Whole-genome resequencing identifies adaptive variation associated with complex terrain in southwestern Chinese ducks.

Qinglian Li, Hehe Liu, Liang Li, Anqi Huang, Jiwei Hu, Lili Bai, Chunchun Han

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Article in Poultry science, 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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1 · What the graph read from it

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5 · Who and what money

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7 authors.

Qinglian LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.

Hehe LiuState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan Province, 625000, China.

Liang LiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.

Anqi HuangCollege of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan Province, 625000, China.

Jiwei HuState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.

Lili BaiState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.

Chunchun HanState Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China. Electronic address: 13839@sicau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The complex and diverse ecological environment of southwestern China has exerted significant influences on the domestication and genetic adaptation of local duck breeds. Although ducks exhibit extensive genetic variation in heterogeneous environments, the genomic mechanisms underlying their adaptation to the complex topography and high-altitude conditions of southwestern China remain unclear. To elucidate the evolutionary processes of genetic differentiation and environmental adaptation in regional duck populations, this study analyzed the genetic diversity, population structure, and selection characteristics based on the whole-genome resequencing data from a total of 500 individuals, encompassing 7 local duck breeds from the southwest region, 2 wild duck breeds, and 6 duck breeds from other regional. Analysis of nucleotide diversity (π) revealed that 2 wild duck breeds exhibited the highest genetic diversity (π = 0.0047-0.0052), Jianchang duck (JC) has the lowest (π = 0.0026). Among domestic breeds, those from plains areas-Sichuan Shelduck (SC), Hanzhong duck (HZ), Kaijiang duck (KJ), and Jianshui yellow-brown duck (JS) (π = 0.00360-0.00377)-showed significantly higher genetic diversity than those from topographically complex regions-Yunnan Sheldrake (YN), Sansui duck (SS), and Jianchang duck (π = 0.00259-0.00311). Populations from complex terrain (JC, YN, and SS) also displayed a high abundance of long runs of homozygosity (ROH). Analysis of the fixation index (Fst) demonstrated low genetic differentiation among YN, SS, and JC, as well as among SC, HZ, and KJ. Genomic scans comparing zFst and the log2(π ratio) identified regions in the top 5% as candidate regions, revealing 20 domestication-related genes, which are functionally associated with nervous system remodeling, angiogenesis, cell adhesion, mitochondrial metabolism, growth and reproduction; 15 regional adaptation-related genes, primarily involved in cell signal transduction, protein synthesis, hormone production, gene expression and DNA damage repair; and 15 candidate genes related to adaptation to the complex high-altitude terrain, participating in nervous system development, immune adaptation, synaptic transmission, sensory systems, cytoskeletal remodeling, and endocrine functions. Collectively, these findings enhance our understanding of evolutionary processes in southwestern Chinese ducks and provide actionable insights for their conservation and breeding programs.

Indexed as

Adaptation, PhysiologicalDucksGenetic VariationAnimalsChinaGenomeWhole Genome SequencingDuckGenomic diversityPopulation genetic structureSouthwest regionWhole-genome resequencing

Identifiers

PMID41980554

DOI10.1016/j.psj.2026.106908

PMCPMC13092077

What Socratic holds

Textmetadata

LicenceCC BY-NC-ND

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.