Genome-wide Diversity, Linkage Disequilibrium, and Admixture in the Main Colombian Creole Pig Breeds

Overview

Journal Trop Anim Health Prod

Publisher Springer

Specialties Tropical Medicine
Veterinary Medicine

Date 2024 Oct 9

PMID 39384642

Authors

Ricardo Jose Ocampo-Gallego

Yolanda Gomez Vargas

Juan Carlos Rincon Florez

Affiliations

Soon will be listed here.

Abstract

Colombian Creole pigs have adapted to tropical conditions for over 500 years. They have been modified by natural and artificial selection in different regions. At present, the diversity and current introgression status are unknown. The objective was to estimate the genomic diversity, linkage disequilibrium, population structure, and admixture of four Colombian pig breeds and their relationship with other breeds worldwide. Three Colombian pig breeds (SPE-San Pedreño, 11 samples; ZUN-Zungo, 11 samples; CM-Casco de Mula, ten samples) from the conservation nucleus and one biotype not recognized as a breed (CCH-Criollo Chocoano, seven samples) were genotyped using the Illumina GGP-Porcine80K chip. Open-access data from seven international breeds were also included. Colombian Creole pigs showed moderate genetic differentiation (F 0.14) globally, but several groups of animals separated, suggesting local clustering due to geographical isolation or different founding effects. Colombian Creole pigs showed breed imprinting and specific grouping in all analyses except for CCH, which, like the Ecuadorian Creole, was a cluster of admixtures. The Colombian Creole pigs revealed a significant relationship with the Iberian pig and some other breeds to varying degrees. However, good maintenance of the conservation nucleus was evidenced. Potential adaptive genes, mainly related to immunological functions, were found, according to F and pcadapt analyses. This study provides a foundation and scientific data for policy decisions on zoogenetic resources.

References

Huang M, Zhang H, Wu Z, Wang X, Li D, Liu S . Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs. Animal. 2021; 15(10):100354. DOI: 10.1016/j.animal.2021.100354. View

Herrero-Medrano J, Megens H, Groenen M, Bosse M, Perez-Enciso M, Crooijmans R . Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds. BMC Genomics. 2014; 15:601. PMC: 4117957. DOI: 10.1186/1471-2164-15-601. View

Ferencakovic M, Solkner J, Curik I . Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genet Sel Evol. 2013; 45:42. PMC: 4176748. DOI: 10.1186/1297-9686-45-42. View

Munoz M, Bozzi R, Garcia-Casco J, Nunez Y, Ribani A, Franci O . Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Sci Rep. 2019; 9(1):13546. PMC: 6753209. DOI: 10.1038/s41598-019-49830-6. View

Cross A, Keel B, Brown-Brandl T, Cassady J, Rohrer G . Genome-wide association of changes in swine feeding behaviour due to heat stress. Genet Sel Evol. 2018; 50(1):11. PMC: 5866911. DOI: 10.1186/s12711-018-0382-1. View

Pickrell J, Pritchard J . Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8(11):e1002967. PMC: 3499260. DOI: 10.1371/journal.pgen.1002967. View

Bjelland D, Weigel K, Vukasinovic N, Nkrumah J . Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci. 2013; 96(7):4697-706. DOI: 10.3168/jds.2012-6435. View

Corbin L, Liu A, Bishop S, Woolliams J . Estimation of historical effective population size using linkage disequilibria with marker data. J Anim Breed Genet. 2012; 129(4):257-70. DOI: 10.1111/j.1439-0388.2012.01003.x. View

Di Gregorio P, Perna A, Di Trana A, Rando A . Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed. Genes (Basel). 2023; 14(7). PMC: 10378754. DOI: 10.3390/genes14071503. View

10.

Fang Y, Hao X, Xu Z, Sun H, Zhao Q, Cao R . Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data. Front Genet. 2021; 12:629966. PMC: 8116706. DOI: 10.3389/fgene.2021.629966. View

11.

Larson G, Liu R, Zhao X, Yuan J, Fuller D, Barton L . Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci U S A. 2010; 107(17):7686-91. PMC: 2867865. DOI: 10.1073/pnas.0912264107. View

12.

Keller M, Visscher P, Goddard M . Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics. 2011; 189(1):237-49. PMC: 3176119. DOI: 10.1534/genetics.111.130922. View

13.

Wang Z, Sun H, Chen Q, Zhang X, Wang Q, Pan Y . A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing. Animal. 2018; 13(4):683-693. DOI: 10.1017/S1751731118001714. View

14.

Sherman B, Hao M, Qiu J, Jiao X, Baseler M, Lane H . DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 2022; 50(W1):W216-W221. PMC: 9252805. DOI: 10.1093/nar/gkac194. View

15.

Revidatti M, Gama L, Martin Burriel I, Cortes Gardyn O, Cappello Villada J, Carolino M . On the origins of American Criollo pigs: A common genetic background with a lasting Iberian signature. PLoS One. 2021; 16(5):e0251879. PMC: 8136715. DOI: 10.1371/journal.pone.0251879. View

16.

Ocampo Gallego R, Florez J, Bejarano Garavito D . Genomic characterization of the nucleus for conservation of the Chino Santandereano breed using SNP markers. Trop Anim Health Prod. 2021; 53(5):492. DOI: 10.1007/s11250-021-02936-4. View

17.

Burgos-Paz W, Souza C, Megens H, Ramayo-Caldas Y, Melo M, Lemus-Flores C . Porcine colonization of the Americas: a 60k SNP story. Heredity (Edinb). 2012; 110(4):321-30. PMC: 3607178. DOI: 10.1038/hdy.2012.109. View

18.

Schiavo G, Bovo S, Bertolini F, Tinarelli S, DallOlio S, Nanni Costa L . Comparative evaluation of genomic inbreeding parameters in seven commercial and autochthonous pig breeds. Animal. 2020; 14(5):910-920. DOI: 10.1017/S175173111900332X. View

19.

Steinig E, Neuditschko M, Khatkar M, Raadsma H, Zenger K . netview p: a network visualization tool to unravel complex population structure using genome-wide SNPs. Mol Ecol Resour. 2015; 16(1):216-27. DOI: 10.1111/1755-0998.12442. View

20.

Chang C, Chow C, Tellier L, Vattikuti S, Purcell S, Lee J . Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015; 4:7. PMC: 4342193. DOI: 10.1186/s13742-015-0047-8. View