Evidence map›Paper›PMID 41750284›Full record

ArticleBiomolecules2026

De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots.

Jiaolong Wen, Haiqi Qiu, Shaoxiong Deng, Shiyuan Wang, Yiyi Liu, Meng Lin, Jie Yang, Zhenfang Wu, Langqing Liu, Yibin Qiu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biomolecules, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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.

Jiaolong WenNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Haiqi QiuNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Shaoxiong DengNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Shiyuan WangNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Yiyi LiuNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Meng LinNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Jie YangNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.ORCID 0000-0002-7031-2160
Zhenfang WuNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Langqing LiuNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.
Yibin QiuNational Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China.ORCID 0009-0005-6982-5427

Funding

China Overseas Postdoctoral Recruitment Program NAKey Technologies R&D Program of Guangdong Province project 2022B0202090002Local Innovative and Research Teams Project of Guangdong Province 2019BTO2N630National Key Research and Development Program of China 2023YFD1300200National Major Agricultural Science and Technology Project NK20221101South China Agricultural University discipline construction and development project 2023B10564001/2023B10564003Young Scientists Fund of the National Natural Science Foundation of China 32502859
6 · The paper itself

Abstract

The Duroc × (Landrace × Yorkshire) (DLY) pig is a cornerstone of three-way crossbreeding system. Nevertheless, advances in commercial crossbred performance have been constrained by the dearth of high-resolution genomic resources for this key population. Here, we report the sequencing and assembly of 16 haplotype-resolved, chromosome-level genome assemblies derived from eight DLY pigs. These assemblies exhibited high continuity (contig N50: 18.17-29.54 Mb) and completeness (BUSCO: 99.3-99.4%), with sequences successfully localized to the 19 chromosomes. Genome annotation revealed an average of 21,922 protein-coding genes and 44.66% repetitive sequences per assembly. Comparative genomic analysis against the current reference genome Sscrofa11.1 enabled the construction of a non-redundant SV catalog comprising 130,416 variants, nearly half of which (48.99%) were novel relative to existing pig pan-genome SV panel. These SVs clustered non-randomly into 231 "SV hotspots" that were significantly enriched in protein-coding genes and putative regulatory elements. Functional analyses further linked these SV hotspots to quantitative trait loci (QTLs) associated with economically important traits. A focused analysis of a 3.43 Mb hotspot on chromosome 1, overlapping a known QTL for average daily gain, revealed eight high-frequency SVs in open chromatin regions near candidate genes (

Indexed as

GenomeAnimalsGenomicsHaplotypesMolecular Sequence AnnotationPolymorphism, Single NucleotideQuantitative Trait LociSwinecomparative analysisDuroc × (Landrace × Yorkshire) piggenome assemblyhaplotype-resolved

Identifiers

PMID41750284
PMCPMC12938368

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.