Identifying QTL for Fiber Yield and Fiber Quality related Traits in Upland RIL population with a High-density Genetic Map on the whole genome

A recombinant inbred line (RIL) population derived from an intraspecific cross between two elite upland cotton cultivars, 0–153 with excellent fiber quanlity and sGK9708 as commercial variety. A genetic map which covered the whole genome of upland cotton was constructed by three types of markers (SLAF-SNP markers, chip-SNP makers and SSR markers). The consensus genetic map harbored 8295 markers included 5521 SLAF SNP markers, 2398 chip –SNP markers and 733 SSR markers). The total distance of genetic map were 5197.17cM and the avenge distance between adjust markers was 0.88 cM. Combined the 22 phenotype data of the RIL population and the genetic map, the QTLs for fiber quality traits (fiber strength, fiber length and micronaire) and yield traits (boll weight, lint percentage and seed index) were identified. The results showed that there were total of 177 QTLs for fiber length, 156 for fiber strength, 201 for micronaire, 253 for boll weight, 179 for lint percentage and 187 for seed index. Among them, 44 for fiber length, 39 for fiber strength, 42 for micronaire, 58 for boll weight, 35 for lint percentage and 38 for seed index were the stable ones which could be detected in at least three environments. And there were 32 QTLs cluster related to fiber length, 29 related to fiber strength, 18 related to micronaire, 30 related to boll weight, 18 related to lint percentage and 29 related to seed index. And there were 18 negtive related QTLs cluster for fiber length, 14 for fiber strength,11 for micronaire, 14 for boll weight, 18 for lint percentage and 12 for seed index.There were also eight QTL clusters between fiber strength and lint percentage and nine QTL clusters between fiber length and lint percentage, all the QTL clusters showed the different additive effect direction for the related traits, which was in accordance with the significant negative genetic corelation between the fiber quality and lint percentage. The QTL cluster of qCluster-chr7-1 could increase fiber length, fiber strength and seed index the qCluster-chr25-1 could increase the fiber length and fiber strength and reduce the lint percentage and boll weight. The further research including function of genes located on the QTL clusters and the interaction between these genes,which would lay foundations for improving the cotton fiber quality and yield simultaneously. Key words: upland cotton; fiber quality, High-density Genetic Map, QTL，RIL population Youlu Yuan as Corresponding authors