Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia

Abstract

Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, while Yakut cattle separated from European taurines ∼5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene, represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.

Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators

“…It is found in many mammals such as rodents, bears, hedgehogs, bats, marsupials ( Heldmaier et al, 2004 ; Geiser et al, 2014 ) and even primates ( Dausmann et al, 2004 ; Blanco et al, 2021 ). Other strategies used by endothermic mammals for coping with low temperature include increased heat production via shivering and non-shivering thermogenesis, reduction of heat loss from the body surface with the help of fur ( Hart, 1956 ) and/or subcutaneous adipose tissue ( Tattersall et al, 2012 ), or modifications of the blood system such as sequence changes of haemoglobin genes ( Campbell et al, 2010 ), counter-current heat exchange ( Ninomiya et al, 2011 ) or the heart’s pumping ability mediated by a missense mutation in the NRAP gene ( Buggiotti et al, 2021 ). Mitogenome adaptations include polymorphisms in mitochondrial genes encoding subunits of the respiratory chain ( Balloux et al, 2009 ; Awadi et al, 2021 ) and stem-loop formation(s) in the major NCR ( Melo-Ferreira et al, 2014 ).…”

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

“…An F ST statistic approach applied to cattle breeds reared in different environments identified several genes under positive selection for thermal tolerance [157]. HapFLK detected the Nebulin Related Anchoring Protein gene (NRAP) to be under selection for adaptation to cold environments [158], ACSS2, ALDOC, EPAS1, EGLN1 and NUCB2 to be under selection for high-altitude adaptation in cattle [159], and DNAJC28, GNRH1 and MREG to be associated with heat stress adaptation in sheep [160].…”

Population genomics reveals that natural variation in <i>PRDM16</i> contributes to cold tolerance in domestic cattle

“…Interestingly, the habitats of these cattle and the average annual temperature in which they were domesticated vary widely. Several recent studies have investigated cold adaptation mechanisms in cattle at the genomic level, providing valuable resources for future research ( Buggiotti et al, 2021 ; Ghoreishifar et al, 2020 ; Hu et al, 2021 ; Igoshin et al, 2021 ); however, most reported candidate genes/variations lack validation. Here, to detect the molecular footprints underlying cold adaptations in domestic cattle, we sequenced the genomes of 28 cattle, including 14 cold-tolerant cattle lineages (annual average temperature of habitat: 2–6 ℃) and 14 cold-intolerant cattle lineages (annual average temperature of habitat: 20–25 ℃).…”