Genome-wide Quantitative Trait Loci And Candidate Gene Identification Reveal Genetic Basis Of Fiber Quality Traits In CCRI70 RIL Population Of Gossypium Hirsutum

Upland cotton（Gossypium hirsutum L.）is an important economic crop which is widely planted for its natural fiber.Due to its excellent environmental adaptability and yield,upland cotton contributes nearly95% of cotton production.With the increasing textile industry’s demand for high-quality fibers continues,development of upland cotton with excellent fiber quality and high yield has been the goal of cotton breeders.Both cotton yield and fiber quality traits are quantitative traits controlled by multiple genes and affected by the environment.Due to the limits of traditional breeding methods,molecular marker-assisted selection has become an important tool for cotton breeding.In recent years,a large number of studies have been reported about the QTLs related to cotton fiber quality and yield traits,which clarified the direction of their additive effects,and indicated the molecular mechanisms of the candidate genes that affect cotton fiber development.However,most of them used germplasm resource as parents while rarely used breeding materials.In this study,the CCRI70 recombinant inbred line（RIL）population was used as plant material,which is developed from the national approved hybrid variety with excellent fiber quality and high yield in China.The genome-wide fiber quality QTL and the candidate genes have been identified.Firstly,identifying the differences at transcription level during fiber initiation and elongation stages for two RILs in CCRI70 RIL population with extreme performances in lint percentage（LP）and fiber length（FL）traits.24 ovule and fiber samples of MBZ70-053（L1）with high FL and low LP,and MBZ70-236（L2）with high LP and low FL,are collected at-3,0,5 and 10 DPA and conducted for RNA-seq analysis.And 49/128,369/206,4296/1198 and 3547/2129 up-/down-regulated differentially expressed genes（DEG）are identified in the two stages.In initiation and elongation stages,DEGs are enriched into energy metabolism and accumulation as well as auxin signaling pathway,respectively.Significant DEGs are identified like PME3,and Sus4,etc.Using WGCNA analysis,7 co-expression networks and 30 hub genes are identified,such as 14-3-3ω,TBL35,ACS6,GAMMA TIP1 and PUM-7,etc.Secondly,construction of a high-density genetic map for CCRI70 RIL population.SLAF-seq of CCRI70 F_8:9 RIL population were carried out,and a high density genetic map with total length of 4850.47centimoles（c M）containing 24425 single nucleotide polymorphism（SNP）markers was constructed,with a marker interval of 0.20 c M on average.The map covers almost of the entire genome of upland cotton,which laid a important foundation for further research such as QTL detection.Thirdly,QTL detection for fiber quality traits on the whole genome.CCRI70 RIL population are developed from two parents of s GK156 and 901-001 with 250 RILs.Using the phenotypic data of fiber length（FL）,fiber strength（FS）and micronaire（FM）in nine environments such as Anyang,Linqing and Alaer during 2015 and 2016,associated with high-density genetic maps,we perform genome-wide QTL identification for the CCRI70 RIL population.A total of 289 QTLs were detected,36 were stable QTLs（17 for FS,11 for FL and 8 for FM）,18 of which were novel.These QTLs formed 7 QTL Clusters,distributed on chromosomes 7,10,14,16,17,24 and 25.The results provided basis for identifying candidate genes and for further study of the genetic mechanisms for fiber traits.Five of these QTL Clusters have the same direction of additive effect for FS and FL QTLs.And one Cluster has the different directions of additive effect for FL and FM QTLs while one has the different directions for FS and FM QTLs.Fourthly,identifying the key candidate genes in QTL intervals.The 36 stable QTLs contained a total of 1476 potential candidate genes.Transcriptome sequencing is performed on a total of 72 fiber samples at 5,10,15,20,25 and 30 DPA from the two parents and the two RILs with extreme performances,and473（320,120 and 83 for FS,FL and FM,respectively）potential candidate genes are DEGs.The study indicated that 10 highly expressed genes enriched into pectin synthesis,phenylpropane synthesis and plant hormone signaling pathways,and annotated as transcription factors,which could have an important impact on fiber strength,such as GAE6,C4H,OMT1,AFR18,EIN3,b ZIP44 and GAI.Fifthly,allelic variation in QTL intervals.Analyzing the genotypic data from DNA sequencing and RNA-seq in QTL intervals,we find that the marker D13＿56413025 in q FS-chr18-4 could significantly increase fiber strength in a nature population,and transcript of the candidate gene GH＿D13G2571（EIN3）in the important QTL q FS-chr18-1 exists 9 allelic variations between elite and poor groups,in which all the allelic variation are consistent with the results of the additive effect direction of QTL.These results provide a theoretical basis for exploring the genetic and molecular mechanisms of upland cotton fiber quality and yield,and provide new genetic information for improving upland cotton fiber quality and yield.