Evidence map›Paper›PMID 42458569›Full record

ArticleGenome biology2026

Multi-parent mapping reveals epistatic architecture and elite haplotypes for multi-trait improvement in cotton.

Peng Han, Chunyuan You, Xinyuan Chen, Yuanlong Wu, Ruipeng Wang, Lu Lu, Jianying Li, Zhongping Xu, Wenyu Gong, Xianlong Zhang and 3 more

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Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

13 authors.

Peng Han *College of Agriculture, Shihezi University, Shihezi, 832003, China.
Chunyuan You *Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
Xinyuan Chen *Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
Yuanlong WuCollege of Agriculture, Shihezi University, Shihezi, 832003, China.
Ruipeng WangHubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
Lu LuCollege of Agriculture, Shihezi University, Shihezi, 832003, China.
Jianying LiHubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
Zhongping XuHubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
Wenyu GongCollege of Agriculture, Shihezi University, Shihezi, 832003, China.
Xianlong ZhangCollege of Agriculture, Shihezi University, Shihezi, 832003, China.
Maojun WangCollege of Agriculture, Shihezi University, Shihezi, 832003, China. mjwang@mail.hzau.edu.cn.
Shuangxia JinCollege of Agriculture, Shihezi University, Shihezi, 832003, China. jsx@mail.hzau.edu.cn.
Xinhui NieCollege of Agriculture, Shihezi University, Shihezi, 832003, China. xjnxh2004130@126.com.

Funding

Development Fund for Xinjiang Talents XL XL202403-06Major Science and Technology Special Project of Xinjiang No. 2024A02002-2National Natural Science Foundation of China No.32001595National Natural Science Foundation of China NO.32260510Science and Technology Planning Project of Tumusuk City-Open Bidding for Selecting the Best Candidates KY2024JBGS09Special Fund of China Postdoctoral Science Foundation No.2022T150249
6 · The paper itself

Abstract

backgroundCotton domestication has fixed favorable alleles, often masking cryptic loci and reinforcing genetic trade-offs, particularly between yield and fiber quality, thereby constraining simultaneous trait improvement.

resultsWe develop an eight-parent MAGIC population comprising 319 recombinant inbred lines through a 12-year breeding program and integrate it with a panel of 318 Xinjiang cotton cultivars released between 1978 and 2024. High-resolution genomic analyses combining SNP-based and identity-by-descent mapping identify 111 sQTLs and 15 hQTLs associated with 19 agronomic traits across multiple environments. Genome-wide epistasis analysis further identifies over 3,000 cryptic loci, highlighting complex genetic interactions underlying trait variation. Parallel population genomic analyses of Xinjiang cultivars reveal 520 genomic regions consistently shaped by modern breeding selection. Integrating these datasets enabled the construction of a multi-trait optimization framework to prioritize elite genotypes with favorable allele combinations. We validate this framework using cultivars derived from MAGIC parental lines, including Zhuangjiahan902 and Huaxin103, demonstrating coordinated improvement in yield and fiber quality.

conclusionsThis study demonstrates the dual utility of MAGIC populations for high-resolution genetic dissection and breeding application. The integrative framework presented here provides a scalable strategy for resolving genetic trade-offs and achieving coordinated multi-trait improvement in cotton and other major crops.

Indexed as

Epistasis, GeneticGossypiumHaplotypesChromosome MappingCotton FiberGenome, PlantPhenotypePlant BreedingPolymorphism, Single NucleotideQuantitative Trait LociCottonGenomic breedingIdentity-by-descent mappingMAGIC populationYield-quality trade-offs

Identifiers

PMID42458569

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