QTL Validation And Exploration Of The Candidate Genes For Fiber Quality Traits In A Gossypium Mustelinum Introgression Line

Cotton is the most important textile resource material in the world.Excellent fiber quality has always been an important demand of the textile industry,and it is also an important goal of breeding improvement.The long time targeted selection of cotton traits has led to the narrow genetic basis of Gossypium hirsutum varieties.Therefore,the introduction of novel genetic resources has become an important means to expand the genetic diversity of upland cotton.Gossypium mustelinum,one of the wild allotetraploid cotton,has a long genetic distance from upland cotton,which is conducive to cross with upland cotton,and the introduction of these related genes into upland cotton will certainly contribute to the improvement of upland cotton varieties.In our previous research,an upland cotton material PD94042 was used as the recurrent parent to cross with G.mustelinum to cultivate 65 introgression lines,and fiber quality QTL were mapped.IL9,an introgression line with elite fiber quality was further selected.Transcriptome analysis（RNA-seq）was performed on cotton fibers of17 and 21 days post anthesis（dpa）of IL9 and its recurrent parent,PD94042,and differential expressed genes（DEGs）were identified.An F₂population containing 1244 individual plants was constructed by crossing of IL9 and PD94042.The phenotypic data of the population was identified and screened,and four DNA mixed pools,namely DNA pool with the strongest fiber strength,the weakest fiber strength,the longest fiber length and the shortest fiber length,together wih the 2 parental DNA pools were obtained,each with 30individuals.The bulked segregation analysis based on genome re-sequencing（BSA-seq）was used for genetic association analysis.Totally 285 individual plants in the F₂population were randomly selected,and molecular marker experiments and phenotypic identification of fiber quality traits were carried out,so as to validate and fine mapping QTLs of fiber quality traits.PD94042 and IL9 were planted and RNAs were extracted from17 and 21 dpa fibers.Part of the RNAs was used in strand-specific transcriptome analysis,and the rest RNAs were used for subsequent RT-q PCR expression verification.In this study,through the QTL mapping of the F₂ subpopulation,we mapped a total of 43 QTL related to cotton fiber quality traits.Compared with the previous QTL results based on the introgression lines of G.mustelinum chromosome fragments,we verified two QTLs,namely q UHM-3-1,which controls cotton fiber length,and qSTR-23-1,which controls cotton fiber.Based on the DEGs of the transcriptome and the results of BSA-seq,candidate genes of fiber quality were further identified with these QTL regions.Using BSA-seq and RNA-seq analysis methods,we also locate candidate gene regions or candidate genes that control different fiber quality traits.By comparing with the QTL mapping results,we have completed a more refined mapping of the target region and identification of candidate genes.Through SNP-Index analysis and ED analysis,we found a total of 26 target genes that control fiber length or fiber strength traits.In addition,according to the results of QTL-mapping and RNA-seq,we have mapped a total of 10 candidate genes that control fiber length or fiber strength.Through the combined analysis of QTL-mapping,BSA-seq and chain-specific transcriptome,we locate a candidate gene Gm PEL-23.1 that controls fiber strength on Chr.23.Based on the results of candidate genes,genome-wide analysis of two gene families were carried out,namely the HD-ZIP-N gene family and the MYB/SANT protein gene family in upland cotton.In terms of the expression verification experiment of the target gene,37 candidate genes were selected to carry out the RT-qPCR verification with the fibers of 17 and 21 dpa.According to the results of expression verification results,17 genes showed differential expression.Compared with the upland cotton fibers of the same period,12 genes were up-regulated,whereas the other 5 genes were down-regulated.In addition,Cot AD＿19764,Cot AD＿70096,Cot AD＿36024 and Gm PEL-23.1 also have differential expression in RNA-seq/strand-specific transcriptome analysis,and the up-down-regulation relationship is consistent with this expression verification.In this study,through the comprehensive use of QTL mapping,transcriptome analysis and BSA-seq analysis,combined with the whole genome sequence information of tetraploid upland cotton,the candidate genes for QTL fiber quality of G.mustelinum were discovered,which provided genetic resources for improving upland cotton fiber quality.