Fine Mapping Of Yield QTL QLPA11 And QSIA11 On Chromosome A11 In Cotton

Cotton is a crop that is related to textile and agriculture.Cotton nourishes the lives of millions of farmers,and supports the vigorous development of the textile industry.With the improvement of people’s living standards,the demand for cotton textile products is increasing day by day.However,a huge gap exists between the supply and demand of cotton in China,and the problem of insufficient supply is becoming increasingly severe.It is an overall objective for the cotton breeding work to cultivate new varieties with high-yielding,high-quality,strong resistance,and adaptable to a wide range of conditions.Gossypium hirsutum rances are semi-wild types that is intermediate between cultivated varieties and wild cotton.They have beneficial characteristics such as drought resistance,insect and disease resistance,and are also tetraploid cotton like cultivated cotton,which can be used for cross breeding,and expanding the genetic basis of cotton.Cotton yield is a quantitative trait controlled by complex genetic mechanisms and easily influenced by the environment.Therefore,traditional breeding methods have made slow progress in cultivating new cotton varieties.Through QTL mapping,molecular markers linked to the main effect genes of yield traits can be identified and used for molecular marker-assisted breeding.Lint percentage and seed index are important yield traits,so analyzing the genetic basis of these traits is of great significance for cotton yield breeding.In our laboratory’previous study,an upland cotton high yield variety,jinnongnong07,as the female parent,and a G.hirsutum race punctatum,accession TX-230,as the male parent were to established a recombinant inbred line population,and QTL for yield trait lint percentage and seed index were deteted on chromosome A11.To fine mapping the QTL for int percentage and seed index on chromosome A11,F₂and F_2:3segregating populations were constructed from a cross beteen RIL 82 and jinnongnong 07,and phenotypic analysis of yield traits was conducted.Meanwhile,InDel markers were developed,and SSR markers and InDel markers were used to fine mapping the major-effect QTL for lint percentage and seed index,and to identify candidate genes for these traits.The main research results are as follows:1.Phenotypic evaluation of secondary segregating populationRecombinant line RIL82 was crossed to jinnongnong07 to produce secondary segregating population in the present study.The result showed that the variation coefficient range for seed index and lint percent was between 11.42%and 17.14%.The mean value of seed index for single plant in the F₂population ranged from 7.05 g to14.96 g,with a mean of 10.94 g,while the mean value of lint percent ranged from20.16%to 45.00%,with a mean of 27.41%.In the F_2:3population,the mean value of seed index ranged from 7.06 g to 15.83 g,with a mean of 10.48 g,while the mean value of lint percent ranged from 35.97%to 49.67%,with a mean of 42.44%.Both traits exhibited a continuous distribution within a large range,with skewness and kurtosis less than 1,indicating a normal distribution.Furthermore,correlation analysis revealed a significant negative correlation between lint percent and seed index.2.Genetic linkage map construction of QTL regionBased on the genetic linkage map constructed in our laboratory previous’study,821 SSR markers were screened for polymorphisms between parent jinnong07 and RIL82,and three pairs of SSR markers with polymorphisms were selected.Three SSR markers and SLAF-SNP were used to constructed the genetic map of chromosome A11,and lint percentage QTL（q LPA11）was located between 117,301,908 bp-120,315,964bp on chromosome A11.Based on sequencing results from parent jinnongnong07 and G.hirtsum race punctatum TX-230,102 pairs of InDel primers were designed,and 45 pairs of InDel primers with polymorphisms were obtained through polymorphism screening between the parents.Forty-five pairs of InDel primers were used to detect the genotypes of the F₂population markers,and the QTL region map on chromosome A11 was constructed,which included 46 markers and covered 37.2 c M,with average distance between markers was 0.808 c M.3.Fine mapping of lint percentage and seed index QTLUtilizing an QTL region genetic map and the phenotype data of lint percent and seed index,the QTL for lint percent and seed index were positioned between marker A11-119.055 and A11-119.999 in F₂population,with a genetic distance of 10.15 c M and an approximate physical distance of 940 Kb.In the F_2:3recombinant individual population,the QTL for lint percent and seed index were further mapped between marker A11-119.49 and A11-119.682,with a genetic distance of 1.67 c M and an approximate physical distance of 190 Kb.Moreover,the QTL region was validated through using the substitution mapping method on the F_2:3recombinant individual population.The results showed that lint percent and seed index QTL were located between markers A11-119.48 and A11-119.682,respectively,with a genetic distance of1.67 c M.The LOD value for lint pecentage QTL in the F_2:3population was significantly higher at 14.57,with an additive effect of 1.03,explaining 7.1%of the phenotypic variation.Similarly,the LOD value for seed index QTL was 8.60,with an additive effect of 0.40,explaining 4.2%of the phenotypic variation.Importantly,favorable alleles for both lint pecentage and seed index QTL were found to be derived from the cultivar jinnongong 07.Furthermore,the accuracy of the fine mapping interval was validated through substitution mapping analysis in the F_2:3population,confirming that both lint pecentage and seed index QTL are located between markers A11-119.48 and A11-119.682.4.Identification of QTL candidate genesIn the genome of upland cotton,the physical distance between InDel markers A11-119.48 and A11-119.682 on the A11 chromosome is determined to be 190 Kb.A total of 12 annotated genes were identified within this interval through transcriptome sequencing and parental resequencing analysis.Subsequent meticulous screening resulted in the identification of five promising candidate genes,namely GH＿A11G3582（b HLH60）,GH＿A11G3583（UVI4）,GH＿A11G3585（SPL17）,GH＿A11G3587（MYB102）and GH＿A11G3588（FAD2）,which are speculated to be associated with lint pecentage and seed index in upland cotton.The fine mapping of QTLs and identification of candidate genes associated with yield in this study provide a solid foundation for the positional cloning and genetic improvement of yield-related genes.