Abstract
Cotton produces natural fiber for the textile industry. The genetic effects of genomic structural variations underlying agronomic traits remain unclear. Here, we generate two high-quality genomes of Gossypium hirsutum cv. NDM8 and Gossypium barbadense acc. Pima90, and identify large-scale structural variations in the two species and 1,081 G. hirsutum accessions. The density of structural variations is higher in the D-subgenome than in the A-subgenome, indicating that the D-subgenome undergoes stronger selection during species formation and variety development. Many structural variations in genes and/or regulatory regions potentially influencing agronomic traits were discovered. Of 446 significantly associated structural variations, those for fiber quality and Verticillium wilt resistance are located mainly in the D-subgenome and those for yield mainly in the A-subgenome. Our research provides insight into the role of structural variations in genotype-to-phenotype relationships and their potential utility in crop improvement.
Highlights
As a widely cultivated fiber crop, cotton produces natural fiber for the textile industry[1]
We obtained 205.18 Gb and 200.62 Gb long reads of NDM8 and Pima[90] genomes, respectively, representing 180.38-fold coverage depth in total on the basis of single-molecule real-time (SMRT) sequencing (Supplementary Table 1)
We focused on all homologous genes between G. barbadense and G. hirsutum, and found thousands of genes diversified in Copia and/or Gypsy insertion, with 6,306 genes only in G. barbadense and 5,268 only in G. hirsutum
Summary
As a widely cultivated fiber crop, cotton produces natural fiber for the textile industry[1]. Thousands of improved cotton varieties have played pivotal roles in yield increases[2]. On this basis, breeders strive to create new varieties by synergistically increasing genetically complex yield and quality while obtaining resistance to numerous adversities, which is limited, by insufficient knowledge and understanding of the genomic basis of key agronomic traits[3]. High-quality genome assembly for modern G. hirsutum varieties, as well as for obsolete varieties TM-1 and ZM24 NDM8 is widely grown in Yellow River Valley cotton-producing areas of China, and Pima[90] has served as a genetic material in molecular breeding[11,12,13,14,15,16]. Analyzing the two genomes and resequences showed that large-scale genomic variations occurred during breeding, providing resources for cotton crop improvement
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