Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions.

Melak Weldenegodguad,Innokentyi Ammosov,Kisun Pokharel,Ruslan Popov,Yao Ming,Juha Kantanen,Zoya Ivanova

doi:10.3389/fgene.2018.00728

Abstract

Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.

Highlights

During their 8,000–10,000 years of domestication, taurine cattle (Bos taurus) have adapted to a wide variety of biogeographic zones and sociocultural environments as a result of natural and human-derived selection (Felius, 1995)
Cattle breeds such as Eastern Finncattle, Icelandic cattle, Swedish Mountain cattle, Yakutian cattle and other northern native cattle breeds are assumed to have their origins in the near-eastern domesticated taurine cattle that once spread to these northern regions (Kantanen et al, 2000, 2009a; Li et al, 2007)
The sequencing depth attained in this study was not ideal for pairwise sequentially Markovian coalescent (PSMC) analysis, our observations regarding the temporal changes in the effective population size (Ne) of the aurochs during the Pleistocene period (Mei et al, 2018) followed the pattern observed for ancestral populations of several other domestic mammalian species, such as pig [Sus scrofa; (Groenen et al, 2012)], horse [Equus caballus; (Librado et al, 2016)], and sheep [Ovis aries; (Yang et al, 2016)]

Summary

Introduction

During their 8,000–10,000 years of domestication, taurine cattle (Bos taurus) have adapted to a wide variety of biogeographic zones and sociocultural environments as a result of natural and human-derived selection (Felius, 1995). In prehistoric and historic times, animal husbandry faced several challenges in these northern climatic conditions, such as short summers and limited vegetation resources for feeding during the long winters, and this practice required well-adapted animals that were suited to the available environmental resources and socioeconomic and cultural conditions (Kantanen et al, 2009a; Bläuer and Kantanen, 2013; Egorov et al, 2015) Cattle breeds such as Eastern Finncattle, Icelandic cattle, Swedish Mountain cattle, Yakutian cattle and other northern native cattle breeds are assumed to have their origins in the near-eastern domesticated taurine cattle that once spread to these northern regions (Kantanen et al, 2000, 2009a; Li et al, 2007). Breeds such as Yakutian cattle exhibit adaptation in demanding environments and may be extremely useful for enabling animal production in marginal regions (Kantanen et al, 2015)

Methods

Results

Discussion

Conclusion