:38235/30001 were correlated with growth period,and2 candidate genes were found;The significance-log(P)threshold distribution ranged from 6.24 to 10.65,and the significant SNPs explained 6.76-12.97%of phenotypic variation.4.Nineteen significant SNP loci and 43 candidate genes were found to be associated with quality-related traits.8 SNPs were correlated with linolenic acid,and they were scaffold86:981127,scaffold242:110610,scaffold313:25935,scaffold729:255875,Scaffold51:164258,scaffold244:33159,scaffold931:286930,scaffold1302:686,and 17 candidate genes were obtained;three SNPs associated with stearic acid were scaffold132:133025,scaffold1216:172262,scaffold11:89557,and 7 candidate genes were obtained;three other SNPs scaffold199:241878/243225/243225 were related to soleic acid,and5 candidate genes were obtained;the SNP scaffold123:2041205 was correlated with linoleic acid,and6 candidate genes were found;two palmitic acid-associated SNPs were scaffold175:581966/580540,and5 candidate genes were found;2 other SNPs scaffoldl96:551524/567328 were associated with crude fat,and3 candidate genes were found;The significance-log(P)threshold distribution ranged from 6.04 to 8.75,and 5.62-11.04%phenotypic variation was explained by the significant SNPs.5.Association analysis of flower and leaf related traits obtained 11 significant SNP loci and 28 candidate genes,of which,3 significant SNPs(scaffold701:840107,scaffold736:250888,scaffold1639:8420),and eight candidate genes were detected for flower color;three significant SNP loci(scaffold811:44136,scaffold1370:15031,scaffold695:22509)and 6 candidate genes were detected for corolla shape;one significant SNP locus Scaffold910:31728was detected for the anther color and5 candidate genes were annotated;one significant SNP locus was detected for leaf color(scaffold211:69126),and 4 candidate genes were annotated;three significant SNP loci were detected for leaf shape(scaffold67:579267,Scaffold76:1474090,scaffold51:1093344),and 5 candidate genes were annotated. |
PDF Full Text Request