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

Rute R Da Fonseca,Lounès Chikhi,Irene Ureña,Catarina Ginja,Ana Elisabete Pires,Sandra Afonso,Emil Jørsboe

doi:10.1186/s12864-019-5685-2

Abstract

BackgroundIberian 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.ResultsWe 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.ConclusionsOur 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.

Highlights

Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space
The Food and Agriculture Organization (FAO) has warned that about 67% of the Iberian cattle breeds are at risk as many of these have less than 1000 breeding females and/or less than 20 breeding males [3], which reinforces the need for a continued conservation strategy
Sequencing error rates for all 48 samples are below 0.2% (Additional file 1: Figure S1)

Summary

Introduction

Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. The complex origin of the Iberian primitive breeds is reflected in their high diversity in Y-chromosome haplotypes, including the major taurine Y1 and Y2 haplogroups [14, 15] and unique patrilines [16], as well as distinct maternal lineages, i.e. common European T3-matrilines along with more distinct Qhaplotypes [15, 17], and a strong influence of T1-lineages of African origin [18] This higher diversity relative to their European counterparts is quite notable, given the geographic distance of this territory from the presumed Near-Eastern center of domestication [4, 14, 15, 19, 20]. This makes Iberian cattle a great example for investigating the genomic impact of the intricate processes of cattle diversification both regarding the last 200 years of specific breed formation and the putative earlier admixture events

Methods

Results

Discussion

Conclusion