Genetic dissection and origin of pleiotropic loci underlying multilevel fiber quality traits in upland cotton(Gossypium hirsutum L.)

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton fiber.Here,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)System.Genome-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits.As a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study.More importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS traits.Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for fineness.The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces.These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G.hirsutum.

Genomic divergence in cotton germplasm related to maturity and heterosis

Commercial varieties of upland cotton(Gossypium hirsutum)have undergone extensive breeding for agronomic traits,such as fiber quality,disease resistance,and yield.Cotton breeding programs have widely used Chinese upland cotton source germplasm(CUCSG)with excellent agronomic traits.A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles.Here,we analyzed 10,522 high-quality singlenucleotide polymorphisms(SNP)with the CottonSNP63 K microarray in 137 cotton accessions(including 12 hybrids of upland cotton).These data were used to investigate the genetic diversity,population structure,and genomic characteristics of each population and the contribution of these loci to heterosis.Three subgroups were identified,in agreement with their knownpedigrees,geographical distributions,and times since introduction.For each group,we identified lineagespecific genomic divergence regions,which potentially harbor key alleles that determine the characteristics of each group,such as early maturity-related loci.Investigation of the distribution of heterozygous loci,among 12 commercial cotton hybrids,revealed a potential role for these regions in heterosis.Our study provides insight into the population structure of upland cotton germplasm.Furthermore,the overlap between lineagespecific regions and heterozygous loci,in the high-yield hybrids,suggests a role for these regions in cotton heterosis.