Fine Mapping And Candidate Gene Analysis Of QLPA13.1 In Cotton

Cotton is a globally significant natural fiber crop that serves as a crucial raw material for the textile industry,which makes it of high research and application value.China is the largest producer of raw cotton worldwide;however,the nation still faces an annual cotton shortfall of approximately 2 million tons,which underscores the need to develop high-yield and high-quality new cotton cultivars.G.hirsutum is the most extensively cultivated cotton species,occupying around 95%of the global planting area due to its high yield and broad adaptability.However,The genetic diversity of G.hirsutum cultivars has been reduced due to the long process of domestication and selection.Wild cotton（G.tomentosum.）,as one of the five allotetraploid wild cotton species,exhibits high levels of genetic diversity.The introduction of G.tomentosum into upland cotton can broaden the genetic basis,providing a significant opportunity for the development of high-yielding,high-quality cotton cultivars.The lint percentage is the ratio of lint to seed cotton,and it is positively related to cotton yield.In the present study,the high yield upland cotton cultivar CCRI35 was used as the recurrent parent,and the G.tomentosum P0601211 was used to detect the genotypes of 559individuals in the BC₃F_2:7 population.QTL mapping were identified for yield and fiber quality.In this study,F₂ and F_2:3 segregating populations were created with a high lint percentage line G.hirsutum variety CCRI 35 and a low lint percentage line HT＿333.The yield of the segregating populations was phenotyped,and extreme single plants were screened to generate the extreme pool of lint percentage.In addition to the pre-laboratory genetic map,primers were tested for single marker association analysis to detect the lint percentage QTL,and In Del markers were designed to encrypt the lint percentage QTL interval for fine mapping of candidate genes.The following are the key findings.（1）Analysis of population traitsA population of 2030 individual plants(（CCRI 35×HT＿333）F₂was generated via hybridization of HT＿333 and CCRI 35.Examination of yield and fiber quality traits demonstrated that these traits exhibited continuous distributions and displayed instances of super-parental separation.The kurtosis and skewness values for all traits within the population were less than 1,and these traits showed near-normal phenotypic distributions in F₂ and F_2:3populations,it was suitable for QTL analysis.Correlation analysis of yield and fiber quality traits within the F₂ population revealed significant associations between lint percentage and other yield and fiber quality traits.（2）QTL of lint percentage correlation was obtained by BSA analysisBased on the lint percentage phenotypes of the（CCRI 35×HT＿333）F₂ population,92extreme individual plants with high or low lint percentages were selected to construct a bulked segregant analysis（BSA）pool for lint percentage.A total of 267 SSR markers covering 26chromosomes were selected from a high-density genetic linkage map constructed previously using the（CCRI 35×Gossypium hirsutum）F₂ population.Polymorphisms between CCRI 35and HT＿333 were detected using these markers,and the genotypes of the 92 individual plants were determined using 34 pairs of polymorphic primers.By combining the genotype data with the lint percentage phenotype data,a lint percentage-associated QTL was identified at the SWU21717 and NAU0856 markers on the telomeric end of chromosome A13.（3）Fine mapping of QTL controlling lint percentage on A13Based on the reference genomes of Gossypium hirsutum TM-1 and G.tomentosum,a set of In Del markers were designed proximal to the telomeric region of chromosome A13,and the region was made denser.A total of 2030 individuals from the（CCRI 35×HT＿333）F₂population were genotyped with seven pairs of polymorphic In Del markers and SSR markers SWU21717 and NAU0856.The phenotype data of lint percentage was integrated with the genotypic data to locate q LPA13.1 between A13-0.0961 and A13-0.296,with a genetic distance of 0.2 c M and an LOD value of 48.56.The additive effect of q LPA13.1 was 1.56%,explaining11%of the phenotypic variation,and the favorable allele was derived from CCRI 35.The QTL was validated in an F_2:3 population containing 486 individuals,with a LOD score of 5.83,an additive effect of 1.01%,and explaining 5.6%of the phenotypic variation,with the favorable allele also coming from CCRI 35.Using substitution mapping to compare the trait and genotype of different recombinant types in the QTL region,q LPA13.1 was finally mapped between markers A13-0.0961 and A13-0.193.（4）Candidate genes identification for lint percentageThe physical distance of In Del markers A13-0.0961 and A13-0.193 on chromosome A13of G.hirsutum is 97 Kb,while the corresponding physical distance on the chromosome of G.tomentosum is 96 Kb,with 11 common annotated genes in the interval.Based on transcriptome data,fluorescence quantification results,functional analysis,and genomics,three candidate genes potentially related to lint percentage were identified:GH＿A13G0010（b ZIP17）,GH＿A13G0011（Gh CYP98A2）and GH＿A13G0019（Gh ORC4）.This study used BSA analysis combined with molecular marker-assisted selection to locate the main QTL related to lint percentage and identify candidate genes,laying a foundation for genetic improvement of lint percentage.