High‐resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets. (17th December 2022)

• Record Type: Journal Article
• Authors: Wang, Nian; Li, Yuanxue; Shen, Chao; Yang, Yang; Wang, Hongya; Yao, Tian; Zhang, Xianlong; Lindsey, Keith; Lin, Zhongxu
• Is Part Of: Plant journal. Volume 113:Number 1(2023)
• Page Start: 145
• Page End: 159
• Publication Date: 2022-12-17
• Subjects: upland cotton -- SV -- inversion -- haplotype -- adaptability -- genetic improvement; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.16041
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s–2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88–1.47 × 10 4 SVs per cultivar were identified, and an SV set was constructed. SVs affected the expression of a large number of genes during fiber elongation, and a transposable element insertion resulted in the glandless phenotype in upland cotton. Six widespread inversions were identified based on nine draft genomes and high‐throughput chromosome conformation capture data. Multiple haplotype blocks that were always associated with aggregated SVs were demonstrated to play a pivotal role in the agronomic traits of upland cotton and drove its adaptation to the northern planting region. Exotic introgression was the source of these haplotype blocks and increased the genetic diversity of upland cotton. Our results enrich the genome resources of upland cotton, and the identified SVs will promote genetic and breeding research in cotton. Significance Statement: The present study uncovered structural variants in upland cottons, many of which affected gene expression in cotton fibers. A transposable element insertion resulting in the glandless phenotype was identified. Inversions affecting population differentiation and adaptation in upland cotton were identified. Haplotype blocks generated from interspecies introgressions associated with upland cotton agronomic traits, providing new ideas for cotton breeding.