Construction Of SNP Genetic Linkage Map And QTL Mapping Of Quality Related Traits In Flax

In this study,The female parent R43?inbred line,homozygous genotype?was crossed to the male parent LH-89?inbred line,homozygous genotype?.The F₁ plants were self-pollinated to develop F₂ map construction population.The selected F₂ were self-pollinated and the seeds from single F₂ plants were planted to construct an F_2:3population for QTL mapping.Based on specific-locus amplified fragment?SLAF?library construction and high-throughput sequencing,the SNP linkage map was constructed and QTL mapping of 13 quality related traits were made.BLAT was used to search against the flax reference genome for alignment of QTL regions with corresponding scaffold of the reference genome.Information of code genes were attained after sequence assembling aligning to Database.Then the genes were annotated using annotation tools based on different Databases.Main results as follows:1.Phenotypic distribution,variance analysis,correlation coefficients and broad sense heritability of 13 traits were made.Results showed that the trait data of H,TL,BN,SPB,TSW,PAL,OLE,OIL were normal distribution and SWPP,BPP,LIO,LIN,OIL were deviated from normal distribution.The variance coefficients of SWPP,BPP,BN,STE,LIN,LIO were significant,data were 0.59,0.56,0.34,0.31,0.32 and 0.39,respectively.There were positive correlations with significance at P<0.01 between H and TL,SWPP.The same with BN and BPP,SWPP,as well as BPP and SWPP.There was negative correlations with significance at P<0.01 between TL and BN.There were negative correlations with significance at P<0.01between PAL and STE,LIN as well as LIO and LIN.There were negative correlations with significance at P<0.05 between OLE and LIO.PAL and LIO was positive correlated with significance at P<0.01.The highest broad sense heritability of LIO and LIN were 88%and86%,respectively.2.After enzyme prediction according to reference genome,Hae?+Rsa?were selected as the suitable enzymes.Through enzyme cutting-PCR-sequencing cycle,196.29M reads were obtained.The reads were GATK aligned and variance tested,and 260,380SNP tags were attained.Among these data,4,638 SNP markers were selected for map construction.3.The linear model of the markers in the linkage map was determined by High Map,and converting the recombination rate to genetic distance.After linkage analysis,4,145 markers were mapped onto the genetic map.The map contains 15 linkage groups.The total length of the map was 2 632.94 cM.The average marker number of linkage groups was 276.33.The integrity of each groups were 93.59%.The average distance between adjacent markers was 0.92 cM.It was the linkage map constructed in flax with the highest marker density and genome coverage.4.Using CIM method,the QTL mapping of 13 agronomic and quality traits were made by R/QTL programme.35 quantitative trait loci?QTL?were identified from 12 linkage groups,except for LG7,LG11 and LG13.Five QTL each for oil content and linoleic acid,four QTL each for linolenic acid and thousand seed weight,three QTL each for palmitic acid,height and technical length,two QTL each for stearic acid and branch number,one each for boll per plant,seeds per boll,seeds weight per plant and oleic acid.There were 21 QTLs whose LOD scores ranged from 3.07 to 12.98,percentage of the phenotypic variation explained by the QTL ranged from 4.65 to 44.08.Among them,18QTL whose percentage of the phenotypic variation explained were exceeded 10%,i.e.,eight for agronomic traits and ten for quality traits,were the main effect QTL.Gene action of QTL loci of linoleic acid and linolenic acid were mainly additive effects,while the gene action of the other QTL loci were mainly Overdominance or partial dominance effects.5.QTL regions were aligned to scaffold of reference genome by BLAT software.130 code genes were attained after sequence alignment,32 for thousand seed weight,26 for palmitic acid,72 for linoleic acid.The QTL for thousand seed weigh,TSW-LG2-1 and TSW-LG6,were each annotated to three associated genes,i.e,Leucine Rich Repeat?LRR?receptor protein kinase.PAL-LG1-2 for palmitic acid was annotated to one transcription factor Myb gene.LIO-LG8 for Linoleic acid was annotated to two transcription factor Myb gene.