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Boschiero C, Neupane M, Yang L, Schroeder SG, Tuo W, Ma L, Baldwin RL, Van Tassell CP, Liu GE. A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle. Animals (Basel) 2024; 14:1921. [PMID: 38998033 PMCID: PMC11240624 DOI: 10.3390/ani14131921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024] Open
Abstract
Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.
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Affiliation(s)
- Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Mahesh Neupane
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Liu Yang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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Roques S, Martinez-Fernandez G, Ramayo-Caldas Y, Popova M, Denman S, Meale SJ, Morgavi DP. Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production. Annu Rev Anim Biosci 2024; 12:321-343. [PMID: 38079599 DOI: 10.1146/annurev-animal-021022-024931] [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: 02/16/2024]
Abstract
Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.
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Affiliation(s)
- Simon Roques
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | | | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, Caldes de Montbui, Spain;
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
| | - Stuart Denman
- Agriculture and Food, CSIRO, St. Lucia, Queensland, Australia; ,
| | - Sarah J Meale
- School of Agriculture and Food Sustainability, Faculty of Science, University of Queensland, Gatton, Queensland, Australia;
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France; , ,
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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Baruselli PS, de Abreu LÂ, de Paula VR, Carvalho B, Gricio EA, Mori FK, Rebeis LM, Albertini S, de Souza AH, D’Occhio M. Applying assisted reproductive technology and reproductive management to reduce CO 2-equivalent emission in dairy and beef cattle: a review. Anim Reprod 2023; 20:e20230060. [PMID: 37720728 PMCID: PMC10503887 DOI: 10.1590/1984-3143-ar2023-0060] [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: 05/16/2023] [Accepted: 07/31/2023] [Indexed: 09/19/2023] Open
Abstract
Methane emission from beef and dairy cattle combined contributes around 4.5-5.0% of total anthropogenic global methane. In addition to enteric methane (CH4) produced by the rumen, cattle production also contributes carbon dioxide (CO2) (feed), nitrous oxide (N2O) (feed production, manure) and other CH4 (manure) to the total greenhouse gas (GHG) budget of beef and dairy production systems. The relative contribution in standard dairy systems is typically enteric CH4 58%, feed 29% and manure 10%. Herds with low production efficiency can have an enteric CH4 contribution up to 90%. Digestibility of feed can impact CH4 emission intensity. Low fertility herds also have a greater enteric CH4 contribution. Animals with good feed conversion efficiency have a lower emission intensity of CH4/kg of meat or milk. Feed efficient heifers tend to be lean and have delayed puberty. Fertility is a major driver of profit in both beef and dairy cattle, and it is highly important to apply multi-trait selection when shifting herds towards improved efficiency and reduced CH4. Single nucleotide polymorphisms (SNPs) have been identified for feed efficiency in cattle and are used in genomic selection. SNPs can be utilized in artificial insemination and embryo transfer to increase the proportion of cattle that have the attributes of efficiency, fertility and reduced enteric CH4. Prepubertal heifers genomically selected for favourable traits can have oocytes recovered to produce IVF embryos. Reproductive technology is predicted to be increasingly adopted to reduce generation interval and accelerate the rate of genetic gain for efficiency, fertility and low CH4 in cattle. The relatively high contribution of cattle to anthropogenic global methane has focussed attention on strategies to reduce enteric CH4 without compromising efficiency and fertility. Assisted reproductive technology has an important role in achieving the goal of multiplying and distributing cattle that have good efficiency, fertility and low CH4.
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Affiliation(s)
- Pietro Sampaio Baruselli
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Laís Ângelo de Abreu
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Vanessa Romário de Paula
- Instituto Paulista de Ensino e Pesquisa, Empresa Brasileira de Pesquisa Agropecuária – EMBRAPA, Juiz de Fora, MG, Brasil
| | - Bruno Carvalho
- Instituto Paulista de Ensino e Pesquisa, Empresa Brasileira de Pesquisa Agropecuária – EMBRAPA, Juiz de Fora, MG, Brasil
| | - Emanuelle Almeida Gricio
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Fernando Kenji Mori
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Lígia Mattos Rebeis
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Sofía Albertini
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brasil
| | | | - Michael D’Occhio
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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Belay Mekonnen G. Technology for Carbon Neutral Animal Breeding. Vet Med Sci 2023. [DOI: 10.5772/intechopen.110383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
Animal breeding techniques are to genetically select highly productive animals with less GHG emission intensity, thereby reducing the number of animals required to produce the same amount of food. Shotgun metagenomics provides a platform to identify rumen microbial communities and genetic markers associated with CH4 emissions, allowing the selection of cattle with less CH4 emissions. Moreover, breeding is a viable option to make real progress towards carbon neutrality with a very high rate of return on investment and a very modest cost per tonne of CO2 equivalents saved regardless of the accounting method. Other high technologies include the use of cloned livestock animals and the manipulation of traits by controlling target genes with improved productivity.
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Host genetics associated with gut microbiota and methane emission in cattle. Mol Biol Rep 2022; 49:8153-8161. [PMID: 35776394 DOI: 10.1007/s11033-022-07718-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
In livestock sector, dairy animals alone produce 18% of the total greenhouse gas emissions globally as methane (CH4). This Enteric methane is the largest component of total carbon footprints produced by livestock production system and its reduction is today's new challenge to make livestock farming sustainable for earth's environment. The production of enteric methane in ruminants is a complex phenomena involving different host factors like host genotype, rumen microbiome, host physiology along with dietary factors. Efforts have been made to reduce methane emissions largely through nutritional interventions and dietary supplements, but permanent reductions can be obtained through genetic means by selecting and breeding of low methane emitting animals. From genome-wide association studies, many important genomic QTL regions and single nucleotide polymorphisms involved in shaping the composition of the ruminal microbiome and thus their carbon footprints have been recognised, implying that methane emission traits are quantitative traits. The major bottleneck in implementation of reduced methane emission traits in the breeding programs is wide variation at phenotypic level, lack of precise methane measurements at individual level. Overall, the heritability for CH4 production traits is moderate, and it can be used in breeding programmes to target changes in microbial composition to reduce CH4 emission in the dairy industry for far-reaching environmental benefits at the cost of a minor reduction in genetic gain in production traits.
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Silpa MV, König S, Sejian V, Malik PK, Nair MRR, Fonseca VFC, Maia ASC, Bhatta R. Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models. Front Vet Sci 2021; 8:625189. [PMID: 33996959 PMCID: PMC8117237 DOI: 10.3389/fvets.2021.625189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/15/2021] [Indexed: 01/02/2023] Open
Abstract
The current changing climate trend poses a threat to the productive efficacy and welfare of livestock across the globe. This review is an attempt to synthesize information pertaining to the applications of various genomic tools and statistical models that are available to identify climate-resilient dairy cows. The different functional and economical traits which govern milk production play a significant role in determining the cost of milk production. Thus, identification of these traits may revolutionize the breeding programs to develop climate-resilient dairy cattle. Moreover, the genotype–environment interaction also influences the performance of dairy cattle especially during a challenging situation. The recent advancement in molecular biology has led to the development of a few biotechnological tools and statistical models like next-generation sequencing (NGS), microarray technology, whole transcriptome analysis, and genome-wide association studies (GWAS) which can be used to quantify the molecular mechanisms which govern the climate resilience capacity of dairy cows. Among these, the most preferred option for researchers around the globe was GWAS as this approach jointly takes into account all the genotype, phenotype, and pedigree information of farm animals. Furthermore, selection signatures can also help to demarcate functionally important regions in the genome which can be used to detect potential loci and candidate genes that have undergone positive selection in complex milk production traits of dairy cattle. These identified biomarkers can be incorporated in the existing breeding policies using genomic selection to develop climate-resilient dairy cattle.
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Affiliation(s)
- Mullakkalparambil Velayudhan Silpa
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität Gießen, Gießen, Germany.,Center for Climate Resilient Animal Adaptation Studies, Indian Council of Agricultural Research-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Veerasamy Sejian
- Center for Climate Resilient Animal Adaptation Studies, Indian Council of Agricultural Research-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Pradeep Kumar Malik
- Center for Climate Resilient Animal Adaptation Studies, Indian Council of Agricultural Research-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Mini Ravi Reshma Nair
- Center for Climate Resilient Animal Adaptation Studies, Indian Council of Agricultural Research-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Vinicius F C Fonseca
- Innovation Group of Thermal Comfort and Animal Welfare (INOBIO-MANERA), Animal Science Department, Universidade Federal da Paraíba, Areia, Brazil.,Brain Function Research Group, Faculty of Health Sciences, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Alex Sandro Campos Maia
- Innovation Group of Thermal Comfort and Animal Welfare (INOBIO-MANERA), Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), São Paulo, Brazil
| | - Raghavendra Bhatta
- Center for Climate Resilient Animal Adaptation Studies, Indian Council of Agricultural Research-National Institute of Animal Nutrition and Physiology, Bangalore, India
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