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Liu D, Yang Y, Chen Z, Fan Y, Liu J, Xu Y, Ahmed Z, Zhang J, Li F, Qi X, Song W, Zhu K, Gongque J, Li G, Huang B, Lei C. Temperature adaptation patterns in Chinese cattle revealed by TRPM2 gene mutation analysis. Anim Biotechnol 2024; 35:2299944. [PMID: 38164963 DOI: 10.1080/10495398.2023.2299944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The TRPM2 gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the TRPM2 gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between TRPM2 genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.
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Affiliation(s)
- Dekai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Yifan Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Zhefu Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Yijie Fan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Yibing Xu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Fuqiang Li
- Hunan Tianhua Industrial Corporation Ltd, Lianyuan, China
| | - Xingshan Qi
- Biyang Xianan Cattle Technology and Development Company Ltd, Biyang, China
| | - Weiru Song
- Animal Disease Prevention and Control Center of Yushu Tibetan Autonomous Prefecture, Yushu, China
| | - Kaixia Zhu
- Animal Disease Prevention and Control Center of Yushu Tibetan Autonomous Prefecture, Yushu, China
| | - Jiangcai Gongque
- Animal Disease Prevention and Control Center of Yushu Tibetan Autonomous Prefecture, Yushu, China
| | - Guomei Li
- Forestry and Grassland Comprehensive Service Center of Yushu Prefecture, Qinghai, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A and F University, Yangling, China
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Colombi D, Perini F, Bettini S, Mastrangelo S, Abeni F, Conte G, Marletta D, Cassandro M, Bernabucci U, Ciampolini R, Lasagna E. Genomic responses to climatic challenges in beef cattle: A review. Anim Genet 2024. [PMID: 39219301 DOI: 10.1111/age.13474] [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: 05/13/2024] [Revised: 07/31/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Climate change is a major concern for the near future and for livestock breeding. Cattle breeding, due to its greenhouse gas emissions, is one of the most implicated industries. Consequently, the main future goals are to breed animals resilient to climate change, with the aim of lowering the livestock impact on the environment and selecting animals that will be able to resist different, unsuitable, and changing climates. The aim of this literature review is to compare the most recent studies on the response and adaptation of beef cattle breeds to extreme environments, in terms of genes and pathways involved. Beef breeding is just starting to implement genomics in its selection plans, and shedding light on the genomic responses to extreme climates could speed up and simplify the adaptation of these breeds to climate change. This review discusses the genes involved in climatic stress responses, including those related to extremely cold climates, in beef and dual-purpose cattle breeds. Genes were associated with productive traits, coat and skin structure and development, thermotolerance, cellular physiology and DNA repair mechanisms, immune system, and fertility traits. The knowledge of genes and pathways involved in climate resilience should be taken into consideration for further selection in beef cattle breeding and could promote the valorization of local breeds adapted to extreme environmental conditions. The use of local or resilient breeds could enhance the environmental and social sustainability, animal welfare, and production, compared with the introduction of cosmopolitan breeds with uncertain adaptation in uncontrolled environmental areas.
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Affiliation(s)
- Daniele Colombi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Francesco Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Stefano Bettini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Fabio Abeni
- Centro di Ricerca Zootecnia e Acquacoltura, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Lodi, Italy
| | - Giuseppe Conte
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| | - Donata Marletta
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
| | - Umberto Bernabucci
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Agriculture and Forest Sciences, Università Della Tuscia, Viterbo, Italy
| | - Roberta Ciampolini
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
- Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
- Interuniversity Center for Adaptability of Livestock Systems to Climate Change (ASIZOCACLI), Catania, Italy
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Li S, Liu L, Ahmed Z, Wang F, Lei C, Sun F. Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data. Front Genet 2024; 15:1435793. [PMID: 39119576 PMCID: PMC11306169 DOI: 10.3389/fgene.2024.1435793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.
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Affiliation(s)
- Shuang Li
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Li Liu
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Fuwen Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fang Sun
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
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Igoshin AV, Romashov GA, Yurchenko AA, Yudin NS, Larkin DM. Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits. Animals (Basel) 2024; 14:2059. [PMID: 39061521 PMCID: PMC11274160 DOI: 10.3390/ani14142059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and FST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds.
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Affiliation(s)
- Alexander V. Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Grigorii A. Romashov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Andrey A. Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, 94800 Villejuif, France
| | - Nikolay S. Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Denis M. Larkin
- Royal Veterinary College, University of London, London NW1 0TU, UK
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Gao Z, Lu Y, Chong Y, Li M, Hong J, Wu J, Wu D, Xi D, Deng W. Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery. Int J Mol Sci 2024; 25:7147. [PMID: 39000250 PMCID: PMC11240973 DOI: 10.3390/ijms25137147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Beef is a major global source of protein, playing an essential role in the human diet. The worldwide production and consumption of beef continue to rise, reflecting a significant trend. However, despite the critical importance of beef cattle resources in agriculture, the diversity of cattle breeds faces severe challenges, with many breeds at risk of extinction. The initiation of the Beef Cattle Genome Project is crucial. By constructing a high-precision functional annotation map of their genome, it becomes possible to analyze the genetic mechanisms underlying important traits in beef cattle, laying a solid foundation for breeding more efficient and productive cattle breeds. This review details advances in genome sequencing and assembly technologies, iterative upgrades of the beef cattle reference genome, and its application in pan-genome research. Additionally, it summarizes relevant studies on the discovery of functional genes associated with key traits in beef cattle, such as growth, meat quality, reproduction, polled traits, disease resistance, and environmental adaptability. Finally, the review explores the potential of telomere-to-telomere (T2T) genome assembly, structural variations (SVs), and multi-omics techniques in future beef cattle genetic breeding. These advancements collectively offer promising avenues for enhancing beef cattle breeding and improving genetic traits.
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Affiliation(s)
- Zhendong Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Lu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yuqing Chong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengfei Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jieyun Hong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiao Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongmei Xi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Kunming 650201, China
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Abdelmanova AA, Deniskova TE, Kharzinova VR, Chinarov RY, Boronetskaya OI, Sölkner J, Brem G, Ai H, Huang L, Trukhachev VI, Zinovieva NA. Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples. Animals (Basel) 2024; 14:1629. [PMID: 38891676 PMCID: PMC11171240 DOI: 10.3390/ani14111629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.
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Affiliation(s)
- Alexandra A. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Tatiana E. Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Veronika R. Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Roman Yu Chinarov
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
| | - Oksana I. Boronetskaya
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine (VMU), Veterinärplatz, 1210 Vienna, Austria;
| | - Huashui Ai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China; (H.A.); (L.H.)
| | - Vladimir I. Trukhachev
- Museum of Livestock, Timiryazev Russian State Agrarian University—Moscow Agrarian Academy, 49, ul. Timiryazevskaya, Moscow 127550, Russia; (O.I.B.); (V.I.T.)
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, Podolsk 142132, Russia; (A.A.A.); (V.R.K.); (R.Y.C.)
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Zhou Y, Tian J, Jiang H, Han M, Wang Y, Lu J. Phylogeography and demographic history of macaques, fascicularis species group, in East Asia: Inferred from multiple genomic markers. Mol Phylogenet Evol 2024; 194:108042. [PMID: 38401812 DOI: 10.1016/j.ympev.2024.108042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0-0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.
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Affiliation(s)
- Yanyan Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Jundong Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Haijun Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Mengya Han
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Yuwei Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Jiqi Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China.
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Upadhyay M, Pogorevc N, Medugorac I. scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses. Mol Biol Evol 2024; 41:msae057. [PMID: 38507648 PMCID: PMC10994858 DOI: 10.1093/molbev/msae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Population genomic analyses such as inference of population structure and identifying signatures of selection usually involve the application of a plethora of tools. The installation of tools and their dependencies, data transformation, or series of data preprocessing in a particular order sometimes makes the analyses challenging. While the usage of container-based technologies has significantly resolved the problems associated with the installation of tools and their dependencies, population genomic analyses requiring multistep pipelines or complex data transformation can greatly be facilitated by the application of workflow management systems such as Nextflow and Snakemake. Here, we present scalepopgen, a collection of fully automated workflows that can carry out widely used population genomic analyses on the biallelic single nucleotide polymorphism data stored in either variant calling format files or the plink-generated binary files. scalepopgen is developed in Nextflow and can be run locally or on high-performance computing systems using either Conda, Singularity, or Docker. The automated workflow includes procedures such as (i) filtering of individuals and genotypes; (ii) principal component analysis, admixture with identifying optimal K-values; (iii) running TreeMix analysis with or without bootstrapping and migration edges, followed by identification of an optimal number of migration edges; (iv) implementing single-population and pair-wise population comparison-based procedures to identify genomic signatures of selection. The pipeline uses various open-source tools; additionally, several Python and R scripts are also provided to collect and visualize the results. The tool is freely available at https://github.com/Popgen48/scalepopgen.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Neža Pogorevc
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
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Cheng X, Li X, Yang M, Zheng C, Li H, Qu L, Ning Z. Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens. BMC Genomics 2023; 24:704. [PMID: 37993775 PMCID: PMC10666442 DOI: 10.1186/s12864-023-09632-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/28/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Eggshell speckle phenotype is an important trait in poultry production because they affect eggshell quality. However, the genetic architecture of speckled eggshells remains unclear. In this study, we determined the heritability of eggshell speckles and conducted a genome-wide association study (GWAS) on purebred Rhode Island Red (RIR) hens at 28 weeks to detect potential genomic loci and candidate genes associated with eggshell speckles. RESULTS The heritability of eggshell speckles was 0.35 at 28 weeks, and the speckle level is not related to other eggshell quality traits in terms of phenotypic correlation. We detected 311 SNPs (6 significantly, and 305 suggestively associated) and 39 candidate genes associated with eggshell speckles. Based on the pathway analysis, the 39 candidate genes were mainly involved in alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, GnRH signaling pathway, vascular smooth muscle contraction, and MAPK signaling pathway. Ultimately, ten genes, LOC423226, SPTBN5, EHD4, LOC77155, TYRO3, ITPKA, DLL4, PLA2G4B, PLA2G4EL5, and PLA2G4EL6 were considered the most promising genes associated with eggshell speckles that were implicated in immunoregulation, calcium transport, and phospholipid metabolism, while its function in laying hens requires further studies. CONCLUSIONS This study provides new insights into understanding the genetic basis of eggshell speckles and has practical application value for the genetic improvement of eggshell quality.
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Affiliation(s)
- Xue Cheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinghua Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mengyuan Yang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chuanwei Zheng
- Beijing Zhongnongbangyang Layer Breeding Co., Ltd, Beijing, 100083, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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10
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Xia X, Zhang F, Li S, Luo X, Peng L, Dong Z, Pausch H, Leonard AS, Crysnanto D, Wang S, Tong B, Lenstra JA, Han J, Li F, Xu T, Gu L, Jin L, Dang R, Huang Y, Lan X, Ren G, Wang Y, Gao Y, Ma Z, Cheng H, Ma Y, Chen H, Pang W, Lei C, Chen N. Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment. Genome Biol 2023; 24:211. [PMID: 37723525 PMCID: PMC10507960 DOI: 10.1186/s13059-023-03052-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. RESULTS In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. CONCLUSIONS Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.
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Affiliation(s)
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Lixin Peng
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, China
| | - Zheng Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, China
| | - Fuyong Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Gang Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yuanpeng Gao
- College of Veterinary Medicine, Northwest A&F University, Xianyang, Yangling, China
| | - Zhijie Ma
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Weijun Pang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
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11
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Gershoni M. Transgenerational transmission of environmental effects in livestock in the age of global warming. Cell Stress Chaperones 2023; 28:445-454. [PMID: 36715961 PMCID: PMC10468476 DOI: 10.1007/s12192-023-01325-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023] Open
Abstract
Recent decades provide mounting evidence for the continual increase in global temperatures, now termed "global warming," to the point of drastic worldwide change in the climate. Climatic change is a long-term shift in temperatures and weather patterns, including increased frequency and intensity of extreme environmental events such as heat waves accompanied by extreme temperatures and high humidity. Climate change and global warming put several challenges to the livestock industry by directly affecting the animal's production, reproduction, health, and welfare. The broad impact of global warming, and in particular heat stress, on-farm animals' performance has been comprehensively studied. It has been estimated that the US livestock industry's loss caused by heat stress is up to $2.4 billion annually. However, the long-term intergenerational and transgenerational effects of climatic change and global warming on farm animals are sparse. Transgenerational effects, which are mediated by epigenetic mechanisms, can affect the animal's performance regardless of its immediate environment by altering its phenotypic expression to fit its ancestors' environment. In many animal species, environmental effects are epigenetically encoded within a narrow time interval during the organism's gametogenesis, and these epigenetic modifications can then be intergenerationally transmitted. Several epigenetic mechanisms mediate intergenerational transmission of environmental effects, typically in a parent-dependent manner. Therefore, exposure of the animal to an extreme climatic event and other environmental stressors during gametogenesis can undergo epigenetic stabilization in the germline and be passed to the offspring. As a result, the offspring might express a phenotype adjusted to fit the stressors experienced by their ancestors, regardless of their direct environment. The purpose of this perspective is to review current evidence for intergenerational and transgenerational transmission of environmental stress effects, specifically in the context of global warming and climate change, and to offer viewpoints on the possible impacts on the livestock industry.
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Affiliation(s)
- Moran Gershoni
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, 7505101, Rishon LeZion, Israel.
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12
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Yudin NS, Larkin DM. Candidate genes for domestication and resistance to cold climate according to whole genome sequencing data of Russian cattle and sheep breeds. Vavilovskii Zhurnal Genet Selektsii 2023; 27:463-470. [PMID: 37867610 PMCID: PMC10587008 DOI: 10.18699/vjgb-23-56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 10/24/2023] Open
Abstract
It is known that different species of animals, when living in the same environmental conditions, can form similar phenotypes. The study of the convergent evolution of several species under the influence of the same environmental factor makes it possible to identify common mechanisms of genetic adaptation. Local cattle and sheep breeds have been formed over thousands of years under the influence of domestication, as well as selection aimed at adaptation to the local environment and meeting human needs. Previously, we identified a number of candidate genes in genome regions potentially selected during domestication and adaptation to the climatic conditions of Russia, in local breeds of cattle and sheep using whole genome genotyping data. However, these data are of low resolution and do not reveal most nucleotide substitutions. The aim of the work was to create, using the whole genome sequencing data, a list of genes associated with domestication, selection and adaptation in Russian cattle and sheep breeds, as well as to identify candidate genes and metabolic pathways for selection for cold adaptation. We used our original data on the search for signatures of selection in the genomes of Russian cattle (Yakut, Kholmogory, Buryat, Wagyu) and sheep (Baikal, Tuva) breeds. We used the HapFLK, DCMS, FST and PBS methods to identify DNA regions with signatures of selection. The number of candidate genes in potentially selective regions was 946 in cattle and 151 in sheep. We showed that the studied Russian cattle and sheep breeds have at least 10 genes in common, apparently involved in the processes of adaptation/selection, including adaptation to a cold climate, including the ASTN2, PM20D1, TMEM176A, and GLIS1 genes. Based on the intersection with the list of selected genes in at least two Arctic/Antarctic mammal species, 20 and 8 genes, have been identified in cattle and sheep, respectively, that are potentially involved in cold adaptation. Among them, the most promising for further research are the ASPH, NCKAP5L, SERPINF1, and SND1 genes. Gene ontology analysis indicated the existence of possible common biochemical pathways for adaptation to cold in domestic and wild mammals associated with cytoskeleton disassembly and apoptosis.
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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
| | - D M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
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13
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Lyu Y, Ren Y, Qu K, Quji S, Zhuzha B, Lei C, Chen N. Local ancestry and selection in admixed Sanjiang cattle. STRESS BIOLOGY 2023; 3:30. [PMID: 37676416 PMCID: PMC10441984 DOI: 10.1007/s44154-023-00101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/29/2023] [Indexed: 09/08/2023]
Abstract
The majority of native cattle are taurine × indicine cattle of diverse phenotypes in the central region of China. Sanjiang cattle, a typical breed in the central region, play a central role in human livelihood and have good adaptability, including resistance to dampness, heat, roughage, and disease, and are thus regarded as an important genetic resource. However, the genetic history of the successful breed remains unknown. Here, we sequenced 10 Sanjiang cattle genomes and compared them to the 70 genomes of 5 representative populations worldwide. We characterized the genomic diversity and breed formation process of Sanjiang cattle and found that Sanjiang cattle have a mixed ancestry of indicine (55.6%) and taurine (33.2%) dating to approximately 30 generations ago, which has shaped the genome of Sanjiang cattle. Through ancestral fragment inference, selective sweep and transcriptomic analysis, we identified several genes linked to lipid metabolism, immune regulation, and stress reactions across the mosaic genome of Sanjiang cattle showing an excess of taurine or indicine ancestry. Taurine ancestry might contribute to meat quality, and indicine ancestry is more conducive to adaptation to hot climate conditions, making Sanjiang cattle a valuable genetic resource for the central region of China. Our results will help us understand the evolutionary history and ancestry components of Sanjiang cattle, which will provide a reference for resource conservation and selective breeding of Chinese native cattle.
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Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yaxuan Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Suolang Quji
- Institute of Animal Husbandry and Veterinary Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Basang Zhuzha
- Institute of Animal Husbandry and Veterinary Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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14
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He H, Yang H, Foo R, Chan W, Zhu F, Liu Y, Zhou X, Ma L, Wang LF, Zhai W. Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto). J Genet Genomics 2023; 50:554-562. [PMID: 37182682 DOI: 10.1016/j.jgg.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the micro-evolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.
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Affiliation(s)
- Haopeng He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hechuan Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Wharton Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Yunsong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore.
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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15
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, Zinovieva NA. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. BIOLOGY 2023; 12:979. [PMID: 37508409 PMCID: PMC10376169 DOI: 10.3390/biology12070979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023]
Abstract
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
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Affiliation(s)
- Michael N Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Alexandra S Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Vladimir I Fisinin
- Center "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Elena A Gladyr
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Natalia A Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Dmitry V Anshakov
- Breeding and Genetic Center "Zagorsk Experimental Breeding Farm"-Branch of the Federal Research Centre "All-Russian Poultry Research and Technological Institute" of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia
| | - Olga I Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Anatoly B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L. K. Ernst Federal Research Center for Animal Husbandry, Pushkin, Saint Petersburg 196601, Russia
| | - Arsen V Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK
| | - Natalia A Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia
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16
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Xia X, Qu K, Wang Y, Sinding MHS, Wang F, Hanif Q, Ahmed Z, Lenstra JA, Han J, Lei C, Chen N. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective. STRESS BIOLOGY 2023; 3:8. [PMID: 37676580 PMCID: PMC10441868 DOI: 10.1007/s44154-023-00085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/26/2023] [Indexed: 09/08/2023]
Abstract
Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.
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Affiliation(s)
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yan Wang
- Qingdao Municipal Bureau of Agriculture and Rural Affairs, Qingdao, 266000, China
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, 12350, Pakistan
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianlin Han
- Livestock Genetic Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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17
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Solodneva E, Svishcheva G, Smolnikov R, Bazhenov S, Konorov E, Mukhina V, Stolpovsky Y. Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:5061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Affiliation(s)
- Evgenia Solodneva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Rodion Smolnikov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Sergey Bazhenov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Evgenii Konorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Gorbatov Federal Research Center for Food Systems, Russian Academy of Sciences, 109316 Moscow, Russia
| | - Vera Mukhina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Koshkina OA, Rodionov AN, Vetokh AN, Gusev IV, Anshakov DV, Stanishevskaya OI, Dotsev AV, Griffin DK, Zinovieva NA. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. J Anim Sci Biotechnol 2023; 14:35. [PMID: 36829208 PMCID: PMC9951459 DOI: 10.1186/s40104-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/27/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.
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Affiliation(s)
- Michael N. Romanov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia ,grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Vladimir I. Fisinin
- grid.4886.20000 0001 2192 9124Federal State Budget Scientific Institution Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Olga A. Koshkina
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Igor V. Gusev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Dmitry V. Anshakov
- grid.4886.20000 0001 2192 9124Breeding and Genetic Centre “Zagorsk Experimental Breeding Farm” – Branch of the Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Olga I. Stanishevskaya
- grid.473314.6Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, St. Petersburg, Russia
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Darren K. Griffin
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
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19
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Huang N, Zhao L, Wang J, Jiang Q, Ju Z, Wang X, Yang C, Gao Y, Wei X, Zhang Y, Xiao Y, Liu W, Lu S, Huang J. Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate. J Anim Sci 2023; 101:skad006. [PMID: 36617259 PMCID: PMC9985157 DOI: 10.1093/jas/skad006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023] Open
Abstract
Cold climate shapes the genome of animals and drives them to carry sufficient genetic variations to adapt to changes in temperature. However, limited information is available about the genome-wide pattern of adaptations to cold environments in cattle. In the present study, we used 777K SNP genotyping (15 Chinese cattle breeds, 198 individuals) and whole genome resequencing data (54 cattle breeds of the world, 432 individuals) to disentangle divergent selection signatures, especially between the cold-adapted (annual average temperature of habitat, 6.24 °C to 10.3 °C) and heat-adapted (20.2 °C to 24.73 °C) Chinese native cattle breeds. Genomic analyses revealed a set of candidate genes (e.g., UQCR11, DNAJC18, EGR1, and STING1) were functionally associated with thermogenesis and energy metabolism. We also characterized the adaptive loci of cattle exposed to cold temperatures. Our study finds new candidate genes and provides new insights into adaptations to cold climates in cattle.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, P. R. China
| | - Lihong Zhao
- Informatic Center, SAAMS, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Jinpeng Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Qiang Jiang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Zhihua Ju
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Xiuge Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Chunhong Yang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yaping Gao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiaochao Wei
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yaran Zhang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Yao Xiao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Wenhao Liu
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Shaoxiong Lu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, P. R. China
| | - Jinming Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
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20
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Noskova E, Abramov N, Iliutkin S, Sidorin A, Dobrynin P, Ulyantsev VI. GADMA2: more efficient and flexible demographic inference from genetic data. Gigascience 2022; 12:giad059. [PMID: 37609916 PMCID: PMC10445054 DOI: 10.1093/gigascience/giad059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/31/2023] [Accepted: 07/05/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Inference of complex demographic histories is a source of information about events that happened in the past of studied populations. Existing methods for demographic inference typically require input from the researcher in the form of a parameterized model. With an increased variety of methods and tools, each with its own interface, the model specification becomes tedious and error-prone. Moreover, optimization algorithms used to find model parameters sometimes turn out to be inefficient, for instance, by being not properly tuned or highly dependent on a user-provided initialization. The open-source software GADMA addresses these problems, providing automatic demographic inference. It proposes a common interface for several likelihood engines and provides global parameters optimization based on a genetic algorithm. RESULTS Here, we introduce the new GADMA2 software and provide a detailed description of the added and expanded features. It has a renovated core code base, new likelihood engines, an updated optimization algorithm, and a flexible setup for automatic model construction. We provide a full overview of GADMA2 enhancements, compare the performance of supported likelihood engines on simulated data, and demonstrate an example of GADMA2 usage on 2 empirical datasets. CONCLUSIONS We demonstrate the better performance of a genetic algorithm in GADMA2 by comparing it to the initial version and other existing optimization approaches. Our experiments on simulated data indicate that GADMA2's likelihood engines are able to provide accurate estimations of demographic parameters even for misspecified models. We improve model parameters for 2 empirical datasets of inbred species.
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Affiliation(s)
- Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
| | | | - Stanislav Iliutkin
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
| | - Anton Sidorin
- Laboratory of Biochemical Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, Moscow 119991, Russia
| | - Vladimir I Ulyantsev
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
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21
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Buggiotti L, Yudin NS, Larkin DM. Copy Number Variants in Two Northernmost Cattle Breeds Are Related to Their Adaptive Phenotypes. Genes (Basel) 2022; 13:genes13091595. [PMID: 36140763 PMCID: PMC9498843 DOI: 10.3390/genes13091595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
Copy number variations (CNVs) are genomic structural variants with potential functional and evolutionary effects on phenotypes. In this study, we report the identification and characterization of CNVs from the whole-genome resequencing data of two northernmost cattle breeds from Russia: the Yakut and Kholmogory cattle and their phylogenetically most related breeds, Hanwoo and Holstein, respectively. Comparisons of the CNV regions (CNVRs) among the breeds led to the identification of breed-specific CNVRs shared by cold-adapted Kholmogory and Yakut cattle. An investigation of their overlap with genes, regulatory domains, conserved non-coding elements (CNEs), enhancers, and quantitative trait loci (QTLs) was performed to further explore breed-specific biology and adaptations. We found CNVRs enriched for gene ontology terms related to adaptation to environments in both the Kholmogory and Yakut breeds and related to thermoregulation specifically in Yakut cattle. Interestingly, the latter has also been supported when exploring the enrichment of breed-specific CNVRs in the regulatory domains and enhancers, CNEs, and QTLs implying the potential contribution of CNVR to the Yakut and Kholmogory cattle breeds’ adaptation to a harsh environment.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London NW1 0TU, UK
| | - Nikolay S. Yudin
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genomics Center, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science (ICG SB RAS), Novosibirsk 630090, Russia
| | - Denis M. Larkin
- Royal Veterinary College, University of London, London NW1 0TU, UK
- Correspondence:
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22
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Ruvinskiy D, Igoshin A, Yurchenko A, Ilina AV, Larkin DM. Resequencing the Yaroslavl cattle genomes reveals signatures of selection and a rare haplotype on BTA28 likely to be related to breed phenotypes. Anim Genet 2022; 53:680-684. [PMID: 35711120 PMCID: PMC9541747 DOI: 10.1111/age.13230] [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: 08/19/2021] [Revised: 03/12/2022] [Accepted: 06/04/2022] [Indexed: 11/29/2022]
Abstract
The genomes of local livestock could shed light on their genetic history, mechanisms of adaptations to environments and unique genetics. Herein we look into the genetics and adaptations of the Russian native dairy Yaroslavl cattle breed using 22 resequenced individuals and comparing them with two related breeds (Russian Kholmogory and Holstein), and to the taurine set of the 1000 Bull Genomes Project (Run 9). HapFLK analysis with Kholmogory and Holstein breeds (using Yakut cattle as outgroup) resulted in 22 regions under selection (q‐value < 0.01) on 11 chromosomes assigned to Yaroslavl cattle, including a strong signature of selection in the region of the KIT gene on BTA6. The FST (fixation index) with the 1000 Bull Genomes Dataset showed 48 non‐overlapping top (0.1%) FST regions of which three overlapped HapFLK regions. We identified 1982 highly differentiated (FST > 0.40) missense mutations in the Yaroslavl genomes. These genes were enriched in the epidermal growth factor and calcium‐binding functional categories. The top FST intervals contained eight genes with allele frequencies quite different between the Yaroslavl and Kholmogory breeds and the rest of the 1000 Bull Genomes Dataset, including KAT6B, which had a nearly Yaroslavl breed‐specific deleterious missense mutation with the highest FST in our dataset (0.99). This gene is a part of a long haplotype containing other genes from FST and hapFLK analyses and with a negative association with weight and carcass traits according to the genotyping of 30 phenotyped Yaroslavl cattle individuals. Our work provides the industry with candidate genetic variants to be focused on in breed improvement efforts.
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Affiliation(s)
- Daniil Ruvinskiy
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Igoshin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Andrey Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Anna V Ilina
- Federal Williams Research Center of Forage Production & Agroecology, Scientific Research Institute of Livestock Breeding and Forage Production, Yaroslavl Region, Russia
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Royal Veterinary College, University of London, London, UK
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23
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Igoshin AV, Romashov GA, Chernyaeva EN, Elatkin NP, Yudin NS, Larkin DM. Comparative analysis of allele frequencies for DNA polymorphisms associated with disease and economically important traits in the genomes of Russian and foreign cattle breeds. Vavilovskii Zhurnal Genet Selektsii 2022; 26:298-307. [PMID: 35774360 PMCID: PMC9167823 DOI: 10.18699/vjgb-22-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 11/19/2022] Open
Abstract
The genetic makeup of a breed including its genetic differences from other breeds determines its appearance and characteristics, including economically important traits and resistance to pathologies. To date, many loci controlling significant phenotypes have been identified, which is successfully used in the world practice of marker-assisted selection to improve breed properties. The aim of this study was a comparative analysis of frequencies for known causative nucleotide substitutions, insertions and deletions associated with disease and economically important traits in Russian and foreign cattle breeds. As a result, we identified frequencies of these DNA polymorphisms in the populations of Russian cattle breeds, compared them with those of foreign populations of the same breed, as well as other foreign breeds. Our results indicate similarities in frequencies for most of such alleles within breeds (populations of Russian and foreign breeding), as well as the relationship between the causative allele prevalence and the presence of phenotypic traits under the effect. We also found an excess of some undesirable alleles in the Russian cattle populations, which should be paid attention to when designing breeding programs. We found that the alleles increasing fertility in the Hereford breed have a higher frequency in the Russian Hereford population compared to the foreign counterpart. Interestingly, unlike for the European breeds, for Asian Turano-Mongolian Wagyu and Yakut cattle, there was a less clear link between phenotypic traits and frequencies of known causative alleles. Our work points to specific genetic variants that could be used to improve and/or maintain the performance of certain cattle breeds bred in the Russian Federation.
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Affiliation(s)
- A. V. Igoshin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - G. A. Romashov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | | | | | - N. S. Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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24
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Aitnazarov RB, Mishakova TM, Yudin NS. Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers. Vavilovskii Zhurnal Genet Selektsii 2022; 25:831-838. [PMID: 35088018 PMCID: PMC8761576 DOI: 10.18699/vj21.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 12/02/2022] Open
Abstract
There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks
to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of
local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great
relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible
to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the
most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations
in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle
populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent
populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of
the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises
in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic
variability parameters were found between individual populations. Private alleles have been identified in five out of
six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity
excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis,
and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic
diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant
differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises,
which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we
recommend focusing on the two populations with significant genetic distinctions from the others.
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Affiliation(s)
- R. B. Aitnazarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - T. M. Mishakova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - N. S. Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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25
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Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
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Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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26
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
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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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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27
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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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