Structural variation(SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.

Genomic insights into the genetic basis of cotton breeding in China

The excellent Upland cotton(Gossypium hirsutum)cultivars developed since 1949 have made a huge contribution to cotton production in China,the world's largest producer and consumer of cotton.However,the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear.In this study,we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent,advanced generation,intercross(MAGiC)population comprising 920 recombinant inbred lines.A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality.Of them,25(46.30%)pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits,revealing complex trade-offs and linkage drags in Upland cotton agronomic traits.Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles.Interestingly,85%oftheseelitealleles were selectedandfixed fromdifferent Americanancestors,consistentwithcotton breeding practices in China.However,seven elite alleles of native origin that are responsible for Fusarium wilt resistance,early maturing,good-quality fiber,and other characteristics were not found in American an-cestors but have greatly contributed to Chinese cotton breeding and wide cultivation.Taken together,these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

A new model system for cotton indoor genetic and genomic research

Dear Editor,As an important fiber and oil crop,cotton has gradually developed into a model plant for studying fiber or seed trichome and polyploid evolution.Thus,strengthening cotton research is essential.Significant progress has been made in the research of cotton genomics(Hu et al.,2019;Huang and Zhu,2021;Wen et al.,2022).However,further research has been hindered due to its long growth period(usually 4–6 months per generation)and large plant size(usually 0.8–1.5 m in height).