Identification Of QTL For Yield And Fiber Traits Using A Popultion From A Cross Between G.hirsutum Cultivar And G.hirsutum Race Latifolium

Cotton is the most important natural fiber crop in the world,as well as an important oil crop and protein crop.Upland cotton is the most widely cultivated species in the world,producing more than 95%of the world’s fiber.However,because of a few germplasm applied in the long-term artificial selection and genetic improvement,intraspecies genetic diversity and base of upland cotton is lost and narrowed,and excellent germplasm resources were scarce,which restricts the new cultivation with high-yield,high-quality,and multi-resistant cotton varieties.The G.hirsutum race is an intermediate type between wild and cultivated species.It has rich genetic diversity,strong boll setting,large boll,and excellent fiber quality.Therefore,identifying superior alleles QTL from G.hirsutum race can provide valuable gene resources for genetic improvement of upland cotton.In this study,we used China Cotton Institute 35（CCRI35）and G.hirsutum race latifolium 19 as parents to construct a[（CCRI35×G.hirsutum race latifolium 19）×CCRI35]BC₁F_2:7 recombinant inbred lines（RIL）containing 171 progenies.A genetic map was constructed using SSR primers and SNP markers developed by SLAF-seq sequencing.The yield and fiber quality-related traits QTL was identified based on the genetic map and the yield and fiber quality trait data from Xinjiang,Chongqing and Hainan for many years.The results are as follows:1.Analysis of yield and fiber quality traitsThe yield and fiber quality traits showed a normal distribution with a large range of variation and a continuous distribution in the seven environments.The results of variance analysis showed that cotton yield and fiber quality traits were not only controlled by genotype,but also had extremely significant environmental effects.Correlation analysis between yield and fiber quality traits showed that:seed index had a very significant negative correlation with lint percent and micronaire value,and a very significant positive correlation with other traits;boll weight had a very significant positive correlation with lint index;lint percent had a significant positive correlation with lint index and micronaire value.Lint percent is extremely significant negative correlation;lint index and fiber quality traits are positively correlated in at least one environment;fiber length,fiber uniformity and fiber strength are extremely significantly positively correlated with micronaire value very significant negative correlation,Micronaire value has nothing to do with fiber elongation;Yield and fiber quality traits are extremely significant positive correlation with seed-related traits except micronaire value.2.Genetic map constructionThe SNP markers obtained by high-throughput sequencing of recombinant inbred lines using SLAF-seq technology,as well as the SSR markers obtained through polymorphism screening between parents and population marker gene detection,were constructed to contain 1771 loci（1728 SNP markers and 43 SSR markers）genetic map,the map genetic distance is 4259.691 c M,the average genetic distance between markers is 4.815 c M,covering 98.75%of the upland cotton genome.There are 938polymorphic markers in the At subgroup,with a genetic distance of 2219.086 c M,and an average distance between markers of 2.366 c M,covering 98.33%of the At subgroup.There are 833 SNP markers in the Dt chromosome subgroup,with a genetic distance of 2040.605 c M.The average genetic distance between the markers was 2.450c M,covering 96.75%of the Dt subgroup.3.QTL mapping of yield traits and fiber quality related traitsA total of 339 QTL for yield and fiber quality related traits were identified baes on the BC₁F_2:7 RIL genetic map and phenotypic data of yield and fiber quality traits in 6different environments.There are 183 QTL for yield traits:31 seed index QTL with6.5-21.4%phenotypic variation explained（PVE）,44 boll weight QTL with 6.6-28.5%PVE,26 lint percentage QTL with 6.7-15.8%PVE,12 lint index QTL for clothing index with 6.6-10.9%PVE,68 QTL for seed-related traits（seed area,seed length,seed width）with 6.6-27.9%PVE.There are 156 QTL for fiber quality:46 fiber length QTLwith 6.6-35.4%PVE,27 fibre uniformity QTL with 6.6-17.3%PVE,46 fiber strength QTLwith 6.5-26.7%PVE,11 micronaire QTL with 6.6-21.6%PVE,26 fiber elongation QTL with 6.5-16.2%PVE.4.Stable QTL for yield traits and fiber quality related traits82 QTLs were repeatedly detected in different environments,including 34 QTL for yield traits and 48 QTL for fiber quality traits.The 34 yield traits included 17 seed index QTL,8 boll weight QTL,8 lint percent QTL,and 1 lint index QTL.The 17favorable alleles QTL come from G.hirsutum race latifolium 19 and 17 favorable alleles QTL from CCRI35.The 48 fiber quality traits included 20 fiber length QTL,22 fiber strength QTL,1 micronaire QTL,3 fibre uniformity QTL and 2 fiber elongation QTL.The 31 favorable alleles QTL 31come from G.hirsutum race latifolium 19 and 17 favorable alleles QTL from from CCRI 35.In addition,246QTL are concentrated in 47 QTL clusters.These multi-environmentally identified QTL（especially the QTL with favorable alleles from G.hirsutum race latifolium 19）can be used for molecular marker-assisted breeding of upland cotton.