QTL Mapping For Fiber Quality Traits And QFS21 Fine-mapping In Upland Cotton

Cotton is the most important natural fiber crop in the world and it is also an important oil and protein resource crop.Furthermore,cotton related industries provide employment to a large number of people around the world.Hence,cotton plays an important role in world economy.Cotton related industries include seed industry,production,transportation,processing,textile,export and other industries.It is not only an important way to increase the income of farmers in cotton cultivated areas,but also an important basis for the development of textile industry,solving a large number of urban and rural labor employment problems.Cotton fiber yield is of primary importance for cotton growers,whereas the textile industry demands high fiber quality.In order to meet the diverse demands of cotton growers and the textile industry,it is necessary for cotton breeders to develop cultivars with both high yield and superior fiber quality.Cotton fiber quality components,important for spinning,primarily include length,strength and micronaire?a measure of fineness?.These traits have genetically complex quantitative inheritance and are substantially influenced by environmental factors.It is difficult to improve synchronously yield and fiber quality traits by traditional breeding approaches.Marker assisted selection?MAS?has proven to be a robust and effective breeding tool to manipulate quantitative trait locus?QTL?controlling quantitative traitsWith the release of genome sequences of cotton species,it is easy to construct high density genetic map and identify QTL.A variety of technologies based on NGS?next-generation sequencing technology?,such as genotyping by sequencing?GBS?,restriction-site associated DNA sequencing?RAD-seq?,specific locus amplified fragment sequencing?SLAF-seq?and resequencing,were widely used to construct high density genetic map and identify QTL in the past years.In this study,a recombiant inbred line population?RIL?was established from a cross between a high fiber quality upland cotton cultivar?Yumian 1?and an American high fiber quality line?CA3084?.SLAF-seq was used to discover SNPs,which were then used to develop a high density genetic map and identify QTL for fiber quality traits.For fine-mapping of qFS21 an F₂ population consisting of 1947 individuals was developed by crossing line RIL041 with Yumian 1.SSRs and InDels were used to genotype this population.Candidate gene of qFS21 was identified through comparing the qFS21 interval with the upland cotton reference genome.The main results are as follows:1.High-density genetic map of upland cottonA high density genetic map containing 6254 SNPs was constructed,covering3141.72 cM with an average distance of 0.5 cM between markers.This map covered96.53%of the genome.All chromosomes showed more than 90%coverage except Chr08 and Chr22 which showed 88.08%and 89.97%coverage,respectively2.Genome-wide QTL mapping for fiber quality traitA total of 95 QTL were detected for fiber quality traits in three environments,explaining 5.5-24.6%of the phenotypic variance.We identified 14 QTL clusters on 13chromosomes,each containing one or more stable QTL.The At genome contained 50QTL,while the Dt genome contained 45 QTL.Among the 95 detected QTL,Yumian1contributed 46 favorable alleles while CA3084 contributed 49.A total of 55 QTL were found in more than one environment with 9 found in all three environments.3.High-density genetic map of chromosome 21A total of 1947 individuals from?RIL041�Yumian 1?F₂ fine-mapping population were genotyped by using 51 SSR polymorphic primers and 40 Indel markers,and a high-density genetic map of chromosome 21 was constructed.The recombinant length was 170.5 cM,and the average distance between markers was 1.87cM.4.Fine-mapping qFS21 for fiber quality traitsThree QTL for fiber strength,fiber elongation and fiber uniformity were fine-mapped on chromosome 21.All of these QTL?qFU21.1,qFS21.1 and qFE21.1?shared a same confidence interval,corresponding the upland cotton reference genome424kb.The nearest markers were D11.58.3489,D11.58.331 and D11.58.3489,which explained 2.5%,3.0%and 1.6%of phenotypic variation,and the additive effects were-0.32,-0.95 and 0.05 respectively.5.Candidate gene identificationThe 424-kb QTL region included 26 annotated genes.The RNA sequencing result showed that three genes expressed differentially at different fiber development stages.These genes might be the QTL candidate gene for fiber quality traits on chromosome 21.