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Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.

Abstract：

:Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Muñoz M,Bozzi R,García-Casco J,Núñez Y,Ribani A,Franci O,García F,Škrlep M,Schiavo G,Bovo S,Utzeri VJ,Charneca R,Martins JM,Quintanilla R,Tibau J,Margeta V,Djurkin-Kušec I,Mercat MJ,Riquet J,Estellé J,Zimmer C,R

doi

10.1038/s41598-019-49830-6

subject

Has Abstract

pub_date

2019-09-19 00:00:00

pages

13546

issue

issn

2045-2322

pii

10.1038/s41598-019-49830-6

journal_volume

pub_type

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Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.