Fine-mapping Of Fiber Strength QTL(qFS_D03) And Cloning Of Candidate Genes

Cotton is one of most economic crops in the world.Cotton fiber is an important nature fiber for the textile industry.Nowadays,with the rapid development of textile industry,the purpose of the cotton breeding has been changed from cotton production to production and quality simultaneously,especially fiber strength,fiber strength has become an important measurement index of fiber quality.Therefore,breeding new varieties with fine fiber strength has being the one of main goal of cotton breeding.However,the genetic narrow in upland cotton with less polymorphism marker,incressing the difficulty of marker-assisted selection in cotton breeding.To overcome this difficulty,here we applied restriction-site associated DNA(RAD)sequencing technology for de novo SNP discovery in allotetraploid cotton.We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines(RILs).Finally,a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result.Using this map quantitative trait locus(QTLs)conferring fiber strength and Verticillium Wilt(VW)resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat(SSR)genetic map.The QTL of fiber strength was located between two RAD-markers with 2-LOD intervals less than 6 cM on D3 chromosome.The major VW resistant QTL was flanked by SSR marker and RAD-marker,with 2-LOD intervals 1.46 cM.Besides,we also tagged more QTLs for these two traits compared with the result by using the same RIL population.This suggests that the newly constructed map has more power and resolution than the previous SSR map.It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits.In order to fine mapping QTL of fiber strength,in this study,we selected4 RILs:RIL168,RIL98,RIL120,RIL43,which with fine fiber strength in diverse enviroments for years.These RILs were used to develope F2 populations with 86-1.The SNP markers identified by RAD-seq,and the InDel markers identified by tanscriptome sequencing were used for fine mapping.We using five F2populations with 1,864individuals analysis markers associated with fiber strength QTL to construction of linkage map.Finaly,the QTL of fiber strength were located between two markers K5219 and K5221,corresponding to the physical distance in 0.93Mb.In addition,transcriptome sequencing of 86-1,which with low fiber strength,and RIL168,which with fine fiber strength during the secondary wall thickening stage of fiber development period were investigated using Illumina HiSeqTM 2000 System.A variety of methods were used to analyze common different expression genes(DEGs)between the meterials,including cluster analysis,MAPMAN functional enrichment analysis,and pathway enrichment analysis.The result shows that,the expression level of genes involved in cellulose synthesis is much higher in RIL168 than in 86-1.The expression pattern of DEGs significantly changed after entering the secondary wall thickening stage,genes related to cellulose precursor synthesis were changed from up-regulated to no difference or down-regulated,which made cellulose mass synthesis in meterials with fine fiber strength.Besides,after searching for structural variation,the result not only contributed polymorphism markers to fine mapping,but also detected several genes with structural variation.Combined the result of fine mapping with transcriptome sequencing,identified five candidate genes with different expression.The relationship between 6bp deletion at N-terminal of GhUBXand fiber strengh was founded by qPCR confirmation,gene cloning,and correlation analyzing.The result indicated that GhUBX,which located in qFSD03intervalplays acritical role in fiber strengthdetermination between materials.