Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

Salvatore Mastrangelo,Baldassare Portolano,Elena Ciani,Rosalia Di Gerlando,Fabio Pilla,Gabriele Senczuk,Marco Tolone,Oscar Cortés,Slim Ben Jemaa,Gianluca Sottile

doi:10.1038/s41598-020-71375-2

Abstract

The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were observed among domesticated bovid populations from different geographic areas, except for Bali cattle. Our findings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic differentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene flow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, reflecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived-breeds, in the past experienced a similar non-European influence, with African and indicine introgression.

Highlights

The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide
The merged dataset used in the analyses consisted of 3,283 individuals from 205 domesticated bovid populations (n = 1 B. javanicus, n = 27 B. t. indicus, n = 165 B. t. taurus, and n = 12 hybrids) (Table S1, Table 1, and Fig. 1) genotyped on 23,313 SNPs
Our results confirmed these findings, as we found that African populations showed mean from runs of homozygosity (FROH) values comparable with those of most European breeds

Summary

Introduction

The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide These comprehensive studies did not include some local European populations, including autochthonous Italian cattle. The availability of genotyping assays has made it possible to conduct a detailed evaluation of cattle genetic diversity globally[2,8,9,10,11,12,13] According to these studies, the European cattle gene pool is mainly of Bos taurus taurus origin. Iberian cattle were shown to have African taurine introgression[10,14], while the Italian Podolica breed is an ancient cross-breed in which indicine introgression has occurred[14] These comprehensive studies did not include several local European cattle characterized in recent investigations[7,15,16], including many Italian cattle b reeds[17]. We determined the population structure and genetic relationship of the new breeds with other populations from around the world

Objectives

Methods

Results

Conclusion