Genomic Insight Into The Genetic Divergence And Adaptative Evolution Of Upland Cotton In China

Upland cotton is the most economically important fiber crop in the modern world.The domestication followed by human-mediated selection has resulted in modern upland cultivars with higher yield and better fiber quality.Diversity is the key to improve cultivars;however,continuous selection and adaptation to the local environment resulted in the loss of genetic variation in upland cotton(Gossypium hirsutum).Wild progenitors and obsolete accessions are an excellent source for strengthening the genetic base and accumulation of desirable traits in modern cultivars.Here we reevaluate a landrace of Gossypium hirsutum,formerly known as Gossypium purpurascens,naturally growing on several islands in South China for centuries.This study seeks to understand the genomic structure,variation,and the adaptive/breeding potential among largely neglected landraces of Gossypium hirsutum ‘purpurascens' in relation to wild G.hirsutum,providing potential insights into the biogeographic history and genomic changes likely associated with domestication.A wide range of differentiation was observed between G.purpurascens and current varieties,obsolete accessions collected from Southwest China,and geographical landraces of upland cotton from Central America,emphasizing the divergent behavior of G.purpurascens.Furthermore,199 genome wide selection sweeps,identified using top 1% threshold Reduction of diversity from G.purpurascens to modern cultivars,overlapped with previously reported QTLs for multiple traits.This study also provides a comprehensive assessment of G.hirsutum landraces,obsolete cultivars,and modern cultivars based on high throughput genome-wide sequencing of the core set of genotypes.As a result of the genome-wide scan,we identified 93 differential regions and 311 selection sweeps associated with domestication and improvement in modern cultivars.Furthermore,we performed genome-wide association studies to identify traits associated with the differential regions and selection sweeps.These GWAS associations resulted in identification of putative QTLs/genes controlling flowering time,fiber quality and other morphological characteristics.Five significant GWAS signals for the flowering time were identified to overlap with the selection sweep and high differentiation regions on chromosome A05,A06,D01,D02,and D10.Furthermore,a pleiotropic locus was identified on chromosome D11 which showed significant association with fiber length,fiber length uniformity,and fiber elongation.Another,non-domesticated trait,anther color showed significant GWAS association on chromosome A05.This study established the primitive nature of G.purpurascens as a vital source of useful variation,the inclusion of which in upland cotton gene pool can enhance the narrowed genetic base of upland cultivars worldwide.Moreover,the conserved nature of G.purpurascens can also provide insight into understanding the evolutionary process of G.hirsutum.This study further the understanding of genetic basis to comprehend the domestication process in Chinese cotton cultivars.It also provides a comprehensive insight into genome structure changes in cotton germplasm due to selection and improvement during the last century.