Open Access Highly Accessed Research article

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

Juan Manuel Herrero-Medrano12*, Hendrik-Jan Megens2, Martien AM Groenen2, Guillermo Ramis1, Mirte Bosse2, Miguel Pérez-Enciso34 and Richard PMA Crooijmans2

Author Affiliations

1 Departamento de Producción Animal, Fac. de Veterinaria, Área de Genética, C.P.30100 Murcia, Spain

2 Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands

3 Centre for Research in Agricultural Genomics, Consortium CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autonoma Barcelona, 08193 Bellaterra, Spain

4 Institut Català de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain

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BMC Genetics 2013, 14:106  doi:10.1186/1471-2156-14-106

Published: 30 October 2013

Additional files

Additional file 1: Table S1:

Fst pairwise (below the diagonal) and Nei’s genetic distances (above the diagonal) between populations. Table S2: Average r2 value for SNP spaced 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0.

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Additional file 2:

Neighbor-Joining tree of pig populations constructed from individual pairwise genetic distance. WBPOR, wild boar from Portugal; WBSPN, wild boar from Spain; RE, Retinto Iberian; NI, Negro Iberian, IB, Iberian (unidentified variant); MJ, Manchado de Jabugo; BI, Bisaro; CM, Chato Murciano.

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Additional file 3:

PCA analysis using exclusively Iberian pigs. IB_Unk, Iberian unknown variant; NI, Negro Iberian; RE, Retinto; MJ, Manchado de Jabugo.

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Additional file 4:

STRUCTURE analysis and Evanno method to determine the optimal number of clusters; Membership coefficient of the breeds tested in the four clusters inferred by STRUCTURE software.

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Additional file 5:

Persistence of phase for intervals of 100 kb ranging from 0 to 10 Mb.

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Additional file 6:

Estimated effective population size (Ne) over time: detail of 10,000 generations ago. WB, wild boar; NI, Negro Iberian; RE, Retinto; MJ, Manchado de Jabugo; BI, Bisaro; CM, Chato Murciano.

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Additional file 7:

Estimation of the percentage covered by ROH in each population. WB, wild boar; IB, Iberian; MJ, Manchado de Jabugo; BI, Bisaro; CM, Chato Murciano.

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