QTL Mapping For Fiber Quality Traits And Fine Mapping And Candidate Gene Identification Of QFS15 In Upland Cotton

Cotton is the most important natural fiber crop.As the most important species,upland cotton yields approximately 95%of all cotton fiber due to its high productivity and wide adaptability.However,comparing with island cotton,its moderate fiber qualities for spinning,especially length,strength and fineness??micronaire�?,are in urgent need of improvement.The most effective methods may be integrate traditional breeding and the high-efficiency method known as marker-assisted selection?MAS?.Cotton fiber quality traits are controlled by multiple quantitative trait loci?QTL?and affected greatly by environments,which leads to inefficient selection of traditional breeding approaches.However,MAS can eliminate environmental effects by selection based on DNA marker genotype,promoting breeding progress.Unfortunately,large gaps still exist between the expectations and actual applications in practical cotton breeding,because of the limited numbers of established molecular markers linked to major QTL controlling fiber quality traits prioritized by breeders.Single-nucleotide polymorphism?SNP?markers with genome-wide abundance characterized by high-throughput genotyping fulfill the need for saturated genetic map construction and are suitable for application to QTL dissection and MAS.The SNP array for hybridization,CottonSNP63K array,has been developed and utilized to evaluate genetic diversity,conduct genome-wide association studies?GWAS?,construct genetic maps and dissect QTL.However,the CottonSNP80K was developed based on upland cotton genome reference sequence,and has been rarely applied in genetic map construction and fiber quality traits QTL mapping.Moreover,among these QTL mapping for fiber quality traits,few of them were conducted for fine mapping and idenfy candidate genes.Therefore,it is urgent to fine mapping fiber quality QTL and identify candidate genes based on high density genetic map and primary mapping,so as to elaborate the molecular mechanisms of cotton fiber development,and application in cotton breeding practice.In the present study,the CottonSNP80K array and SSR primer identified in previous study in our lab were implemented to genotype?Yumian 1�Acala Maxxa?recombinant inbred lines?RILs?population and construct a high-density intraspecific genetic map for upland cotton,then identify genome-wide fiber quality QTL based on the genetic map and fiber quality traits test,fine mapping fiber quality traits QTL and indentify candidate genes on chromosome 15.The main results as following:1.High-density intraspecific genetic map construction for upland cottonThe CottonSNP80K array and 343 SSR primers pairs were implemented to genotype?Yumian 1�Acala Maxxa?recombinant inbred lines?RILs?and construct a high-density intraspecific genetic map for upland cotton,which contained 12462polymorphic loci and spanned 3741.81 cM with an average distance of 0.30 cM between consecutive loci,and the genetic map was corresponded to 1934.65 Mb of the physical map,spanning 97.99%of the upland cotton genome reference sequence.2.Genome-wide QTL mapping for fiber quality trait in upland cottonA total of 104 QTL controlling fiber quality traits were detected based on genetic map and fiber tests for?Yumian 1�Acala Maxxa?recombinant inbred lines population in three environments?2015CQ,2016CQ and 2016HN?,these QTL included 21 fiber length QTL,16 fiber uniformity QTL,27 fiber strength QTL,18 fiber micronaire QTL and 22 fiber elongation QTL,explaining 5.0-18.8%of the total phenotypic variance.Yumian 1 contributed positive additive effects at 48 QTL to increase relevant trait values,whereas 56 QTL alleles with negative additive effects derived from Acala Maxxa.Significantly,Thirty-five QTL were detected in 2 environments,25 in three environments,and 74 QTL were concentrated distributed on 19 QTL clusters.3.High-density genetic map construction on chromosome 15In total,ninety-three polymorphic primer pairs were used to genotype 409inviduals from?RIL138�Acala Maxxa?F₂ fine mapping population,and at final,a high-density genetic map for chromosome 15 was constructed,which contained 93 loci,spanned 160.03 cM with an average distance of 1.72 cM between consecutive loci,and the genetic map was accordant to the corresponding physical map,showing the accuracy and good reliability for QTL fine mapping.4.Fine mapping for fiber quality traits on chromosome 15A total of 6 QTL controlling fiber quality traits were detected based on genetic map and fiber tests for?RIL138�Acala Maxxa?F₂ fine mapping population,six QTL concentrated distributed on 2 QTL clusters with two set of QTL controlling fiber length,fiber strength and fiber micronaire respectively,all these favorable alleles for 6 QTL were origined from Acala Maxxa.Ultimately,qFL15.1 and qFS15.1 were mapped on6.40 cM region,with the additive efforts of-0.36 mm and-0.84 cN/tex respectively,the corresponding physical region?1767206 bp?contained 69 annotation genes.qFL15.2and qFS15.2 were mapped on 7.47 cM region,with the additive efforts of-0.40 mm and-0.96 cN/tex respectively,the corresponding physical region?648288 bp?contained 43annotation genes.5.Candidate gene identificationAccording to the corresponding reference sequence annotation genes in QTL confidence interval,and the results of DEGs and re-sequencing of mapping parents,candidate genes Gh_D01G1679 and Gh_D01G1705 were identified for qFS15.1,Gh_D01G1953 and Gh_D01G1970 for qFS15.2.Gh_D01G1679 encodes expansin-like A2 protein,Gh_D01G1705 encodes RWP-RK family protein,Gh_D01G1953 encodes TPX2 domain protein,known as microtubule binding protein,Gh_D01G1970 encoded Med27 domain protein.These fuctions of four candidate genes were closely related to fiber quality traits.