Evidence map›Paper›PMID 40684225›Full record

ArticleJournal of animal science and biotechnology2025

Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.

Guangquan Lv, Peiyu Yang, Ao Guo, Minghao Cao, Dong Li, Zhe Liu, Mingyu Wang, Jingchun Sun, Rongrong Ding, Taiyong Yu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of animal science and biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
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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

10 authors.

Guangquan Lv *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Peiyu Yang *Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Ao GuoKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Minghao CaoKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Dong LiKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Zhe LiuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Mingyu WangKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Jingchun SunKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Rongrong DingKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China. dingrongrong92@nwafu.edu.cn.
Taiyong YuKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China. yutaiyong310@nwsuaf.edu.cn.

Funding

Key Technologies Research and Development Program 2021YFD1301200Key Technologies Research and Development Program 2021YFF1000602
6 · The paper itself

Abstract

backgroundTraditional genomic analysis relies on a single reference genome, which struggles to effectively characterize the genetic diversity among populations. This is due to the substantial genetic differences between the genome of the studied species and the reference genome, potentially introducing reference bias.

resultsIn this study, we focused on Guanzhong Black pigs (GZB), Danish Large White pigs (DLW), and their hybrid offspring, Qinchuan Black pigs (QCB). We provided two high-quality parental genomes at the chromosomal level and constructed a parental genomic reference panel to detect SNPs (single nucleotide polymorphisms), INDELs (insertions and deletions), and SVs (structural variations). Compared with the single-reference method, the integrated parental genomic strategy identified 5.48% more SNPs and 67.84% more INDELs. The uniformity of variant distribution and genome functional annotation remained consistent before and after integration, while the ratio of non-reference/non-reference genotypes was also improved. In population genetic structure analysis, principal component analysis (PCA) of the three variant types (SNPs, INDELs, and SVs) exhibited good clustering effects, and ADMIXTURE analysis demonstrated consistent stratification. Selection signal analysis based on the integrated parental genomic strategy successfully identified more differentiated windows and positively selected genes. By leveraging multiple variant types and employing two selection signal methods, we jointly identified several novel intramuscular fat candidate genes (MSMO1, SMC6, CCDC158, KIT, CCNC, etc.), which could not be identified by the single-reference method alone. Functional validation of the gene MSMO1 revealed its role in promoting intramuscular adipocyte proliferation and inhibiting adipogenic differentiation.

conclusionsThis study is the first to construct a parental genomic reference panel specifically for pig hybrid populations, which significantly reduces reference bias and exhibits superior performance in downstream analyses. This strategy offers new possibilities for genomic selection breeding of livestock and establishes a methodological foundation for precisely dissecting complex traits in hybrid populations.

Indexed as

GenotypingIntramuscular fatParental genomePig

Identifiers

PMID40684225
PMCPMC12276683

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

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 Socratic graph.