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Structural variations (SVs) have long been described as being involved in the origin, adaption, and domestication 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 182 593 non-redundant SVs, including 2236 inversions, 97 398 insertions, and 82 959 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 species and highlights the importance of SVs during the speciation, domestication, and improvement of cultivated crop species. In this study, the authors constructed a structural variation (SV)-based pan-genome and four segregation mapping populations of cotton. Through SV-based GWAS and QTL analysis, this study provides insights into genome-wide, gene-scale SVs linked to important agronomic traits in cotton and highlights the importance of SVs during the speciation, domestication, and improvement of cultivated crop species. [ABSTRACT FROM AUTHOR]

Background: Advances in genome sequencing technology, particularly restriction-site associated DNA sequence (RAD-seq) and whole-genome resequencing, have greatly aided the construction of cotton interspecific genetic maps based on single nucleotide polymorphism (SNPs), Indels, and other types of markers. High-density genetic maps can improve accuracy of quantitative trait locus (QTL) mapping, narrow down location intervals, and facilitate identification of the candidate genes. Result: In this study, 249 individuals from an interspecific F2 population (TM-1 and Hai7124) were re-sequenced, yielding 6303 high-confidence bin markers spanning 5057.13 cM across 26 cotton chromosomes. A total of 3380 recombination hot regions RHRs were identified which unevenly distributed on the 26 chromosomes. Based on this map, 112 QTLs relating to agronomic and physiological traits from seedling to boll opening stage were identified, including 15 loci associated with 14 traits that contained genes harboring nonsynonymous SNPs. We analyzed the sequence and expression of these ten candidate genes and discovered that GhRHD3 (GH_D10G0500) may affect fiber yield while GhGPAT6 (GH_D04G1426) may affect photosynthesis efficiency. Conclusion: Our research illustrates the efficiency of constructing a genetic map using binmap and QTL mapping on the basis of a certain size of the early-generation population. High-density genetic map features high recombination exchanges in number and distribution. The QTLs and the candidate genes identified based on this high-density genetic map may provide important gene resources for the genetic improvement of cotton. [ABSTRACT FROM AUTHOR]

Genotyping platforms provide robust support for genomics, genetics, and molecular breeding. Given the economic importance of cotton, it is urgent to develop a cotton genotyping platform that features high throughput, precision, efficiency, and cost-effectiveness. Here we reported the development of a liquid SNP chip named "ZJU CottonSNP40K" through genotyping by target sequencing, along with its utility. Representative SNPs of this chip were selected by screening more than 3,828,396 SNPs extracted from the abundance of resequencing data available from nearly 1000 cotton accessions. After strict selection, the final array includes 40,071 core SNPs evenly distributed across 26 chromosomes, 27.64 % of which are within genic regions. Testing on 13 cotton accessions showed the chip has high genotyping efficiency and accuracy. The SNP array was further used to genotype 328 (TM-1 × latifolium)F 2 individuals and a high-density genetic map was constructed for QTL mapping. The genetic map covered 2963.8 cM with an average distance of 0.57 cM, and yielded a total of 116 QTLs associated with ten agricultural traits. As an accurate high-throughput genotyping SNP array, ZJU CottonSNP40K will facilitate cotton functional studies and molecular breeding. • A high throughput, precision, efficiency, and cost-effectiveness cotton liquid SNP chip named "ZJU CottonSNP40K" were developed through genotyping by target sequencing. • A high-density genetic map was constructed that covered 2963.8 cM with an average distance of 0.57 cM. • A total of 116 QTLs associated with ten agricultural traits were detected on the basis of this new constructed genetic map. [ABSTRACT FROM AUTHOR]