Format

Send to

Choose Destination
BMC Genomics. 2019 May 3;20(1):334. doi: 10.1186/s12864-019-5685-2.

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle.

Author information

1
Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. rfonseca@snm.ku.dk.
2
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark. rfonseca@snm.ku.dk.
3
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
4
LARC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisbon, Portugal.
5
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
6
Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062, Toulouse cedex 9, France.
7
Instituto Gulbenkian de Ciência, Rua da Quinta Grande n°6, P-2780-156, Oeiras, Portugal.
8
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal. catarinaginja@cibio.up.pt.

Abstract

BACKGROUND:

Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.

RESULTS:

We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow.

CONCLUSIONS:

Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.

KEYWORDS:

Animal breeding; Cattle genomes; Genetic differentiation; Genomic diversity; Iberia; Native breeds; Sex chromosome diversity; population structure

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center