Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia.
Laura Buggiotti,Andrey A. Yurchenko,N. S. Yudin,Christy J. Vander Jagt,N.V. Vorobieva,Mariya A. Kusliy,Sergei K. Vasiliev,Andrey N. Rodionov,Oksana I. Boronetskaya,Natalia A Zinovieva,Alexander S. Graphodatsky,Hans D. Daetwyler,Denis M. Larkin,Denis M. Larkin +13 more
TL;DR: In this article, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated, highlighting Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 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.
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Abstract: Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the 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, whereas Yakut cattle separated from European taurines approximately 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.
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The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock.
Matilde Maria Passamonti,Elisa Somenzi,Mario Barbato,Giovanni Chillemi,Licia Colli,Stéphane Joost,Marco Milanesi,Riccardo Negrini,Monia Santini,Elia Vajana,John L. Williams,Paolo Ajmone-Marsan +11 more
Abstract: Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations
TL;DR: In this paper, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, the authors report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations.
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Population genomics reveals that natural variation in PRDM16 contributes to cold tolerance in domestic cattle
Chunlong Yan,Jun Lin,Yuan-Fei Huang,Qing-Shan Gao,Zhengyu Piao,Shouli Yuan,Li Chen,Xue Ren,Rongcai Ye,Meng Dong,Hanlin Zhang,Huiqiao Zhou,Xiaoxiao Jiang,Wangjie Jin,Xuming Zhou,Chang-Guo Yan +15 more
TL;DR: Functional analysis identified a substitution of PRDM16 (p.P779L) in northern cattle, which maintains brown adipocyte formation by boosting thermogenesis-related gene expression, indicating a vital role of this gene in cold tolerance.
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GADMA2: more efficient and flexible demographic inference from genetic data
Ekaterina Noskova,Nikita Abramov,Stanislav Iliutkin,Anton V. Sidorin,Pavel Dobrynin,Vladimir Ulyantsev +5 more
TL;DR: GADMA2 is a software tool for efficient and flexible demographic inference from genetic data. It offers a common interface for several likelihood engines, global parameters optimization based on a genetic algorithm, and flexible model construction.
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References
Adaptation to hot climate and strategies to alleviate heat stress in livestock production.
TL;DR: The objective of this paper was to review the effective strategies to alleviate heat stress in the context of tropical livestock production systems and those involving genetic selection for heat tolerance.
909
RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference.
TL;DR: RFMix, a powerful discriminative modeling approach that is faster and more accurate than existing methods and capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors, is presented.
890
Robust and scalable inference of population history from hundreds of unphased whole genomes
TL;DR: SMC++ is presented, a new statistical tool capable of analyzing orders of magnitude more samples than existing methods while requiring only unphased genomes and employing a novel spline regularization scheme that greatly reduces estimation error.
860
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
Hans D. Daetwyler,Aurélien Capitan,Hubert Pausch,Paul Stothard,Rianne van Binsbergen,R.F. Brøndum,Xiaoping Liao,Anis Djari,Sabrina Rodriguez,Cécile Grohs,Diane Esquerre,Olivier Bouchez,Marie-Noelle Rossignol,Christophe Klopp,Dominique Rocha,Sébastien Fritz,André Eggen,Phil J. Bowman,David Coote,Amanda J. Chamberlain,Charlotte Anderson,Curt P VanTassell,Ina Hulsegge,Michael E. Goddard,Bernt Guldbrandtsen,M.S. Lund,Roel F. Veerkamp,Didier Boichard,Ruedi Fries,Ben J. Hayes +29 more
TL;DR: The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls.
844
Evidence for two independent domestications of cattle
TL;DR: Application of a molecular clock suggests that the two major mtDNA clades diverged at least 200,000, and possibly as much as 1 million, years ago, as evidence for two separate domestication events of different subspecies of the aurochs, Bos primigenius and Bos taurus.
819
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