Graph Pangenome And GWAS Reveal The Impacts Of Structural Variations On The Speciation And Diversification Of Allotetraploid Cottons

Structural variation(SV)plays an important role in species formation,intraspecific diversification,and environmental adaptation.However,the impact of SVs on the formation and diversification of allotetraploid cottons is still unclear.In this study,we assembled a high-quality reference genome of G.barbadense acc.Tanguis,a Peruvian landrace closely related to the formation of modern ELS cottons.By integrating 11 published allotetraploid cotton genomes and 1,158 resequencing data,we constructed an SV-based graph pangenome(Pan SV)and performed GWAS.Pan SV and GWAS revealed the impact of SV on the speciation and diversification of allotetraploid cottons.The main results were as follows:1.A high-quality reference genome of Tanguis was assembled.The genome size was 2.33 Gb and the Scaffold N50 was 93.79 Mb.The integrity and continuity of the genome assembly were good according to the results of Hi-C data,genetic mapping synteny comparisons,and BUSCOs assessment.2.A Pan SV containing 2,236 inversions,97,398 insertions and 82,959 deletions was constructed.Among them,there were 98 large inversions greater than 1 Mb,unevenly distributed on the chromosomes.The largest inversion(~32 Mb)was identified and verified by Hi-C data on chromosome A06,and was present in G.tomentosum,G.mustelinum,G.darwinii,and G.barbadense(Tanguis,3-79 and Pima90).In addition,recombination rate within this region was suppressed in the(XH21×Tanguis)F2.The above results suggest that great changes in genome sequences occurred during divergence in cotton,and these SVs may have led to changes in agronomic traits,environmental adaptations,species divergence and cultivar formation.3.Based on the Pan SV-based GWAS analysis(SV-GWAS),a number of new associated loci for high yield and fiber quality were identified.Compared with SNPGWAS,SV-GWAS has potential to identify more new loci,as well as the ability to detect stable loci in different environments.Our SV-GWAS results provide the evidence that the increased yield in America Pima cottons is based on genetic contributions from Tanguis cotton,and that the improved fiber quality in Chinese cottons stems from genetic contributions of Egyptian/Central Asian cottons and G.hirsutum introgression.4.Different types of ELS cotton,such as Karnak and Xinhai 21,were crossed with South American landrace with median fiber quality,such as Tanguis and VIR29 TV,to construct mapping populations.A total of 299 QTLs were identified for high yield and fiber quality.QTL co-localization analysis with SV-GWAS identified a stable,fiber length-associated QTL locus(q FL/D11).The most significantly associated SV was an83-bp deletion located 540 bp downstream of GH_D11G3495.This SV was able to significantly enhance fiber length.These candidate loci were the genetic basis for the formation of ELS cottons and an important genetic resource for the next step of genetic improvement.This study provides insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop species and highlights the importance of SVs during the speciation,domestication,and improvement of cultivated crop species.