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Medeiros GC, Ferraz JBS, Pedrosa VB, Chen SY, Doucette JS, Boerman JP, Brito LF. Genetic parameters for udder conformation traits derived from Cartesian coordinates generated by robotic milking systems in North American Holstein cattle. J Dairy Sci 2024; 107:7038-7051. [PMID: 38762108 DOI: 10.3168/jds.2023-24208] [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: 09/18/2023] [Accepted: 04/01/2024] [Indexed: 05/20/2024]
Abstract
Udder conformation is directly related to milk yield, cow health, workability, and welfare. Automatic milking systems (AMS, also known as milking robots) have become popular worldwide, and the number of dairy farms adopting these systems has increased considerably over the past years. In each milking visit, AMS record the location of the 4 teats as Cartesian coordinates in an xyz plan, which can then be used to derive udder conformation traits. Because AMS generate a large amount of data for individual cows per milking visit, they can contribute to an accurate assessment of important traits such as udder conformation without the addition of human classifier errors (in subjective scoring systems). Therefore, the primary objectives of this study were to estimate genomic-based genetic parameters for udder conformation traits derived from AMS records in North American Holstein cattle and to assess the genetic correlation between the derived traits for evaluating the feasibility of multitrait genomic selection for breeding cows that are more suitable for milking in AMS. The Cartesian teat coordinates measured during each milking visit were collected by 36 milking robots in 4,480 Holstein cows from 2017 to 2021, resulting in 5,317,488 records. A total of 4,118 of these Holstein cows were also genotyped for 57,600 SNPs. Five udder conformation traits were derived: udder balance (UB, mm), udder depth (UD, mm), front teat distance (FTD, mm), rear teat distance (RTD, mm), and distance front-rear (DFR, mm). In addition, 2 traits directly related to cow productivity in the system were added to the study: daily milk yield (DY) and milk electroconductivity (EC; as an indicator of mastitis). Variance components and genetic parameters for UB, UD, FTD, RTD, DFR, DY, and EC were estimated based on repeatability animal models. The estimates of heritability (± SE) for UB, UD, FTD, RTD, DFR, DY, and EC were 0.41 ± 0.02, 0.79 ± 0.01, 0.53 ± 0.02, 0.40 ± 0.02, 0.65 ± 0.02, 0.20 ± 0.02, and 0.46 ± 0.02, respectively. The repeatability estimates (± SE) for UB, UD, FTD, RTD, and DFR were 0.82 ± 0.01, 0.93 ± 0.01, 0.87 ± 0.01, 0.83 ± 0.01, and 0.88 ± 0.01, respectively. The strongest genetic correlations were observed between FTD and RTD (0.54 ± 0.03), UD and DFR (-0.47 ± 0.03), DFR and FTD (0.32 ± 0.03), and UD and FTD (-0.31 ± 0.03). These results suggest that udder conformation traits derived from Cartesian coordinates from AMS are moderately to highly heritable. Furthermore, the moderate genetic correlations between these traits should be considered when developing selection subindexes. The most relevant genetic correlations between traits related to cow milk productivity and udder conformation traits were between UD and EC (-0.25 ± 0.03) and between DFR and DY (0.30 ± 0.04), in which both genetic correlations are favorable. These findings will contribute to the design of genomic selection schemes for improving udder conformation in North American Holstein cattle, especially in precision dairy farms.
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Affiliation(s)
- Gabriel C Medeiros
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Jose Bento S Ferraz
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jarrod S Doucette
- Agriculture Information Technology (AgIT), Purdue University, West Lafayette, IN 47907
| | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Medina JE, Castañeda S, Camargo M, Garcia-Corredor DJ, Muñoz M, Ramírez JD. Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Vet Res Commun 2024; 48:2029-2049. [PMID: 38865041 DOI: 10.1007/s11259-024-10403-2] [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: 10/10/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Mosquera, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Weller RB. Sunlight: Time for a Rethink? J Invest Dermatol 2024; 144:1724-1732. [PMID: 38661623 DOI: 10.1016/j.jid.2023.12.027] [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: 12/01/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 04/26/2024]
Abstract
UVR is a skin carcinogen, yet no studies link sun exposure to increased all-cause mortality. Epidemiological studies from the United Kingdom and Sweden link sun exposure with reduced all-cause, cardiovascular, and cancer mortality. Vitamin D synthesis is dependent on UVB exposure. Individuals with higher serum levels of vitamin D are healthier in many ways, yet multiple trials of oral vitamin D supplementation show little benefit. Growing evidence shows that sunlight has health benefits through vitamin D-independent pathways, such as photomobilization of nitric oxide from cutaneous stores with reduction in cardiovascular morbidity. Sunlight has important systemic health benefit as well as risks.
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Affiliation(s)
- Richard B Weller
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom; Department of Dermatology, The University of Edinburgh, Edinburgh, United Kingdom.
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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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Estrada R, Figueroa D, Romero Y, Alvarez-García WY, Rojas D, Alvarado W, Maicelo JL, Quilcate C, Arbizu CI. Complete Mitogenome of "Pumpo" ( Bos taurus), a Top Bull from a Peruvian Genetic Nucleus, and Its Phylogenetic Analysis. Curr Issues Mol Biol 2024; 46:5352-5363. [PMID: 38920992 PMCID: PMC11201737 DOI: 10.3390/cimb46060320] [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: 04/22/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices.
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Affiliation(s)
- Richard Estrada
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (D.F.); (Y.R.); (W.Y.A.-G.); (D.R.); (C.Q.)
| | - Deyanira Figueroa
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (D.F.); (Y.R.); (W.Y.A.-G.); (D.R.); (C.Q.)
| | - Yolanda Romero
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (D.F.); (Y.R.); (W.Y.A.-G.); (D.R.); (C.Q.)
| | - Wuesley Yusmein Alvarez-García
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (D.F.); (Y.R.); (W.Y.A.-G.); (D.R.); (C.Q.)
| | - Diorman Rojas
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (D.F.); (Y.R.); (W.Y.A.-G.); (D.R.); (C.Q.)
| | - Wigoberto Alvarado
- Facultad de Ingeniería Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru; (W.A.); (J.L.M.)
| | - Jorge L. Maicelo
- Facultad de Ingeniería Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru; (W.A.); (J.L.M.)
| | - Carlos Quilcate
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (D.F.); (Y.R.); (W.Y.A.-G.); (D.R.); (C.Q.)
| | - Carlos I. Arbizu
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Amazonas 01001, Peru
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6
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Loureiro B, Ereno RL, Pupulim AGR, Tramontana MCVB, Tabosa HP, Barros CM, Favoreto MG. Genome-wide association study of Nelore and Angus heifers with low and high ovarian follicle counts. Anim Reprod 2024; 21:e20230110. [PMID: 38384724 PMCID: PMC10878542 DOI: 10.1590/1984-3143-ar2023-0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/06/2023] [Indexed: 02/23/2024] Open
Abstract
The number of antral follicles is considered an important fertility trait because animals with a high follicle count (HFC) produce more oocytes and embryos per cycle. Identification of these animals by genetic markers such as single nucleotide polymorphisms (SNPs) can accelerate selection of future generations. The aim of this study was to perform a genome wide association study (GWAS) on Nelore and Angus heifers with HFC and low (LFC) antral follicle counts. The groups HFC and LFC for genotyping were formed based on the average of total follicles (≥ 3 mm) counted in each breed consistently ± standard deviation. A total of 72 Nelore heifers (32 HFC and 40 LFC) and 48 Angus heifers (21 HFC and 27 LFC) were selected and the DNA was extracted from blood and hair bulb. Genotyping was done using the Illumina Bovine HD 770K BeadChip. The GWAS analysis showed 181 and 201 SNPs with genotype/phenotype association (P ≤ 0.01) in Nelore and Angus heifers, respectively. Functional enrichment analysis was performed on candidate genes that were associated with SNPs. A total of 97 genes were associated to the 181 SNPs in the Nelore heifers and the functional analysis identified genes (ROBO1 and SLIT3) in the ROBO-SLIT pathway that can be involved in the control of germ cell migration in the ovary as it is involved in lutheal cell migration and fetal ovary development. In the Angus heifers, 57 genes were associated with the 201 SNPs, highlighting Fribilin 1 (FBN1) gene, involved in regulation of growth factors directly involved in follicle activation and development. In summary, GWAS for Nelore and Angus heifers showed SNPs associated with higher follicle count phenotype. Furthermore, these findings offer valuable insights for the further investigation of potential mechanism involved in follicle formation and development, important for breeding programs for both breeds.
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Affiliation(s)
- Bárbara Loureiro
- Laboratório de Fisiologia da Reprodução Animal, Universidade Vila Velha - UVV, Vila Velha, ES, Brasil
| | - Ronaldo Luiz Ereno
- Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, SP, Brasil
| | | | | | - Henrique Passos Tabosa
- Laboratório de Fisiologia da Reprodução Animal, Universidade Vila Velha - UVV, Vila Velha, ES, Brasil
| | - Ciro Moraes Barros
- Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, SP, Brasil
| | - Maurício Gomes Favoreto
- Laboratório de Fisiologia da Reprodução Animal, Universidade Vila Velha - UVV, Vila Velha, ES, Brasil
- Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Botucatu, SP, Brasil
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Kim K, Kim D, Hanotte O, Lee C, Kim H, Jeong C. Inference of Admixture Origins in Indigenous African Cattle. Mol Biol Evol 2023; 40:msad257. [PMID: 37995300 PMCID: PMC10701095 DOI: 10.1093/molbev/msad257] [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: 04/07/2023] [Revised: 10/12/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
Present-day African cattle retain a unique genetic profile composed of a mixture of the Bos taurus and Bos indicus populations introduced into the continent at different time periods. However, details of the admixture history and the exact origins of the source populations remain obscure. Here, we infer the source of admixture in the earliest domestic cattle in Africa, African taurine. We detect a significant contribution (up to ∼20%) from a basal taurine lineage, which might represent the now-extinct African aurochs. In addition, we show that the indicine ancestry of African cattle, although most closely related to so-far sampled North Indian indicine breeds, has a small amount of additional genetic affinity to Southeast Asian indicine breeds. Our findings support the hypothesis of aurochs introgression into African taurine and generate a novel hypothesis that the origin of indicine ancestry in Africa might be different indicine populations than the ones found in North India today.
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Affiliation(s)
- Kwondo Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghee Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Midlothian, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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Kambal S, Tijjani A, Ibrahim SAE, Ahmed MKA, Mwacharo JM, Hanotte O. Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Anim Genet 2023; 54:689-708. [PMID: 37697736 DOI: 10.1111/age.13353] [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: 07/28/2023] [Revised: 07/28/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.
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Affiliation(s)
- Sumaya Kambal
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Sabah A E Ibrahim
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Joram M Mwacharo
- Scotland's Rural College and Centre for Tropical Livestock Genetics and Health, Edinburgh, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Singh VK, Singh S, Nandhini PB, Bhatia AK, Dixit SP, Ganguly I. Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent. Anim Biotechnol 2023; 34:3483-3494. [PMID: 36592947 DOI: 10.1080/10495398.2022.2162910] [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: 01/04/2023]
Abstract
Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1-13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.
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Affiliation(s)
- V K Singh
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Singh
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - P B Nandhini
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - A K Bhatia
- Animal Genetic Resources Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - I Ganguly
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Demir E, Moravčíková N, Kaya S, Kasarda R, Bilginer Ü, Doğru H, Balcıoğlu MS, Karslı T. Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye. Anim Genet 2023; 54:721-730. [PMID: 37789609 DOI: 10.1111/age.13361] [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: 04/22/2023] [Revised: 09/01/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST ) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP-EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP-EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3-1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.
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Affiliation(s)
- Eymen Demir
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Sarp Kaya
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Ümit Bilginer
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Huriye Doğru
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - Murat Soner Balcıoğlu
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Taki Karslı
- Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, Eskisehir, Türkiye
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11
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Jevit MJ, Castaneda C, Paria N, Das PJ, Miller D, Antczak DF, Kalbfleisch TS, Davis BW, Raudsepp T. Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 2023; 13:20180. [PMID: 37978222 PMCID: PMC10656420 DOI: 10.1038/s41598-023-47583-x] [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: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
We generated single haplotype assemblies from a hinny hybrid which significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes. We added over 15 Mb of missing sequence to both X chromosomes, 60 Mb to donkey autosomes and corrected numerous errors in donkey and some in horse reference genomes. We resolved functionally important X-linked repeats: the DXZ4 macrosatellite and ampliconic Equine Testis Specific Transcript Y7 (ETSTY7). We pinpointed the location of the pseudoautosomal boundaries (PAB) and determined the size of the horse (1.8 Mb) and donkey (1.88 Mb) pseudoautosomal regions (PARs). We discovered distinct differences in horse and donkey PABs: a testis-expressed gene, XKR3Y, spans horse PAB with exons1-2 located in Y and exon3 in the X-Y PAR, whereas the donkey XKR3Y is Y-specific. DXZ4 had a similar ~ 8 kb monomer in both species with 10 copies in horse and 20 in donkey. We assigned hundreds of copies of ETSTY7, a sequence horizontally transferred from Parascaris and massively amplified in equids, to horse and donkey X chromosomes and three autosomes. The findings and products contribute to molecular studies of equid biology and advance research on X-linked conditions, sex chromosome regulation and evolution in equids.
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Affiliation(s)
- Matthew J Jevit
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Caitlin Castaneda
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Nandina Paria
- Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA
| | - Pranab J Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Theodore S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Brian W Davis
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Terje Raudsepp
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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12
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Chakraborty A, Bisht MS, Saxena R, Mahajan S, Pulikkan J, Sharma VK. Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genomics 2023; 45:1399-1408. [PMID: 37231295 DOI: 10.1007/s13258-023-01401-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Indian cattle breeds (Bos indicus) are known for their remarkable adaptability to hot and humid climates, higher nutritious quality of milk, better disease tolerance, and greater ability to perform in poor feed compared to taurine cattle (Bos taurus). Distinct phenotypic differences are observed among the B. indicus breeds; however, the whole genome sequences were unavailable for these indigenous breeds. OBJECTIVE We aimed to perform whole genome sequencing to construct the draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur (the smallest cattle of the world). METHODS We sequenced the whole genomes using Illumina short-read technology, and constructed de novo and reference-based genome assemblies of these native B. indicus breeds for the first time. RESULTS The draft de novo genome assemblies of B. indicus breeds ranged from 1.98 to 3.42 Gbp. We also constructed the mitochondrial genome assemblies (~ 16.3 Kbp), and yet unavailable 18S rRNA marker gene sequences of these B. indicus breeds. The genome assemblies helped to identify the bovine genes related to distinct phenotypic characteristics and other biological processes for this species compared to B. taurus, which are plausibly responsible for providing better adaptive traits. We also identified the genes that showed sequence variation in dwarf and non-dwarf breeds of B. indicus compared to B. taurus. CONCLUSIONS The genome assemblies of these Indian cattle breeds, the 18S rRNA marker genes, and identification of the distinct genes in B. indicus breeds compared to B. taurus will help in future studies on these cattle species.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Joby Pulikkan
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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13
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Ginja C, Guimarães S, da Fonseca RR, Rasteiro R, Rodríguez-Varela R, Simões LG, Sarmento C, Belarte MC, Kallala N, Torres JR, Sanmartí J, Arruda AM, Detry C, Davis S, Matos J, Götherström A, Pires AE, Valenzuela-Lamas S. Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle. iScience 2023; 26:107196. [PMID: 37485357 PMCID: PMC10359934 DOI: 10.1016/j.isci.2023.107196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/22/2022] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.
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Affiliation(s)
- Catarina Ginja
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Silvia Guimarães
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Luciana G. Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Cindy Sarmento
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Maria Carme Belarte
- ICREA, Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
- ICAC, Institut Català d'Arqueologia Clàssica, Tarragona, Spain
| | - Nabil Kallala
- INP, Institut National du Patrimoine, Tunis, Tunisia
- Faculté des Sciences Humaines et Sociales, Université de Tunis, Tunis, Tunisia
| | | | - Joan Sanmartí
- In memoriam, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Ana Margarida Arruda
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Cleia Detry
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Simon Davis
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- LARC/DGPC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisboa, Portugal
| | - José Matos
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P, Oeiras, Portugal
- CE3C, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | | | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | - Silvia Valenzuela-Lamas
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
- Archaeology of Social Dynamics, Consejo Superior de Investigaciones Científicas-Institució Milà i Fontanals d'Humanitats (CSIC-IMF), Barcelona, Spain
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14
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Powell J, Talenti A, Fisch A, Hemmink JD, Paxton E, Toye P, Santos I, Ferreira BR, Connelley TK, Morrison LJ, Prendergast JGD. Profiling the immune epigenome across global cattle breeds. Genome Biol 2023; 24:127. [PMID: 37218021 DOI: 10.1186/s13059-023-02964-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages. RESULTS We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. CONCLUSIONS Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds.
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Affiliation(s)
- Jessica Powell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Johanneke D Hemmink
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
| | - Edith Paxton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Philip Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, PO Box 30709, Nairobi, 00100, Kenya
| | - Isabel Santos
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Beatriz R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Tim K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
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15
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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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16
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Ren Y, Tseng E, Smith TPL, Hiendleder S, Williams JL, Low WY. Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies. BMC Genomics 2023; 24:108. [PMID: 36915055 PMCID: PMC10012480 DOI: 10.1186/s12864-023-09212-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU). However, the higher cost of Iso-Seq relative to RNA-seq has limited the comparison of both methods. Transcript abundance estimated by RNA-seq and deep Iso-Seq data for fetal liver from two cattle subspecies were compared to evaluate concordance. Inter-sample correlation of gene- and transcript-level abundance was higher within technology than between technologies. Identification of DEGs between the cattle subspecies depended on sequencing method with only 44 genes identified by both that included 6 novel genes annotated by Iso-Seq. There was a pronounced difference between Iso-Seq and RNA-seq results at transcript-level wherein Iso-Seq revealed several magnitudes more transcript abundance and usage differences between subspecies. Factors influencing DEG identification included size selection during Iso-Seq library preparation, average transcript abundance, multi-mapping of RNA-seq reads to the reference genome, and overlapping coordinates of genes. Some DEGs called by RNA-seq alone appear to be sequence duplication artifacts. Among the 44 DEGs identified by both technologies some play a role in immune system, thyroid function and cell growth. Iso-Seq revealed hidden transcriptional complexity in DEGs, DETs and DTU genes between cattle subspecies previously missed by RNA-seq.
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Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia
| | | | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Clay Center, Nebraska, USA
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.,Robinson Research Institute, The University of Adelaide, North Adelaide, Adelaide, SA, 5006, Australia
| | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.,Department of Animal Science, Food and Nutrition, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.
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17
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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:ijms24055061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [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: 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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18
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Serum Oxytocin, Cortisol and Social Behavior in Calves: A Study in the Impossible Task Paradigm. Animals (Basel) 2023; 13:ani13040646. [PMID: 36830435 PMCID: PMC9951757 DOI: 10.3390/ani13040646] [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: 01/23/2023] [Revised: 02/07/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
In this study, we explored the correlations between circulating levels of oxytocin, cortisol, and different social behaviors toward humans in 26 Italian Red Pied calves (all females, with an average age of 174 ± 24 days) using the impossible task paradigm. This paradigm has proved fruitful in highlighting the effect of socialization on the willingness to interact with humans in several domesticated species. The test consists of the violation of an expectation (recovering food from an experimental apparatus) while a caregiver and a stranger are present. Immediately after the end of the test (less than one minute), blood was collected from the coccygeal vein. Statistics were performed by the Spearman's rank correlation; significant differences were adjusted according to Bonferroni's correction. Cortisol correlates positively (ρ = 0.565; p < 0.05) with the latency of behaviors directed at the caregiver, and the duration of behaviors directed at the apparatus correlates negatively with both the caregiver (ρ = -0.654; p < 0.05) and a stranger (ρ = -0.644; p < 0.05). Contrary to what is reported in the literature on cows, no correlations were found between oxytocin levels and direct behaviors toward the caregiver. This highlights a different behavioral strategy between calves and cows when placed in front of an impossible task.
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19
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Cortez T, Montenegro H, Coutinho LL, Regitano LCA, Andrade SCS. Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus). PLoS One 2022; 17:e0279091. [PMID: 36548260 PMCID: PMC9778527 DOI: 10.1371/journal.pone.0279091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families' turnover rate (λ). Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (λ = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
| | - Horácio Montenegro
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luiz L. Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luciana C. A. Regitano
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
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20
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Riggio V, Tijjani A, Callaby R, Talenti A, Wragg D, Obishakin ET, Ezeasor C, Jongejan F, Ogo NI, Aboagye-Antwi F, Toure A, Nzalawahej J, Diallo B, Missohou A, Belem AMG, Djikeng A, Juleff N, Fourie J, Labuschagne M, Madder M, Marshall K, Prendergast JGD, Morrison LJ. Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle. Genet Sel Evol 2022; 54:58. [PMID: 36057548 PMCID: PMC9441065 DOI: 10.1186/s12711-022-00751-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. RESULTS We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. CONCLUSIONS Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.
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Affiliation(s)
- Valentina Riggio
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK. .,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, P.O Box 5689, Addis Ababa, Ethiopia
| | - Rebecca Callaby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Emmanuel T Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria.,Biomedical Research Centre, Ghent University Global Campus, Songdo, Incheon, South Korea
| | - Chukwunonso Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Frans Jongejan
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ndudim I Ogo
- National Veterinary Research Institute, Vom, Nigeria
| | - Fred Aboagye-Antwi
- Department of Animal Biology and Conservation Sciences, University of Ghana, Accra, Ghana
| | - Alassane Toure
- Laboratoire National d'Appui Au Dévéloppement Agricole(LANADA)/Laboratoire Central Vétérinaire de Bingerville, Bp: 206, Bingerville, Côte d'Ivoire
| | - Jahashi Nzalawahej
- Department of Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Ayao Missohou
- Ecole Inter-Etats des Sciences et Médecine Vétérinaires (EISMV) de Dakar, Dakar, Senegal
| | - Adrien M G Belem
- Université Polytechnique de Bobo-Dioulasso (UPB), Bobo -Dioulasso, Burkina Faso
| | - Appolinaire Djikeng
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Nick Juleff
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Michel Labuschagne
- Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa.,Clinvet, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa
| | - Maxime Madder
- Clinglobal, B03/04, The Tamarin Commercial Hub, Jacaranda Avenue, Tamarin, 90903, Mauritius
| | - Karen Marshall
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya.,International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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21
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22
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Zhou Y, Yang L, Han X, Han J, Hu Y, Li F, Xia H, Peng L, Boschiero C, Rosen BD, Bickhart DM, Zhang S, Guo A, Van Tassell CP, Smith TPL, Yang L, Liu GE. Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Res 2022; 32:1585-1601. [PMID: 35977842 PMCID: PMC9435747 DOI: 10.1101/gr.276550.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 07/21/2022] [Indexed: 02/03/2023]
Abstract
A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in the cattle reference genome, representing 3.1% novel sequence compared with the 2.71-Gb reference. A catalog of structural variants developed from this cattle population identified 3.3 million deletions, 0.12 million inversions, and 0.18 million duplications. Estimates of breed ancestry and hybridization between cattle breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism-based analysis. Hundreds of deletions were observed to have stratification based on subspecies and breed. For example, an insertion of a Bov-tA1 repeat element was identified in the first intron of the APPL2 gene and correlated with cattle breed geographic distribution. This insertion falls within a segment overlapping predicted enhancer and promoter regions of the gene, and could affect important traits such as immune response, olfactory functions, cell proliferation, and glucose metabolism in muscle. The results indicate that pangenomes are a valuable resource for studying diversity and evolutionary history, and help to delineate how domestication, trait-based breeding, and adaptive introgression have shaped the cattle genome.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaotao Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingwei Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, ARS USDA, Madison, Wisconsin 53706, USA
| | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, ARS USDA, Clay Center, Nebraska 68933, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
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23
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Leonard AS, Crysnanto D, Fang ZH, Heaton MP, Vander Ley BL, Herrera C, Bollwein H, Bickhart DM, Kuhn KL, Smith TPL, Rosen BD, Pausch H. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun 2022; 13:3012. [PMID: 35641504 PMCID: PMC9156671 DOI: 10.1038/s41467-022-30680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Michael P Heaton
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA.
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
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24
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Dorji J, Vander Jagt CJ, Chamberlain AJ, Cocks BG, MacLeod IM, Daetwyler HD. Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle. Sci Rep 2022; 12:5582. [PMID: 35379858 PMCID: PMC8980051 DOI: 10.1038/s41598-022-09427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.
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Affiliation(s)
- Jigme Dorji
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Benjamin G Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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25
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Mulim HA, Brito LF, Pinto LFB, Ferraz JBS, Grigoletto L, Silva MR, Pedrosa VB. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics 2022; 23:209. [PMID: 35291953 PMCID: PMC8925140 DOI: 10.1186/s12864-022-08384-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023] Open
Abstract
Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08384-0.
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Affiliation(s)
| | - Luiz F Brito
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA
| | | | - José Bento Sterman Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Lais Grigoletto
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA.,Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Bahia, Brazil. .,Department of Animal Science, State University of Ponta Grossa, Av. General Carlos Cavalcanti, 4748 - Uvaranas, Ponta Grossa, PR, 84030-900, Brazil.
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A cattle graph genome incorporating global breed diversity. Nat Commun 2022; 13:910. [PMID: 35177600 PMCID: PMC8854726 DOI: 10.1038/s41467-022-28605-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/20/2022] [Indexed: 11/28/2022] Open
Abstract
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research. Cattle reference genomes are valuable resources but are currently heavily biased towards European breeds. Here the authors integrate assemblies for African breeds into a more representative cattle graph genome capturing global breed diversity.
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Association Between Natriuretic Peptide Receptor 2 (NPR2) RS208158047 Polymorphism and Fattening Performance of Young Bulls. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2021-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The objective of this study was to determine fattening performance data for Charolais, Limousin and Blonde d’Aquitaine beef cattle and associate these data with NPR2 gene 8:g.59961937 T>C (rs208158047) mutation. Experiments were conducted with 176 beef cattle (77 Charolais, 66 Limousin and 33 Blonde d’Aquitaine) at nine months of age. Experiments lasted for 9 months and animals were slaughtered at the age of 18 months. Cattle body weights were determined at four different periods: beginning of fattening (d0), 60th day of fattening (d60), 120th day of fattening (d120) and at the end of fattening (sw). In terms of rs208158047 mutation of Charolais, Limousin and Blonde d’Aquitaine breeds, TT and CT genotypes were identified, and CC genotype was not encountered. The association of average daily gain (ADG) in d0-d60, d0-d120 and d0-sw periods with the genotypes of rs208158047 mutation was found to be significant (P<0.05). Greater ADGs were observed in rs208158047-CT genotypes compared to rs208158047-TT genotypes. These results indicate that the selection of bovine NPR2 gene could be used to ensure the breeding direction for growth related traits of the beef cattle.
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Deleterious protein-coding variants in diverse cattle breeds of the world. Genet Sel Evol 2021; 53:80. [PMID: 34654372 PMCID: PMC8518297 DOI: 10.1186/s12711-021-00674-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary. We investigated this question by using whole-genome data from 432 animals belonging to 54 worldwide cattle breeds. Our analysis revealed a negative correlation between genomic heterozygosity and nonsynonymous-to-silent diversity ratio, which suggests a higher proportion of single nucleotide variants (SNVs) affecting proteins in low-diversity breeds. Our results also showed that low-diversity breeds had a larger number of high-frequency (derived allele frequency (DAF) > 0.51) deleterious SNVs than high-diversity breeds. An opposite trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, the number of high-frequency deleterious SNVs was larger in the genomes of taurine cattle breeds than of indicine breeds, whereas the number of low-frequency deleterious SNVs was larger in the genomes of indicine cattle than in those of taurine cattle. Furthermore, we observed significant variation in the counts of deleterious SNVs within taurine breeds. The variations in deleterious mutation load between taurine and indicine breeds could be attributed to the population sizes of the wild progenitors before domestication, whereas the variations observed within taurine breeds could be due to differences in inbreeding level, strength of artificial selection, and/or founding population size. Our findings imply that the incidence of genetic diseases can vary between cattle breeds.
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29
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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30
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Wanner NM, Faulk C. Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. Genes (Basel) 2021; 12:1223. [PMID: 34440397 PMCID: PMC8391136 DOI: 10.3390/genes12081223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 02/01/2023] Open
Abstract
Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human-animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.
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Affiliation(s)
- Nicole M. Wanner
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA;
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agriculture, and Natural Resource Sciences, University of Minnesota, 277 Coffey Hall, 1420 Eckles Avenue, St. Paul, MN 55108, USA
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Perea C, Ciaravino G, Stuber T, Thacker TC, Robbe-Austerman S, Allepuz A, de Val BP. Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain. Microorganisms 2021; 9:microorganisms9081629. [PMID: 34442709 PMCID: PMC8401651 DOI: 10.3390/microorganisms9081629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.
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Affiliation(s)
- Claudia Perea
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
- Correspondence:
| | - Giovanna Ciaravino
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (G.C.); (A.A.)
| | - Tod Stuber
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Tyler C. Thacker
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Alberto Allepuz
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (G.C.); (A.A.)
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), 08197 Bellaterra, Spain;
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - Bernat Pérez de Val
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), 08197 Bellaterra, Spain;
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
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Liu R, Tearle R, Low WY, Chen T, Thomsen D, Smith TPL, Hiendleder S, Williams JL. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. BMC Genomics 2021; 22:410. [PMID: 34082698 PMCID: PMC8176687 DOI: 10.1186/s12864-021-07667-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses. Results In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. Conclusions These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07667-2.
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Affiliation(s)
- Ruijie Liu
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Tong Chen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Dana Thomsen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Timothy P L Smith
- USMARC, USDA-ARS-US Meat Animal Research Center, Clay Center, NE, USA
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Present address: Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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Senczuk G, Mastrangelo S, Ajmone-Marsan P, Becskei Z, Colangelo P, Colli L, Ferretti L, Karsli T, Lancioni H, Lasagna E, Marletta D, Persichilli C, Portolano B, Sarti FM, Ciani E, Pilla F. On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data. Genet Sel Evol 2021; 53:48. [PMID: 34078254 PMCID: PMC8173809 DOI: 10.1186/s12711-021-00639-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00639-w.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Zsolt Becskei
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, Bulevar Oslobodjenja street 18, 11000, Belgrade, Serbia
| | - Paolo Colangelo
- National Council of Research (CNR), Research Institute On Terrestrial Ecosystems (IRET), Via Salaria km 29.300, Montelibretti, 00015, Rome, Italy
| | - Licia Colli
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Italy, Pavia
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di sotto, 06123, Perugia, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donata Marletta
- Department of Agriculture, Food and Environment, University of Catania, 95125, Catania, Italy
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Baldassare Portolano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceuticals, University of Bari, 70124, Bari, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
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Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
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Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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Male mice and cows perceive human emotional chemosignals: a preliminary study. Anim Cogn 2021; 24:1205-1214. [PMID: 33839953 DOI: 10.1007/s10071-021-01511-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/04/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022]
Abstract
Olfactory cues of individuals of the same species or from different species may induce changes in behaviors and physiological reactions in mammals. However, there are few studies on the influence of human odor on animal behavior and welfare, especially those of rodents and farm animals. The present study aimed to investigate whether the odor of a stressed human (in sweat) would modify the behavior of mice and cows. We hypothesized that laboratory and farm animals can perceive human emotions though olfactory cues and that human emotional chemosignals can modify their behavioral reactions and welfare. Two odors of human axillary sweat were collected from engineering students (n = 25, 14 females and 11 males; 21.1 ± 0.7 years old, range: 19-23 years old): a "stress" odor collected after an exam and a "non-stress" odor collected after a standard class. Two experiments were then conducted to test the discrimination of these two odors by male mice (n = 20) under standard conditions and by cows (n = 10) under farm conditions. During the experiments, the behavioral responses of the animals to both odors (through a dispenser for the mice and a bucket for the cows) were observed. The mice produced significantly (p = 0.004) more fecal pellets with the stress odor dispenser than with the non-stress-odor dispenser. The cows spent significantly (p = 0.04) more time smelling the non-stress-odor bucket than control. For both species, the other behaviors observed did not differ significantly between the odors. Mice and cows seemed to perceive and react to stressful human chemosignals. Mice showed physiological reactions that indicated stress in response to the stress odor of humans, while cows showed preference reactions in response to the non-stress odor of humans. This preliminary study showed that laboratory and farm animals, such as male mice and cows, seemed to discriminate certain odors emitted by humans that were likely related to different emotions. Animals may recognize stressful human chemosignals, associate these signals with negative husbandry practices or human-animal relationships, and consequently modify their behavior.
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Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT, Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Davenport KM, Kuhn KL, Green RE, Shapiro B, Rosen BD. A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. J Hered 2021; 112:184-191. [PMID: 33438035 PMCID: PMC8006815 DOI: 10.1093/jhered/esab002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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Affiliation(s)
| | | | | | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TX
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD
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Krovvidi S, Metta M. Evaluation of non-synonym mutation in DGAT1 K232A as a marker for milk production traits in Ongole cattle and Murrah buffalo from Southern India. Trop Anim Health Prod 2021; 53:118. [PMID: 33439326 DOI: 10.1007/s11250-021-02560-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/05/2021] [Indexed: 11/25/2022]
Abstract
Various candidate genes have been reported to affect milk yield and composition in dairy cattle. A non-synonymous mutation in the DGAT1 gene, i.e., K232A was reported to have a strong association with milk yield and milk composition of Bos taurus. A study has been undertaken on 502 unrelated individuals belonging to indigenous Ongole cattle, crossbred cattle, and Murrah buffaloes from the Indian sub-continent with the objective to determine the polymorphism of the K232A locus and their association with milk yield and composition. Typing DGAT1 K232A allelic variation by PCR-RFLP using CfrI restriction enzyme revealed three genotypes in crossbred cattle. Genotype KK was more prevalent (0.60) in Jersey crossbred, whereas in Holstein Friesian crossbred it was KA genotype (0.48). In Ongole cattle and Murrah buffaloes, the locus did not exhibit polymorphism. The least-square mean of milk yields pooled over lactations across the DGAT1 variants was significantly (P < 0.05) higher among the homozygous (AA) genotypes, both in Jersey crossbred and HF crossbred cattle after adjusting for the effects of farm, parity, and season. The fat, SNF, and protein content values of AA genotypes were less than the KK genotypes in both the genetic groups (P > 0.05). The fixation of the DGAT1K allele at the locus in Bos indicus cattle and Bubalus bubalis in the present study did not support its use as a reliable universal marker for milk production and composition traits.
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Affiliation(s)
- Sudhakar Krovvidi
- Department of Animal Genetics and Breeding, NTR College of Veterinary Science (Sri Venkateswara Veterinary University), Gannavaram, Andhra Pradesh, 521 102, India.
| | - Muralidhar Metta
- Department of Animal Genetics and Breeding, NTR College of Veterinary Science (Sri Venkateswara Veterinary University), Gannavaram, Andhra Pradesh, 521 102, India
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Gebrehiwot NZ, Strucken EM, Aliloo H, Marshall K, Gibson JP. The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data. BMC Genomics 2020; 21:869. [PMID: 33287702 PMCID: PMC7720612 DOI: 10.1186/s12864-020-07270-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07270-x.
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Affiliation(s)
- N Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - E M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - H Aliloo
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - K Marshall
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - J P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Hu Y, Xia H, Li M, Xu C, Ye X, Su R, Zhang M, Nash O, Sonstegard TS, Yang L, Liu GE, Zhou Y. Comparative analyses of copy number variations between Bos taurus and Bos indicus. BMC Genomics 2020; 21:682. [PMID: 33004001 PMCID: PMC7528262 DOI: 10.1186/s12864-020-07097-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. RESULTS Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. CONCLUSIONS This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.
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Affiliation(s)
- Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxun Li
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Chang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaowei Ye
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruixue Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
| | | | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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41
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Mastrangelo S, Tolone M, Ben Jemaa S, Sottile G, Di Gerlando R, Cortés O, Senczuk G, Portolano B, Pilla F, Ciani E. Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle. Sci Rep 2020; 10:14522. [PMID: 32883980 PMCID: PMC7471305 DOI: 10.1038/s41598-020-71375-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
The availability of genotyping assays has allowed the detailed evaluation of cattle genetic diversity worldwide. However, these comprehensive studies did not include some local European populations, including autochthonous Italian cattle. In this study, we assembled a large-scale, genome-wide dataset of single nucleotide polymorphisms scored in 3,283 individuals from 205 cattle populations worldwide to assess genome-wide autozygosity and understand better the genetic relationships among these populations. We prioritized European cattle, with a special focus on Italian breeds. Moderate differences in estimates of molecular inbreeding calculated from runs of homozygosity (FROH) were observed among domesticated bovid populations from different geographic areas, except for Bali cattle. Our findings indicated that some Italian breeds show the highest estimates of levels of molecular inbreeding among the cattle populations assessed in this study. Patterns of genetic differentiation, shared ancestry, and phylogenetic analysis all suggested the occurrence of gene flow, particularly among populations originating from the same geographical area. For European cattle, we observed a distribution along three main directions, reflecting the known history and formation of the analyzed breeds. The Italian breeds are split into two main groups, based on their historical origin and degree of conservation of ancestral genomic components. The results pinpointed that also Sicilian breeds, much alike Podolian derived-breeds, in the past experienced a similar non-European influence, with African and indicine introgression.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de La Recherche Agronomique de Tunisie, Université de Carthage, 2049, Ariana, Tunisia
| | - Gianluca Sottile
- Dipartimento Scienze Economiche, Aziendali e Statistiche, University of Palermo, 90128, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Oscar Cortés
- Departamento de Produccion Animal, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
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42
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Papachristou D, Koutsouli P, Laliotis GP, Kunz E, Upadhyay M, Seichter D, Russ I, Gjoko B, Kostaras N, Bizelis I, Medugorac I. Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genet Sel Evol 2020; 52:43. [PMID: 32727375 PMCID: PMC7391618 DOI: 10.1186/s12711-020-00560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
Background The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
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Affiliation(s)
- Dimitris Papachristou
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Panagiota Koutsouli
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - George P Laliotis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Bunevski Gjoko
- Livestock Department, Faculty of Agricultural Sciences and Food Institute of Animal Biotechnology, University Ss. Cyril and Methodius, 16-ta Makedonska Brigada 3, 1000, Skopje, North Macedonia
| | - Nikolaos Kostaras
- AMALTHIA, Network for the Protection of Greek Indigenous Farm Animals, 51 Argyrokastrou, 15669, Athens, Greece
| | - Iosif Bizelis
- Laboratory of Animal Husbandry, Faculty of Animal Sciences, Department of Animal Production, Agricultural University of Athens, 75 Iera Odos, 11855, Athens, Greece
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Lena-Christ-Str. 48, 82152, Martinsried, Germany.
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43
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Barrera-Redondo J, Piñero D, Eguiarte LE. Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners. Front Genet 2020; 11:742. [PMID: 32760427 PMCID: PMC7373799 DOI: 10.3389/fgene.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023] Open
Abstract
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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Affiliation(s)
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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44
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Düx A, Lequime S, Patrono LV, Vrancken B, Boral S, Gogarten JF, Hilbig A, Horst D, Merkel K, Prepoint B, Santibanez S, Schlotterbeck J, Suchard MA, Ulrich M, Widulin N, Mankertz A, Leendertz FH, Harper K, Schnalke T, Lemey P, Calvignac-Spencer S. Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science 2020; 368:1367-1370. [PMID: 32554594 DOI: 10.1126/science.aba9411] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022]
Abstract
Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.
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Affiliation(s)
- Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Sebastian Lequime
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Livia Victoria Patrono
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Bram Vrancken
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sengül Boral
- Institute for Pathology, Charité, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Antonia Hilbig
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - David Horst
- Institute for Pathology, Charité, Berlin, Germany
| | - Kevin Merkel
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Baptiste Prepoint
- Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany.,Département de Biologie, Ecole Normale Supérieure, PSL Université Paris, Paris, France
| | - Sabine Santibanez
- National Reference Centre for Measles, Mumps, and Rubella, Robert Koch Institute, Berlin, Germany
| | | | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - Navena Widulin
- Berlin Museum of Medical History, Charité, Berlin, Germany
| | - Annette Mankertz
- National Reference Centre for Measles, Mumps, and Rubella, Robert Koch Institute, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - Kyle Harper
- Department of Classics and Letters, University of Oklahoma, Norman, OK, USA
| | | | - Philippe Lemey
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany. .,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
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45
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Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus). Sci Rep 2020; 10:9412. [PMID: 32523018 PMCID: PMC7287098 DOI: 10.1038/s41598-020-66272-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/12/2020] [Indexed: 11/22/2022] Open
Abstract
Most of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical adaptation and productive traits. Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) mutations were identified using the newest bovine reference genome ARS_UCD1.2, and variant functional consequences were predicted using the Ensembl VEP software. A total of 35,753,707 SNPs and 4,492,636 INDELs were detected and annotated to their functional effects. We identified 400 genes that comprised both, a SNP and an INDEL, of high functional impact on proteins (i.e. variants that cause protein truncation, loss of function or triggering nonsense-mediated decay). Among these, we highlight the following genes: BoLA, associated with cattle immune response to infections and reproduction aspects; HSPA8, DNAJC27, and DNAJC28, involved with thermoregulatory protective mechanisms in mammals; and many olfactory signaling pathway related genes that are important genetic factors in the evolution of mammalian species. All these functional aspects are directly related to cattle adaptability to tropical environments.
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46
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Naval-Sánchez M, Porto-Neto LR, Cardoso DF, Hayes BJ, Daetwyler HD, Kijas J, Reverter A. Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genet Sel Evol 2020; 52:27. [PMID: 32460767 PMCID: PMC7251699 DOI: 10.1186/s12711-020-00546-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
Background Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. Conclusions Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.
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Affiliation(s)
- Marina Naval-Sánchez
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia. .,Institute of Molecular Biosciences, The University of Queensland, 306 Carmody Road, St. Lucia, Brisbane, QLD, 4067, Australia.
| | - Laercio R Porto-Neto
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Diercles F Cardoso
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia.,Department of Animal Science, School of Agricultural and Veterinarian Sciences, Sao Paulo State University (UNESP), Jaboticabal, SP, Brazil.,Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - James Kijas
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
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Carter AM. Evolution of placentation in cattle and antelopes. Anim Reprod 2020; 16:3-17. [PMID: 33936288 PMCID: PMC8083812 DOI: 10.21451/1984-3143-ar2018-00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Bovids have enjoyed great evolutionary success as evidenced by the large number of extant species. Several important domestic animals are from this family. They derive from both subfamilies: cattle and their kin belong to Bovinae and sheep and goats to Antilopinae. The premise of this review, therefore, is that evolution of reproduction and placentation is best understood in a context that includes antelope-like bovines and antelopes. Many key features of placentation, including hormone secretion, had evolved before bovids emerged as a distinct group. Variation nevertheless occurs. Most striking is the difference in fusion of the binucleate trophoblast cell with uterine epithelium that yields a transient trinucleate cell in bovines and many antelopes, but a more persistent syncytium in wildebeest, sheep and goat. There is considerable variation in placentome number and villus branching within the placentome. Many antelopes have right-sided implantation in a bicornuate uterus whilst others have a uterus duplex. Finally, there has been continued evolution of placental hormones with tandem duplication of PAG genes in cattle, differences in glycosylation of placental lactogen and the emergence of placental growth hormone in sheep and goats. The selection pressures driving this evolution are unknown though maternal-fetal competition for nutrients is an attractive hypothesis.
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Affiliation(s)
- Anthony M Carter
- Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
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48
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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49
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Barbato M, Reichel MP, Passamonti M, Low WY, Colli L, Tearle R, Williams JL, Ajmone Marsan P. A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel. PLoS One 2020; 15:e0231162. [PMID: 32271816 PMCID: PMC7145104 DOI: 10.1371/journal.pone.0231162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.
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Affiliation(s)
- Mario Barbato
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
| | - Michael P. Reichel
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Matilde Passamonti
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Licia Colli
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rick Tearle
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - John L. Williams
- School of Animal and Veterinary Sciences, Davies Research Centre, University of Adelaide, Roseworthy, Australia
| | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Technology–DIANA, and Nutrigenomics and Proteomics Research Center–PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Research Center on Biodiversity and Ancient DNA–BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
- * E-mail: (MB); (PAM)
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Barbato M, Hailer F, Upadhyay M, Del Corvo M, Colli L, Negrini R, Kim ES, Crooijmans RPMA, Sonstegard T, Ajmone-Marsan P. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep 2020; 10:1279. [PMID: 31992729 PMCID: PMC6987186 DOI: 10.1038/s41598-020-57880-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/26/2019] [Indexed: 11/19/2022] Open
Abstract
Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
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Affiliation(s)
- Mario Barbato
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcello Del Corvo
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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