High‐resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets

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 × 104 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.

Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement

“…The modern upland cotton cohort in China consists of accessions of high genetic, phenotypic and geographical diversities [ 38 , 39 , 40 , 41 ]. Previous genetic research revealed that large inversions caused the geographical divergence of cultivated cotton accessions [ 5 , 6 , 8 , 42 , 43 ]. We inferred that functional genomic sites may also have geographical bias and result in phenotypic divergence among cultivars from different regions.…”

Worldwide cotton production and trade during COVID-19 pandemic: An empirical analysis for a three-year observation

“…Allotetraploid G. hirsutum L., also known as upland cotton, is the most widely cultivated species and emerged in the U.S. 1-1.5 million years ago as a result of hybridization of G. herbaceum or G. arboretum genome with the G. raimondii genome. Due to its high adaptability and yields, it is grown in 95% of the world's cotton fields today (Ali et al, 2020;Xun et al, 2021;Jan et al, 2022;Tokel et al, 2022a;Chen et al, 2023;Wang et al, 2023).…”