High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement

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.

Subgenome Bias and Temporal Postponement of Gene Expression Contributes to the Distinctions of Fiber Quality in Gossypium Species

“…RNA-based gene expression assays comparing tetraploid domesticated species and wild species have revealed artificial domestication caused more fiber development-related genes to be expressed and involved in various basic metabolism pathways such as fatty acid, amino acid, and organic acid metabolism ( Yoo et al, 2013 ; Nomaguchi et al, 2018 ). In addition, complete whole-genome sequencing and assembly of several allotetraploid cotton species has provided key references for functional genomics research ( Li et al, 2015 ; Zhang et al, 2015 ; Hu et al, 2019 ; Wang et al, 2019 ; Ma et al, 2021 ). Using these and other data, differences in gene expression and regulation networks can be identified, which is necessary to elucidate the global genetic and molecular bases of interspecies differences in fiber quality.…”

Identification of the CesA Subfamily and Functional Analysis of GhMCesA35 in Gossypium hirsutum L.

“…Five allopolyploid cotton species have been sequenced and assembled in recent years, including economically significant upland cotton [30,46]. Therefore, we used the genome of upland cotton from previous studies and identified 38 CesA genes in upland cotton.…”

A Calmodulin-Like Gene (GbCML7) for Fiber Strength and Yield Improvement Identified by Resequencing Core Accessions of a Pedigree in Gossypium barbadense

“…In 2015, the first sea island cotton genome (lines 3-79) was sequenced successfully, opening a new chapter of sea island cotton genomic analyses (Yuan et al, 2015). Since that time, 3-79 was the subject of additional sequencing and/or genome updates (Wang et al, 2018;Chen et al, 2020), while genomes for additional sea island cotton accessions, i.e., Hai7124 (Hu et al, 2019) and Pima90 (Ma et al, 2021), were generated. In addition, resequencing of multiple accessions has provided insight into the diversity and domestication of this species (Fang et al, 2017a(Fang et al, , 2021Yuan et al, 2021), laying the foundation for precise genetic mapping of agronomic traits.…”