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Yudin NS, Yurchenko AA, Larkin DM. [Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:190-201. [PMID: 34901717 PMCID: PMC8627871 DOI: 10.18699/vj21.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Yurchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia The Royal Veterinary College, University of London, London, United Kingdom
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Igoshin A, Yudin N, Aitnazarov R, Yurchenko AA, Larkin DM. Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations. Life (Basel) 2021; 11:959. [PMID: 34575108 PMCID: PMC8467296 DOI: 10.3390/life11090959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/30/2022] Open
Abstract
Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, 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, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.
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Affiliation(s)
- Alexander Igoshin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Nikolay Yudin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ruslan Aitnazarov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Andrey A. Yurchenko
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Denis M. Larkin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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Liu YX, Ma XM, Xiong L, Wu XY, Liang CN, Bao PJ, Yu QL, Yan P. Effects of Intensive Fattening With Total Mixed Rations on Carcass Characteristics, Meat Quality, and Meat Chemical Composition of Yak and Mechanism Based on Serum and Transcriptomic Profiles. Front Vet Sci 2021; 7:599418. [PMID: 33553278 PMCID: PMC7859351 DOI: 10.3389/fvets.2020.599418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
The objective of this study was to investigate the effects of intensive fattening with total mixed rations (TMR) on carcass characteristics, meat quality, and chemical composition of the yak meat. Theoretical data has been provided for evaluating the quality of yak meat during natural grazing and short-term fattening. Based on the analysis, we found that in fattening yak, the carcass weight (CWT) was increased by 106.43%, whereas the cooking loss, tenderness, and drop loss were significantly improved due to higher intramuscular fat content and lower moisture (P < 0.05). Protein, fat, calcium, and amino acids were also much higher (P < 0.01) in fattening yak compared with the grazing yak. The levels of albumin (ALB), lactate dehydrogenase (LDH), triglyceride (TRIG), and amylase (AMYL) in serum indicated better nutritional status for fattening yaks. The transcriptomics analysis showed that the high expression of ACSL1 and ACACB genes improved the synthesis and deposition of fat in fattening yak, whereas the regulation of SLC7A8, ATP1A4, ATP1A1, SLC3A2, and CPA3 gene expression weakened the proteolysis. These results indicated that fattening with TMR improves the yield and quality of the yak meat.
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Affiliation(s)
- Yi-Xuan Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Xiao-Ming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Lin Xiong
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xiao-Yun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Chun-Nian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Peng-Jia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Qun-Li Yu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
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Zhang GW, Wang L, Huang D, Chen H, Li B, Wu Y, Zhang J, Jiang A, Zhang J, Zuo F. Inheritance patterns of leukocyte gene expression under heat stress in F 1 hybrid cattle and their parents. J Dairy Sci 2020; 103:10321-10331. [PMID: 32896393 DOI: 10.3168/jds.2020-18410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/15/2020] [Indexed: 11/19/2022]
Abstract
Crossbreeding capitalizes on heterosis effects and results in increased performance of crossbred animals. Dominance hypothesis and overdominance hypothesis are 2 common models proposed to explain heterosis. Differential gene expression between parents and hybrids is hypothesized to be responsible for heterosis. This study aimed to investigate the heat tolerance and inheritance patterns of leukocyte transcriptomics in F1 hybrid cattle (Angus males × Droughtmaster females) and their parents Red Angus (AN) and Droughtmaster (DR) under heat stress. According to the respiratory rate and heat tolerance coefficient index, DR was better adapted to heat stress than AN. The physiological responses to heat stress of F1 hybrids were similar to AN. We identified 802 differentially expressed genes in leukocytes between AN and DR under heat stress using mRNA sequencing. Compared with AN, upregulated genes in DR were enriched in biological processes of response to stress, external and chemical stimulus, and cytokine, cell surface receptor signaling pathway, and cardiovascular system development. In contrast, upregulated genes in AN were enriched in B cell activation and regulation of B cell activation. Gene expression levels can be inherited additively or nonadditively and are classified into additive (35%), dominance (44%), and overdominance and underdominance (18%) modes in F1 hybrids and their parents. Inheritance patterns of gene expression showed that 97% (249/255) of the dominant genes were classified as paternal AN dominant in hybrids. The paternal imprinted PEG10 gene and its regulatory transcription factor MYC showed an AN dominant expression pattern. The MYC interacted with most AN dominant genes. These transcriptomic analyses revealed that DR and AN had specific cellular and humoral immunity and cardiovascular systems development function under heat stress. Inheritance pattern analyses from gene expression partly explained phenotypic differences between parents and F1 hybrids. The paternal imprinted PEG10 gene interaction with transcription factor MYC may contribute to explaining paternal dominant gene expression in hybrids.
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Affiliation(s)
- Gong-Wei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460.
| | - Ling Wang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460
| | - Dejun Huang
- ChongQing Academy of Animal Sciences, Rongchang, Chongqing, China, 402460
| | - Huiyou Chen
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460
| | - Baisen Li
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460
| | - Yuhui Wu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460
| | - Jianmin Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460
| | - An Jiang
- ChongQing Academy of Animal Sciences, Rongchang, Chongqing, China, 402460
| | - Jian Zhang
- ChongQing Academy of Animal Sciences, Rongchang, Chongqing, China, 402460
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing, China, 402460; Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing, China, 402460.
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Yudin NS, Larkin DM. Whole genome studies of origin, selection and adaptation of the Russian cattle breeds. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.
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Affiliation(s)
| | - D. M. Larkin
- Royal Veterinary College, University of London; Institute of Cytology and Genetics, SB RAS
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Alshawi A, Essa A, Al-Bayatti S, Hanotte O. Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle. Front Genet 2019; 10:609. [PMID: 31379916 PMCID: PMC6646475 DOI: 10.3389/fgene.2019.00609] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 06/11/2019] [Indexed: 01/03/2023] Open
Abstract
The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently, four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq, while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at the genome level. Here, we report at a genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho), and admixture. Signatures of selection were studied using extended haplotype homozygosity (EHH) (iHS and Rsb) and inter-population Wright's Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine, and taurine indicate that the two breeds are crossbreed zebu × taurine, with more zebu background in Jenoubi cattle compared with Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signatures of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g., tick resistance and heat stress), and genes of commercial interest (e.g., marbling score).
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Affiliation(s)
- Akil Alshawi
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, Faculty of Medicine and Health Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Baghdad, Iraqi Ministry of Higher Education and Scientific Research, Baghdad, Iraq
| | - Abdulameer Essa
- Animal Genetics Resources Department, Directorate of Animal Resources, the Ministry of Iraqi Agriculture, Baghdad, Iraq
| | - Sahar Al-Bayatti
- Animal Genetics Resources Department, Directorate of Animal Resources, the Ministry of Iraqi Agriculture, Baghdad, Iraq
| | - Olivier Hanotte
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, Faculty of Medicine and Health Sciences, University Park Campus, University of Nottingham, Nottingham, United Kingdom.,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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