Reveal genomic insights into cotton domestication and improvement using gene level functional haplotype-based GWAS
Guoan Qi,
Yiqian Li,
Wanying Zhang,
Zegang Han,
Jinwen Chen,
Ziqian Zhang,
Lisha Xuan,
Rui Chen,
Lei Fang,
Yan Hu and
Tianzhen Zhang ()
Additional contact information
Guoan Qi: Zhejiang University
Yiqian Li: Zhejiang University
Wanying Zhang: Zhejiang University
Zegang Han: Zhejiang University
Jinwen Chen: Zhejiang University
Ziqian Zhang: Zhejiang University
Lisha Xuan: Zhejiang University
Rui Chen: Zhejiang University
Lei Fang: Zhejiang University
Yan Hu: Zhejiang University
Tianzhen Zhang: Zhejiang University
Nature Communications, 2025, vol. 16, issue 1, 1-14
Abstract:
Abstract Genome-wide association studies (GWAS) are widely used to detect associations between genetic variants and phenotypes. However, few studies have thoroughly analyzed genes, the fundamental and most crucial functional units. Here, we develop an innovative strategy to translate genomic variants into gene-level functional haplotypes (FHs), effectively reducing the interference from complex genome structure and linkage disequilibrium (LD) present in the conventional genetic mapping framework. Using refined mixed linear models, gene-level FH is regressed with 20 cotton agronomic traits across 245 sets of phenotypic values in 3,724 accessions, directly identifying 532 quantitative trait genes (QTGs) with significant breeding potential. The biological function of a superior fiber quality QTG encoding ferulic acid 5-hydroxylase 1 is experimentally validated. Thereafter, we systematically analyze the genetic basis of cotton domestication and improvement at the gene level. This report provides genomic insight into the genetic dissection and efficient mapping of functional genes in plants.
Date: 2025
References: Add references at CitEc
Citations:
Downloads: (external link)
https://www.nature.com/articles/s41467-025-59983-w Abstract (text/html)
Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.
Export reference: BibTeX
RIS (EndNote, ProCite, RefMan)
HTML/Text
Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59983-w
Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/
DOI: 10.1038/s41467-025-59983-w
Access Statistics for this article
Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie
More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().