Construction Of Genetic Linkage Map And QTL Analysis Of Fiber Quality In Upland Cotton (Gossypium Hirsutum L.)

Upland Cotton (Gossypium hirsutum L.) is the leading natural fiber crop in the world. To promote the cotton genetics and breeding, a high-density genetic linkage map is required. Recent advances in DNA markers have proved that the combination of conventional breeding and biotechnology can provide a new way for crop improvement. Through molecular marker-assisted selection, the improvement of economically important agronomic trait could be implemented on molecular level. The first step for detecting molecular markers that are closely linked with target quantitative trait loci (QTL) is the construction of a genetic linkage map. At present, the maps developed from interspecific population in allotetraploid cotton tend to be saturated. However, the maps developed from intraspecific population in upland cotton currently are not so genome widely-covered and marker high-density enough to be employed in marker-assisted breeding. Therefore, the present study constructed a genetic linkage map with SSR, SRAP and IT-ISJ (Intron Targeted Intron-exon Splice Junction) and with morphological markers using 270 F_2:7 recombinant inbred lines (RILs) developed from a cross between two high-polymorphic parents of upland cotton cultivar, Yumianl and T586, and then fiber quality QTL were analysed.This may offer an theoretical basis for the genetic linkage map comparison as well as melocular marker-assisted selection for fiber quality in upland cotton. The main results showed as following:Fiber quality performances of mapping parents and F_2:7 RILsThe fiber quality of RIL population was determined across five environments (Chongqing-Chongqing-Hainan-Chongqing- Chongqing, 2004-2007). The two mapping parents were markedly different in fiber quality. Except fiber elongation, the fiber quality of cultivar Yumian 1 was significantly higher than that of cultivar T586. The fiber elongation displayed lower transgressive segregation beyond both parents in chongiqng, 2007, and other fiber quality traits of RILs population were all the intermediate between two parents. Fiber quality segregated continuously in five environments, and the result suggested that the fiber quality was controlled by multiple genes. The significant variances of genotype and environment tested in five environments indicated fiber quality was affected by both genotype and environment.Primer pair polymorphismA total of 236 polymorphic primer pairs were found among 4041 primer pairs including 2917 SSR primer pairs, 384 SRAP primer pairs and 740 IT-ISJ primer pairs between the two mapping parents, and the polymorphic primer pairs were 160, 27 and 49 for SSR, SRAP and IT-ISJ, respectively. The polymorphic ratio of the total primer pairs amounted to 5.84%. The average polymorphic ratio of SSR, SRAP and IT-ISJ were 5.49%, 7.03% and 6.62%, respectively. Polymorphic ratio varied between different primer types.Genotyping the recombinant inbred lines270 recombinant inbred lines were genotyped with 236 primer pairs that showed polymorphism between two parents and 253 polymorphic loci were detected, including 165 SSR, 29 SRAP and 59 IT-ISJ. Together with 365 loic obtained in our lab in the past, 618 loci are available for map construction. Chi-square examination demonstrated that 197 of 618 locideviated from the expected 1:1 Mendelian segregation, accounting for 31.88% of total loci, and most of these distorted loci revealed slight deviation(x²<10). Only 46 (7.44%) loci deviated severely (x²>10), including 1 morphological loci (12.50% of total morphological loci), 35 SSR (6.70% of total SSR loci), 3 SRAP (10.34% of total SRAP loci) and 7 IT-ISJ (11.86% of total IT-ISJ loci).Linkage map618 loci were conducted on genetic linkage analysis and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 57 linkage groups was constructed. The 57 linkage groups are ordered into the all 26 chromosomes except chromosome 4, spanning 3106.9 cM, and approximately accounting for the 69.87% of the whole cotton genome with an average genetic distance of 5.15 cM between two markers. This genetic linkage map is to date the most extensively genome-covered and most highly loci-mapped linkage map in upland cotton.Fiber quality QTL analysisBased on interval mapping method of mapping software MapQTL5.0 with LOD=2.0, the genetic linkage map and fiber quality of 270 RIL population across five environments were used to identified QTL for fiber quality, and 35 QTL affecting fiber quality were identified, Of these 35 QTL, 7 were fiber length QTL (FL), 7 were fiber uniformity QTL (FU), 7 were fiber fineness QTL (FF), 4 were fiber elongation QTL (FE) and 10 were fiber strength QTL (FS). Each QTL explained 4.1%～41.5% of the fiber quality variance. 22 QTL were distributed on A-Chromosome while other 13 on D-Chromosome. 5 QTL (FL1, FL4, FU1, FU3 and FF2) were detected in five environments and they concentrated on Ch6 and Ch7. As for fiber quality traits, the addictive effects of cultivar Yumian 1 were much significant than cultivar T586 and supplied more favorable allele gene for population.