Evidence map›Paper›PMID 41299239›Full record

ArticleBMC genomics2025

Genome-wide adaptive selection and functional annotation of regulatory variation in the Yangxin pig.

Sha Liu, Qiong Chen, Huanhuan Zhou, Caichun Yang, Liangyu Shi, Hongbo Chen

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Article in BMC genomics, 2025. 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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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Sha Liu *Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.
Qiong Chen *Huangmei Qiangli Livestock Co., Ltd, Huanggang, Huangmei, 435500, China.
Huanhuan ZhouLaboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.
Caichun YangHuangmei Qiangli Livestock Co., Ltd, Huanggang, Huangmei, 435500, China.
Liangyu ShiLaboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China. liangyu_shi@whpu.edu.cn.
Hongbo ChenLaboratory of Genetic Breeding, Reproduction and Precision Livestock Farming & Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China. chenhongbo@whpu.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundLocal adaptation drives complex traits in domestic animals, but the roles of positive and balancing selection in Chinese indigenous pig breeds remain unclear. We performed whole-genome resequencing of 79 Yangxin pigs and applied positive and balance selection, integrated findings with PigQTLdb and FarmGTEx.

resultsIn this study, we detected ~ 98 Mb of the genome under adaptive selection, mainly involving non-coding variants. Positive selection signals were concentrated in regulatory regions affected to muscle traits, whereas balancing selection was enriched at loci associated with reproduction. The strongest overlap with regulatory elements was observed in muscle tissue. Additionally, significant enrichment of the Hippo signaling pathway was detected in testis. DNA-level annotation revealed reproductive QTL to be most overrepresented in balancing-selection regions. Notable candidate genes and pathways include VGLL3 and Hippo signaling, and oxytocin, circadian entrainment, vascular smooth muscle contraction, and adrenergic signaling.

conclusionThese results underscore a regulatory basis for muscle phenotype variation, and the role of balancing selection in preserving fertility-related diversity. Our findings provide genomic markers for breeding and conservation strategies aimed at enhancing productivity in the Yangxin pig.

Indexed as

Molecular Sequence AnnotationSelection, GeneticAnimalsGenomeMalePolymorphism, Single NucleotideQuantitative Trait LociSwineWhole Genome SequencingAdaptative selectionMuscle traitNon-coding variantsReproductive QTLSelective signaturesYangxin pig

Identifiers

PMID41299239
PMCPMC12751906

What Socratic holds

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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.