Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse periphe
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RESEARCH ARTICLE
Open Access
Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle Rute R. da Fonseca1,2* , Irene Ureña3, Sandra Afonso3, Ana Elisabete Pires3,4, Emil Jørsboe2, Lounès Chikhi5,6 and Catarina Ginja3*
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: Cattle genomes, Iberia, Native breeds, Genomic diversity, Animal breeding, Sex chromosome diversity, population structure, Genetic differentiation
Background The biological resources of the Mediterranean sub-region of the Palaearctic include a diversity of domesticated animals [1] comprising 53 officially recognized local breeds of taurine cattle (Bos taurus) in the Iberian Peninsula alone (Additional file 1: Table S1). Taurine cattle are thought to have been domesticated by Neolithic farmers * Correspondence: [email protected]; [email protected] 1 Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark 3 CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal Full list of author information is available at the end of the article
from Bos primigenius populations in the Fertile Crescent around 10,000 years [2], and have since diversified into more than 1000 breeds [3]. Cattle genomes have been shaped not only by human-d
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