Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.

Andrey Yurchenko,Andrey Yurchenko,Andrey Yurchenko,Vladimir Brukhin,Denis M Larkin,Denis M Larkin,Denis M Larkin,Denis M Larkin,Nikolay Yudin,Bulat Lhasaranov,Ruslan Aitnazarov,Alexandra Plyusnina,Alexandra Plyusnina,Ivan A Paronyan,Vladimir Soloshenko,Ruslan Popov,Kirill V Plemyashov

doi:10.1038/s41437-017-0024-3

Abstract

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

Highlights

Thousands of years of artificial selection coupled with human-driven migration and adaptation to diverse environmental conditions resulted in ~1000 cattle breeds worldwide, which are tailored to local economic needs, aesthetic demands and possess unique genetic profiles (Mason 1969)
Single nucleotide polymorphism diversity (SNP), diversity, inbreeding, and linkage disequilibrium (LD) within the Russian breeds. Both the GGP HD150K and BovineSNP50K SNP arrays were found highly informative for the Russian cattle breeds (Supplementary Table 1)
The advent of cost-efficient genotyping SNP arrays has made it possible to reveal the genetic profiles of various breeds of domesticated species, develop informed strategies of their improvement on one hand, and learn about the genetic processes accompanying domestication and breed formation on the other

Summary

Introduction

Thousands of years of artificial selection coupled with human-driven migration and adaptation to diverse environmental conditions resulted in ~1000 cattle breeds worldwide, which are tailored to local economic needs, aesthetic demands and possess unique genetic profiles (Mason 1969). There is a tendency to replace or ‘improve’ local breeds with the genetic material from superior commercial ones, meaning that genetic diversity, signatures of adaptations to local conditions, and the history of formation encoded in native breed genomes often diminish before being recorded and properly studied (Gaouar et al 2015). The genetic diversity of domestic cattle stems from the two main sources of domestication of the ancient Bos subspecies: B. taurus and B. indicus originating from the Fertile Crescent and the Indus Valley, respectively, and adapted to distinct environments (Loftus et al 1994). Some extant breeds originate from old and/or recent interbreeding between the B. taurus and B. indicus resulting in a wide geoclimatic adaptation of the hybrids (Larkin and Yudin 2016)

Methods

Results

Conclusion