Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population.

Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.

Direct visualization of horizontal gene transfer in cotton plants.

Plant mitochondrial and chloroplast genes that underwent horizontal transfer have been identified by parasite and grafting systems, respectively. Here, we directly observed 3 horizontal gene transfer (HGT) events in the 45 second axillary shoots of grafted cotton plants (Gossypium barbadense and Gossypium hirsutum) after extirpating the first axillary bud. The second axillary shoots showed phenotypic variations in cotton flowers and seeds that were evidence of spontaneous development from cells in the grafting site. As the progeny segregated and did not show stable inheritance across 3 generations, inheritance of traits in our study differed from the stable heredity of HGT plants in previous studies. In those studies, plants were artificially regenerated from the graft junctions, and inheritance involved only the movement of chloroplast DNA or genomic material between cells. Our findings may provide a feasible method to enhance plant breeding and the study of HGT.