Construction of a High-Density Genetic Map via Genome Resequencing and QTL Detection for Key Fiber Traits in Asiatic Cotton

Background: Asiatic cotton (Gossypium arboreum, genome A2) is one of diploid cotton species producing spinnable fibers. However, few studies on the genetic mechanism of key fiber traits of Asiatic cotton have been reported. Sequencing technology advancement and the release of Asiatic cotton genome made it possible to construct a high-density SNP genetic map and further untapped QTL detection.Results: The Asiatic cotton cultivars SXY No.1 and CSLZ were crossed to develop a recombinant inbred line (RIL) population with 189 lines. Whole genome resequencing technology was employed to construct a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. Based on fiber quality and yield component trait data from three environments, a total of 177 QTL were identified for 8 key fiber traits explaining 5.0-37.4% of the phenotypic variance. Besides, 48 stable QTL, including 15 for upper quartile length (UQL), 18 for fiber fineness (FF), 1 for immature fiber content (IFC), 4 for fiber neps count (FNC), 3 for lint percentage (LP), 7 for seed index (SI), were detected in more than one environment.Conclusions: Using a RIL population and whole genome resequencing strategy, this study presented a high-density genetic map of G. arboreum and identified 48 stable QTL for 6 key fiber traits (UQL, FF, IFC, FNC, LP, SI). Our work laid solid foundation for subsequent fine mapping of QTL for key fiber traits and cloning of controlling genes.

Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers

Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.