Genetic Map Construction And QTL Identification For Fiber Related Traits In Upland Cotton(Gossypium Hirsutum L.)

Cotton,as a multi-uses crop,is playing a significant role in the international economy on different areas of several countries.The cotton fibers,which are formed by the elongation of single cells on the surface of cotton seeds,are the main natural source of textile industry and the main part of cotton economic value.The increase of population and the improvement of living stands made high requires to the fiber quality and yield of cotton.Increasing the fiber quality and yield of cotton have always been the goals of breeders.However,the fiber quality traits of cotton are complicated quantitative traits that were controlled by multiple loci and were strongly affected by environment.Besides,the negative genetic correlation between fiber quality and yield component traits added many difficulties and challenges to improving these traits simultaneously through the classic breeding procedure.With the development of biological techniques,molecular markers assisted selective(MAS)breeding is gradually applied in cotton breeding,which provides a powerful tool to improve cotton fiber quality and yield.Genetic linkage map construction and QTL identification are the two main parts of MAS.Markers that were used to construct genetic map are also gradually changed from traditional markers like Simple Sequence Repeats(SSR)markers to Single Nucleotide Polymorphism(SNP)markers and Insertion-Deletion(InDel)markers with the development of sequencing technologies.Genetic maps that constructed by SNP markers are often with high-density and high-resolution than other markers,which are widely applied in MAS research currently.Obtaining SNP markers through Specific-Locus Amplified Fragment Sequencing(SLAF-seq)is the most widely used method.Based on a high-density genetic map,the detection of QTLs of fiber quality traits under several environments and generations could help improving cotton fiber quality through identifying stable and major QTLs.In the present study,a recombinant inbred lines(RIL)population was established from two G.hirsutum cultivars M11 and Yumian 1.A high-density genetic linkage map was constructed with SNP and SSR markers,and QTLs for cotton fiber quality were detected.The main results are as follows: 1.Genetic linkage map constructionA total of 7211 loci(including SNP and SSR marker),that distributed on the whole cotton genome with 26 chromosomes,were applied to construct a high-density genetic linkage map.This genetic map totally covered 3485.7cM with an average distance of 0.51 cM between adjacent markers.The total number of loci for A-subgenome was 4369,covering 1830.2 cM.with an average distance of 0.42 cM between adjacent markers.Among them,chromosome A13 contained the maximum number of loci,which is 707.While chromosome A11 with 114 loci was the minimum.The total number of loci on D-subgenome was 2842,and they covered 1655.5 cM with an average distance 0.6 cM between adjacent markers.The biggest number of loci was founded on chromosome D10 with 425 loci,and the least number of loci was located on chromosome D08 with 116 loci.2.Physical length of the genetic mapThe physical positions of SNP loci were obtained from sequencing data,and the physical positions of SSR loci were obtained through Blast with the reference genome of G.hirsutum.The physical length of each chromosome on the genetic map was analyzed.On the whole,the total physical length of 26 chromosomes was 1934.8 million bases(Mb),and the physical length of each chromosome ranged from 46.7 to 103.6 Mb.3.QTL identification for fiber related traitsTotally six traits,including fiber length(FL),fiber strength(FS),fiber uniformity(FU),fiber micronaire(FM),fiber elongation(FE)and lint percentage(LP)were collected from four different environments,and 47 QTLs were detected.The phenotypic variation explained(PVE)value and LOD value of these QTLs ranged from 10.1%-21.1% and 2.0-4.4,respectively.These QTLs distributed on most chromosomes expect chromosome A06,D02,D06,D07 and D13.In addition,two QTLs of lint percentage(qLP-D03-1,qLP-D09-1)were identified in three environments,and two QTLs for fiber length(qFL-A07-2,qFL-D11-1)and two QTLs for fiber micronaire(qFM-A08-1,qFM-D11-1)were identified in two environments.These six QTLs were thought to be stable QTLs.4.QTL clustersA total of four QTL clusters were detected in the present study,and they distributed on chromosome A05,A10,D09 and D11,respectively.All of these four QTL clusters contained three kinds of QTL.In addition,Cluster-D09 contained the stable lint percentage QTL qLP-D09-1,and Cluster-D11 contained the stable fiber micronaire QTL qFM-D11-1.5.QTL by environment interaction analysisA total of 13 QEI were identified in the present study,including one QEI for lint percentage and 12 QEI for fiber quality traits.Except for QEI-FS-A03-2,of which phenotypic value was mostly explained by environment effect,the phenotypic value of the other QEI were all significantly affected by the average additive effect.In addition,QEI-FM-A08-1 located in the same region with qFM-A08-1,this fiber micronaire QTL region was identified with stability in both two methods,could be beneficial for further study of fiber micronaire.