Evidence map›Paper›PMID 39962408›Full record

ArticleBMC genomics2025

Genomic consequences of intensive inbreeding in miniature inbred pigs.

Hong-Man Chen, Heng Zhao, Qun-Yao Zhu, Chen Yan, Ya-Qi Liu, Si Si, Muhammad Ameen Jamal, Kai-Xiang Xu, De-Ling Jiao, Min-Juan Lv and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Gene therapy: The current trajectory of clinical and commercial translation.Progress in biophysics and molecular biology · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Hong-Man Chen *Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Heng Zhao *Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Qun-Yao ZhuYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Chen YanKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Ya-Qi LiuShaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Si SiKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Muhammad Ameen JamalYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Kai-Xiang XuYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
De-Ling JiaoYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Min-Juan LvYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Wen WangShaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
Hong-Ye ZhaoYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
Lei ChenShaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China. chen_lei@nwpu.edu.cn.
Ming-Shan WangKey Laboratory of Genetic Evolution & Animal Models, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. wangmingshan@mail.kiz.ac.cn.
Hong-Jiang WeiYunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China. hongjiangwei@126.com.

Funding

Major Science and Technology Projects in Yunnan Province 202102AA100054National Key Research and Development Program of China 2022YFF1000100Yunnan Fundamental Research Projects 202301AW070012Yunnan Province 202305AH340006
6 · The paper itself

Abstract

backgroundInbreeding, a central theme in evolutionary and conservation biology, is a crucial practice in breeding to stabilize and enhance the specific traits or to establish inbred lines. It also carries the risk of inbreeding depression, reduced fitness, and increased potential for extinction. Nevertheless, inbreeding has been extensively studied in small and endangered populations but its effects in large domesticated animals are poorly understood. Here, we aim to investigate the genomic consequences of inbreeding in the Banna miniature inbred pig (BN), a breed that has been inbred for over 40 years.

resultsWe have sequenced 41 genomes of BN and Diannan miniature pig (DN) at high-coverage (> 31×) and combined them with published whole-genomes of swine to comprehensively investigate the genetic consequences of inbreeding. We find that BN is genetically closely related to DN, which is consistent with breeding records. All families of BN have undergone an extreme bottleneck due to intensive inbreeding, resulting in higher genomic inbreeding coefficients, reduced genetic diversity, and a lower effective population size (Ne) compare to non-inbred pigs. Furthermore, BN and DN exhibit an increased genetic load relative to Asian wild boars. Prolonged inbreeding and bottlenecks have led to some purging of deleterious mutations in BN compared to DN, and a conversion from masked load to realized load.

conclusionsWe present a comprehensive analysis to understand and assess the consequences of inbreeding in miniature inbred pigs from a perspective of population genomics. Utilizing genomic measurements proves effective in estimating the consequences of inbreeding, especially when a detailed and accurate historical record of pedigree are lacking. Our results provide valuable resources and a detailed perspective on the genomic impacts of inbreeding, potentially guiding efforts in breeding, breed improvement, and conservation.

Indexed as

GenomeGenomicsInbreedingSwine, MiniatureAnimalsGenetic VariationSwineGenetic loadInbreedingMiniature inbred pigsRuns of homozygosity

Identifiers

PMID39962408
PMCPMC11834389

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

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 OpenQuestion graph.