QTL Mapping For Fiber Quality Traits Using Recombinant Inbred Lines With High-quality Fiber

Fiber quality is an important target trait in cotton breeding improving.As the fiber quality is easy affected by the environment,the breeding selection becomes very complex.Molecular markers are associated with the trait based DNA level,which directly reflects the difference of the DNA.Using marker-assisted selection could avoid the blindness of conventional breeding which depends on phenotypic selection,and improve the efficiency of breeding selection.Therefore,marker assisted selection plays an important role in the breeding process.QTL mapping for important agronomic traits in crops is one of the hot spots in crop genetics and breeding.A lot of important traits have been mapped in the rice,tomato,corn and other crops.With the development of molecular marker technology,construction of genetic map and QTL mapping of important agronomic traits in cotton have made great progress,and QTL mapping for fiber quality is one of the hot spots.In this study,we crossed the high-quality fiber germplasm,Luyuan 343 and high-yielding germplasm,Lumianyan 22 to construct recombinant inbred lines andused SSR and SLAF tags to construct a high density genetic map.QTLfor fiber quality and yield traits were mapped based on the high density genetic map.This study would be beneficial to fine mapping the fiber quality QTL and clone genes related to fiber quality based genetic map.The main results are as follows:The genetic effects of fiber length,strength and fineness were higher,with more than 30%.The three traits were mainly controlled by genetic factors.The genetic effect of the fiber length was the highest(52.04%),followed the fiber strength and fineness.Compared with fiber length,environmental effect on fiber strength and fineness were larger.The genetic effect of fiber elongation wasthe lowest(5.08%),but the environmental effect was the highest(71.82%).Fiber elongation was most easily affected by the environmental factors,and genetic selection efficiency for elongation was lower.Among the yield traits,genetic effect of lint percentage was higher(48.48%),and the effect of environmental value was lower(5.04%),so the genetic improvement efficiency of lint percentage was high.The genetic effect of boll weight was 26.48%and the environmental effect was 33-04%,suggesting the boll weight phenotype resulted by the interaction of genetic effect and environment.The genetic effects of fiber quality and yield traits were mainly additive inheritance.we compared phenotypic variation in main fiber quality parameters(including fiber length,fiber strength and fiber micronaire)and dissected the molecular genetic basis using a recombinant inbred line(RIL)population containing 282 individual lines grown at three locations in two major cotton-producing regions;i.e.,the Yellow River Valley and the Yangtze River Valley in China,over two cotton planting seasons.We found that fibers produced from the Yangtze River Valley location appeared shorter,stronger and thicker relative to that from the Yellow River Valley location.A total of 27 Quantitative Trait Loci(QTL)were identified for the main fiber quality parameters.Six QTLs were detected in more than five datasets,which explained 5.09%-23.17%of the phenotypic variance.One QTL(qFL16.1)was detected at the Yellow River Valley location over two planting seasons while three QTLs(qFL19.1,qFS03.1 and qFM19.1)were detected at the Yangtze River Valley location over the two years of planting seasons.Nine QTLs with significant additive × environment interactions(QEI)were also identified,and eight of these QTLs were detected at the Yangtze River Valley location,Moreover,four of twenty-three QTLs for boll weight and lint percentage were identified in more than five environments.A total of 623.61M reads data were obtained using high-throughput sequencing,the average Q30 was 80.40%,and the average GC content was 38.12%.After bioinformatics analysis,this project developed 432870 SLAF tags,the average sequencing depth of SLAF tag for parents was 37.4x,the average depth for offspring was 6.08x.Of the 432,870 SLAF tags,polymorphic SLAF tag was 25,280.The polymorphism ratio reached to 5.84%.The 3,749 high-quality SLAF markers integrating with 226 polymorphic SSR markers which identified in our previous study,were distributed on 26 linkage groups(LGs)according to cotton genome database.A total of 3755 markers including 3556 SLAFs and 199 SSR markers were finally mapped to LGs,spanning a total distance of 3,426.57cM with an average marker interval of 1.5 cM.The longest LG was Chr.16,which was 194.67 cM in length with 490 markers and a 0.4 cM marker interval.The shortest LG was Chr.6,which was 40.62 cM in length with 24 markers and a 1.69 cM marker interval.Chr.2 harbored the greatest marker number of 788,followed by Chr.16,while the number of markers on chromosome 6 was the least.Among the mapped markers,1,951 markers showed significant segregation distortion,and 73.8%of them tend to the female parent.Chromosome 2,on which all the markers are biased except one,had the larest number of segregation distortion markers(SDMs),and account for 40.3%of the total SDMs.Based on the high density genetic map,WinQTLCart QTL 2.5 was used to map the fiber quality and yield trait QTL.A total of 104 QTLs were detected for five fiber quality traits and three yield traits,67 of the QTLs were related to fiber quality,and 37 QTLs were related to yield traits.Twenty-four stable QTLscould be detected in more than 3 environments,of which 15 were related to fiber quality traits,9 related to yield traits.Of the stable QTLs for fiber quality,9 stable QTLs distributed in the A sub-genome group,and 6 stable QTLs were in the D sub-genome.Of the stable QTLs for yield traits,one stable QTL mapped in A sub-genome,8 stable QTLs mapped in the D sub-genome.The stable QTLs related to the fiber quality traits were distributed both in A sub-genome and D sub-genome,and the QTLs in A sub-genome were more thanthat in D sub-genome.The stable QTLs related to yield traits were mainly distributed in D sub-genome.In addition,19 QTL-clusters were identified,which distributed on 12 chromosomes.Twevle of the QTL-clusters contained fiber quality QTLs as well as yield QTLs,and the favorable alleles were from different parents,suggesting the negative correlation between fiber quality and yield traits.