Evidence map›Paper›PMID 37041265›Full record

ArticleTropical animal health and production2023

Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing.

Rafael Suárez-Mesa, Roger Ros-Freixedes, Houda Laghouaouta, Ramona N Pena, Byron Hernández-Ortiz, Iang Rondón-Barragán, Joan Estany

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Tropical animal health and production, 2023. 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, top 88% of its field
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, 0 citations in OpenAlex.

  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

7 authors at 2 institutions in 2 countries.

Rafael Suárez-MesaDepartment of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain. rafael.suarez@udl.cat.ORCID http://orcid.org/0000-0003-1092-164X
Roger Ros-FreixedesDepartment of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.ORCID http://orcid.org/0000-0002-3745-6736
Houda LaghouaoutaDepartment of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.ORCID http://orcid.org/0000-0002-8578-120X
Ramona N PenaDepartment of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.ORCID http://orcid.org/0000-0002-3558-7302
Byron Hernández-OrtizResearch and Innovation Group in Animal Health and Welfare Germplasm Animal Bank, Agrosavia, Bogotá, 250047, Colombia.ORCID http://orcid.org/0000-0002-2390-4323
Iang Rondón-BarragánResearch Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.ORCID http://orcid.org/0000-0001-6980-892X
Joan EstanyDepartment of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain. joan.estany@udl.cat.ORCID http://orcid.org/0000-0002-5660-5709
Universitat de Lleida · ESUniversity of Tolima · CO

Funding

Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS) 755Ministerio de Ciencia e Innovación PID2021-125689OB-I00Ministerio de Ciencia e Innovación RTI2018-101346-B-I00Universitat de Lleida 401
6 · The paper itself

Abstract

Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.

Indexed as

AcclimatizationGenomeAnimalsColombiaGenomicsPhenotypeSwineAnimal genetic resourcesConservationCreole pigsGenetic variabilityLEPRWhole-genome sequencing

Identifiers

PMID37041265
PMCPMC10089996
OpenAlexW4364377073

What OpenQuestion holds

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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 OpenQuestion graph.