Genome Wide QTL Mapping For Resistance To Verticillium Wilt,Fiber Quality And Yield Traits In Cotton Chromosome Segment Substitution Lines

Cotton is an important economic crop worldwide.It provides important natural fibers for the textile industry.Of the two most economically important tetraploid cultivated species,Upland cotton,which has high yield and wide adaptability,makes up about 95 % of the total cotton yield worldwide.Sea-island cotton(G.barbadense)has strong resistance to Verticillium wilt(VW)and extra-long,fine,strong,fibers.Using conventional breeding,breeders have made interspecific crosses between Upland cotton and seaisland cotton to synchronously improve the VW resistance,yield and fiber quality of Upland cotton for many years,but no breakthrough has been reported because of the negative genetic correlation between yield and fiber quality,between yield and disease resistance,as well as linkage drag and hybrid breakdown.By MAS,the development of Chromosome Segment Substitution Lines(CSSLs)from Sea-island cotton in Upland cotton provided ideal and optimal materials for breeders and locating the quantitative trait loci(QTL)for yield,fiber quality and disease resistance.In this study,a CSSL population comprising of 300 lines derived from an interspecific backcross between the highly resistant line Hai1(Sea-island cotton)and the susceptible variety CCRI36(Upland cotton)as the recurrent parent were used as plant materials.A total of 597 markers selected from the a high-density simple sequence repeat(SSR)genetic linkage map from the CCRI36 � Hai1 BC1F1 population were used to identify the genotypes of 300 CSSLs.Quantitative trait loci(QTL)related to yield and fiber quality and VW resistance were detected in the whole cotton genome using these data.Based the disease index(DI)data obtained from three dates of 300 CSSLs in greenhouse with six replications in 2015 and eight dates of 300 CSSLs in Anyang and Xinjiang with two replications in 2015 and 2016,a total of 60 disease index(DI)QTLs for VW resistance were identified on 21 chromosome of cotton genome except chromosome 04,08,13,16 and 18,explaining 3.8�11.9% of the observed PV.Among them,32 DI QTLs were consistently detected in at least two environments,which were regarded to be stable ones.Biomercator 4.2 has been used to integrate QTL data of our CSSL population and QTL data with previous studies to perform meta-analysis.Meta �analysis indicated that the 10 QTLs were consistent with those identified previously and another 50 were new and unreported QTLs.By meta-analysis,30 QTL hotspot regions were identified and 13 of them were new,unreported hotspot regions.These stable or consensus QTLs and QTL hotspot regions warrant further investigation to better understand the genetics and molecular mechanisms underlying VW resistance.This study provides useful information for further comparative analysis and MAS in the breeding of disease-resistant cotton.It may also lay an important foundation for fine mapping,gene cloning and further genome-wide molecular design breeding program.Based the data yield and fiber quality of 300 CSSLs in 4 environments(Anyang and Xinjiang in 2015;Anyang and Xinjiang in 2016,with two replications each year),a total of 191 QTLs were identified on 23 chromosomes.Among them,98 QTLs of the fiber quality traits and 93 QTLs of the yield traits.94 QTLs were mapped on At sub-genome while 97 were mapped on Dt sub-genome.Three chromosomes Chr03,Chr05 and Chr20 contained more QTLs as compared to remained chromosomes,while three chromosomes Chr04,Chr08 and Chr21 have no QTL.Among them,54 QTLs was consistence or stable.In total,34 colocated QTL regions or clusters were observed on 15 chromosomes which contained 99 QTLs for fiber and yield traits.Most of the stable QTLs were located in these cluster regions.So,these cluster regions could be used as target for fiber quality and yield improvement through marker assisted selection in cotton breeding program.Compared with previous reports,out of 191 QTLs,53 QTLs were identified with 15 for FL,11 for FS,5 for FM,4 for FE,5 for FU,4 for LP,4 for BW,3 for SI and 2 for PH.138 QTLs could be consider as new discover.These stable and common QTLs lay a solid foundation for MAS breeding.We found 7 large clusters namely,C01-cluster-1,C05-cluster-4,C07-cluster-1,C19-cluster-2,C20-cluster-1,C22-cluster-1 and C22-cluster-2,which had positive correlation between VW resistance and fiber quality traits.It means the donor parent G.barbadense increased both VW resistance and fiber quality,and decreased Verticillium wilt disease index.Another three clusters(C10-cluster-1,C20-cluster-1 and C25-cluster-1)which had also positive correlation between VW resistance and yield related traits.One cluster,C20-cluster-1 is important for VW resistance,fiber quality and yield.So,these clusters and QTLs are very important for fiber quality improvement including yield and VW disease resistance as well as breeding improvements in cotton.