Exploration Of Interspecific Variation,Application Of QTL Mapping And Genome-Wide Interpretation Of Recombination Variation In Cotton

Cotton is an important cash crop,its own commercialization rate is more than 95%,and has played an important role in China and the world’s economic development.Upland cotton,as the main cultivated species,has high yield but low genetic diversity.The wild cotton germplasm is resistant to disease and insect,drought and cold,salt and alkali.How to use the excellent characteristics of wild germplasm to improve upland cotton,broaden its genetic diversity and cultivate new cotton varieties with high yield and high quality is a key point of cotton breeding and genetic improvement in the future.Genetic variation produced by recombination can be screened through natural selection,which determines the adaptive evolution of organisms,and thus indirectly determines the genome evolution.Recombination variation is common in natural populations,and is an important part of evolution and breeding.Therefore,this study includes into two parts,the main results are as follows: 1.Exploration and utilization of interspecific variation in cottonSLAF-seq was performed on G.hirsutum Emian22（Gh_E22）,G.barbadense 3-79（Gb₃-79）,G.tomentosum（Gt）,G.mustelinum（Gm）and G.darwinii（Gd）.The phylogenetic relationship of five cotton species was constructed,and a large number of interspecific variations were identified.On this basis,an introgression line population of the wild germplasm G.mustelinum containing 71 families in a background of the upland cotton was constructed.The genomic coverage of introgression fragments was 36.3%.The analysis of 15 phenotypic traits showed that the yield and fiber quality traits demonstrated a relatively continuous normal distribution and the separation variation was large.A total of 48 QTL were detected,including 19 QTL related to yield,29 QTL related to fiber quality with the 2,839 high-quality SNPs.A candidate gene（Gh_A09G0372）that might be related to yield（boll weight or lint percentage）was identified.2.Genome-wide recombination rate variation in cottonThe variation of cotton genome-wide recombination rate was analyzed by linkage mapping and linkage disequilibrium mapping.It was found that at the genome-wide level,recombination showed an uneven distribution pattern.There was a significant positive correlation between recombination rate and gene density,marker density,and the distance from centromeres,but a significant negative correlation with TE density.The recombination rate of upland cotton cultivars was higher than that of Asian cotton.The variation of recombination rate within species was less than that between species.The recombination rate of the structural variation region was relatively high and varied greatly.Recombination was relatively less affected by geographic sources and breeding periods.A genome-wide association study of 15 agronomic traits was carried out using 267 upland cotton materials,163 QTL were detected,and a candidate gene,Ghir_COL2 which was located between two high recombination intervals and related to cotton early maturity was identified.Compared with yield and early maturity traits,fiber quality traits were more strongly selected,suggesting that recombination promoted cotton domestication and genetic improvement,which provided new insights into cotton recombination rate variation studies.