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

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.

Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

“…In spite of the small population size, the nucleotide diversity (π = 1.6 × 10 − 3 ) is higher in OB than many taurine cattle breeds with considerably more breeding animals including Holstein, Jersey and Fleckvieh (∼1.2-1.4 × 10 − 3 ) [43,44]. However, nucleotide diversity is lower in OB than African indigenous cattle breeds (2.0-4.0 × 10 − 3 ), New Danish Red (1.7 × 10 − 3 ) and Yakutian cattle breeds (1.7 × 10 − 3 ) [44][45][46]. The average F ROH estimated from WGS data was 0.14 in OB.…”

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

“…The Finnish reference reindeer was found to belong to the cluster of northern Fennoscandian reindeer distinct from the "eastern" and North American genetic cluster. It is recommended that phylogenetically different animal populations have their own reference assemblies 23 . With our GO family-based comparisons with nine other mammalian genomes, we identified hundreds of genes and gene families that are unique, under positive selection and rapidly expanding in reindeer.…”

“…The genetic basis of specific R. tarandus characteristics, such as adaptation to marked annual regulation in daylight, exceptional vitamin D metabolism and behavioural traits, was identified. In the present study, we provide an alternative draft reference genome for reindeer studies and particularly those representing arctic and sub-arctic regions which show phylogenetic distinctiveness compared to existing reference assemblies [21][22][23] . Here, we deep-sequenced and de novo assembled the genome of a male reindeer originating from Sodankylä, northern Finland by using the Illumina HiSeq platform.…”

Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

“…Наибольший сигнал был выявлен в районах генов, белки которых контролируют энергетический метаболизм (COX7C), пентозофосфатный путь окисления глюкозы (FBP1 и FBP2), васкулогенез (RASA1), ионный транспорт (CACNG3 и PRKCB), работу рецепто ра тиреоидного гормона (TRIP11) и тепловой шок (HSBP1). C помощью полногеномного секвенирования были идентифицированы потенциальные гены холодовой адаптации у представителей западного (CD14, COBL, JMJD1C, KCNMA1, PLA2G4, SERPINF2, SRA1, TAF7) и восточного (DNAJC28, HSP90B1, AGTRAP, TAF7, TRIP13, NPPA, NPPB) финского скота, традиционно разводимого в Фенноскандии (Weldenegodguad et al, 2019). Ранее было показано, что некоторые из этих генов, вовлеченные в энергетический метаболизм, сокращение гладкой мускулатуры, температурную рецепцию и другие физиологические реакции, могли участвовать в адаптации к холоду у коренных народностей Сибири (Cardona et al, 2014).…”