ArticleNature communications2025
Reveal genomic insights into cotton domestication and improvement using gene level functional haplotype-based GWAS.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Feasibility and pitfalls of combining small subpopulations for genome-wide association analysis of maize (Zea mays L.) kernel traits.The plant genome · 2026Article
- Cotton Salt Stress Resilience: Integrating Physiological, Molecular, and Agronomic Strategies for Next-Generation Breeding.Plant, cell & environment · 2026Review
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- MianxinNo.1: a modern cultivar genome-informed SNP array based on cGPS technology for genomics-assisted breeding in cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Functional Characterization ofPlants (Basel, Switzerland) · 2026Article
- A fast method for breeding by design via G × E interactions detected in large-scale climatic, phenomic and genomic data.National science review · 2026Article
- Genome-wide association study reveals novel SNP loci and candidate genes linked to flowering time in upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
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Authors and funding
11 authors.
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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.
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