Genome Wide QTL Mapping for Resistance to Verticillium Wilt, Fiber Quality and Yield Traits in Cotton Chromosome Segment Substitution Lines

The development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for further genome research and crop improvement through MAS. We had developed BC5F3:5 population with the donor parent Hai1 and the recurrent parent CCRI36. In this study，300 CSSLs and their two parents CCRI36 and Hai1 were planted in a randomized complete block design with 2 replications in two Ecological locations(Anyang and Xinjiang) in 2015 and 2016, respectively. Phenotypic evaluation included Verticillium wilt disease resistance(disease index), fiber yield(plant height,boll weight, lint percentage and seed index) and fiber quaility(fiber length, fiber strength, micronaire,fiber uniformity and fiber elongation). Verticillium wilt disease resistance were collected at the time of July and August.A total of 597 pairs SSR markers screened from 2292 pairs of markers in the whole genome high density map from a BC2F1 population of G. hirsutum×G. barbadense were used to identify the polymorphisms among the BC5F3:5 lines.A total of 56 QTLs for Verticillium wilt disease resistance were detected, 30 of them are stable.,38 QTLs (68%) had negative additives effects, which indicate that the G. barbadense alleles increased Verticillium wilt resistance and decrease DI by about 2.64 to 13.23. The highest number of QTLs (15) for Verticillium wilt disease resistance was detected on Chromosome 05. By meta-analysis, 30 QTL hotspot regions for VW resistance were identified and 13 of them were new, unreported hotspot regions.191 QTLs have been detected for fiber yield and fiber quality, 98 for the fiber quality traits and 93 for the yield related traits, 54 of them are stable(12 for fiber length, 8 for fiber strength, 5 for micronaire,2 for fiber elongation, and 6 for plant height,10 for boll weight,6 for lint percentage and 5 for seed index). Three chromosomes Chr05, Chr10 and Chr20 contained more QTLs.30 clusters with disease index and fiber related traits were identified on 16 chromosomes.Most of the fiber traits were clustered with the disease index stable QTLs. We found 6 clusters namely, C01-cluster-1, C05-cluster-4, C07-cluster-1, C19-cluster-2, C22-cluster-1 and C22-cluster-2, which had positive correlation between VW resistance and fiber quality traits. Two clusters, C10-cluster-1 and C25-cluster-1 had also positive correlation between VW resistance and yield related traits( boll weight and lint percentage). One cluster, C20-cluster-1 is important for VW resistance, fiber quality and fiber yield.So, these clusters and related QTLs are very important for breeding improvement of fiber quality and yield, VW disease resistance. Key words: CSSL, Verticillium wilt disease index, fiber quality, yield, QTL, SSR markers. Correspondence: shiyuzhen@caas.cn,yuanyouluyuan@caas.cn