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Akinsola OM, Musa AA, Muansangi L, Singh SP, Mukherjee S, Mukherjee A. Genomic insights into adaptation and inbreeding among Sub-Saharan African cattle from pastoral and agropastoral systems. Front Genet 2024; 15:1430291. [PMID: 39119582 PMCID: PMC11306176 DOI: 10.3389/fgene.2024.1430291] [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: 05/09/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background In Sub-Saharan Africa (SSA), cattle are crucial for socioeconomic stability yet face numerous environmental stressors such as diseases, parasites, and extreme heat within pastoral and agropastoral systems. Despite their significance, gaps remain in understanding how genetic diversity and inbreeding influence traits essential for disease resistance and environmental adaptability. This study examines the genomic adaptations that enable SSA cattle to thrive under these conditions and assesses the impact of inbreeding on such adaptive traits. Methods We analyzed genomic data from 113 cattle across four breeds-Kuri, N'dama, Zebu-Fulani, and Zebu-Bororo-employing Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) analyses to identify historical and recent genetic selections. Strict quality controls using PLINK software ensured accurate genomic pattern identification related to adaptation and inbreeding. Results ROH analysis revealed islands with genes such as RSAD2, CMPK2, and NOTCH1, which are involved in immune response and cellular stress management, highlighting regions of historical selection that have likely provided adaptive advantages in overcoming environmental and pathogenic stresses. In contrast, iHS analysis identified genes under recent selection like HIPK1, involved in stress response regulation, and EPHA5, which plays a crucial role in neural development and synaptic functions, potentially equipping these breeds with novel adaptations to ongoing and emergent environmental challenges. Conclusion This research confirms that selective pressures inherent in pastoral and agropastoral systems profoundly influence the genetic structure of SSA cattle. By delineating the genetic bases of key adaptive traits, our study offers crucial insights for targeted breeding programs to enhance cattle resilience and productivity. These findings provide a valuable framework for future genetic improvements and conservation strategies, crucial for sustainable livestock management and economic stability in SSA.
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Affiliation(s)
- Oludayo M. Akinsola
- Department of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos, Nigeria
| | | | - Lal Muansangi
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sanchit P. Singh
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sabyasachi Mukherjee
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Anupama Mukherjee
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
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Song X, Zhao M, Cao Q, Wang S, Li R, Zhang X, Zhang L, Shi K. Transcriptome provides insights into bovine mammary regulatory mechanisms during the lactation cycle. JOURNAL OF APPLIED ANIMAL RESEARCH 2022. [DOI: 10.1080/09712119.2022.2064865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Xuyang Song
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Meng Zhao
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Qiaoqiao Cao
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Shengxuan Wang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Ranran Li
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Xuan Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Letian Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
| | - Kerong Shi
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, People’s Republic of China
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Sutera AM, Di Gerlando R, Mastrangelo S, Sardina MT, D’Alessandro E, Portolano B, Tolone M. Genome-wide association study for milk production traits in an economically important local dairy sheep breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1963865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Anna Maria Sutera
- Dipartimento di Scienze Veterinarie, Università di Messina, Messina, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | | | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
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Vijayakumar P, Bakyaraj S, Singaravadivelan A, Vasanthakumar T, Suresh R. Meta-analysis of mammary RNA seq datasets reveals the molecular understanding of bovine lactation biology. Genome 2019; 62:489-501. [PMID: 31071269 DOI: 10.1139/gen-2018-0144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A better understanding of the biology of lactation, both in terms of gene expression and the identification of candidate genes for the production of milk and its components, is made possible by recent advances in RNA seq technology. The purpose of this study was to understand the synthesis of milk components and the molecular pathways involved, as well as to identify candidate genes for milk production traits within whole mammary transcriptomic datasets. We performed a meta-analysis of publically available RNA seq transcriptome datasets of mammary tissue/milk somatic cells. In total, 11 562 genes were commonly identified from all RNA seq based mammary gland transcriptomes. Functional annotation of commonly expressed genes revealed the molecular processes that contribute to the synthesis of fats, proteins, and lactose in mammary secretory cells and the molecular pathways responsible for milk synthesis. In addition, we identified several candidate genes responsible for milk production traits and constructed a gene regulatory network for RNA seq data. In conclusion, this study provides a basic understanding of the lactation biology of cows at the gene expression level.
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Affiliation(s)
- Periyasamy Vijayakumar
- a Veterinary College and Research Institute, TANUVAS, Orathanadu-614 625, Thanjavur, Tamil Nadu, India
| | - Sanniyasi Bakyaraj
- b College of Poultry Production and Management, TANUVAS, Hosur-635 110, Krishnagiri, Tamil Nadu, India
| | | | - Thangavelu Vasanthakumar
- a Veterinary College and Research Institute, TANUVAS, Orathanadu-614 625, Thanjavur, Tamil Nadu, India
| | - Ramalingam Suresh
- a Veterinary College and Research Institute, TANUVAS, Orathanadu-614 625, Thanjavur, Tamil Nadu, India
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Zhao J, Xu Z, Chen A, You X, Zhao Y, He W, Zhao L, Yang S. Identification of meat from yak and cattle using SNP markers with integrated allele-specific polymerase chain reaction-capillary electrophoresis method. Meat Sci 2018; 148:120-126. [PMID: 30388476 DOI: 10.1016/j.meatsci.2018.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 07/22/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
Correct species identification is necessary for meat product quality assurance. Genetic markers are useful tools to accurately determine the animal source of meat products. To better protect yak meat and its products, ten single nucleotide polymorphism (SNP) loci from bovine meat-related genes and one positive control primer set were selected to discriminate meat sourced from yak or cattle. A multiplex allele-specific polymerase chain reaction and capillary electrophoresis method was employed for SNP genotyping. The samples were identified as from yak or cattle based on the number of amplicons. Yak samples generally produced one to three amplicon peaks, and the cattle samples yielded five or more peaks in the electropherogram. This method could be useful to distinguish yak meat from cattle beef, and would protect consumers and yak meat producers.
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Affiliation(s)
- Jie Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Zhenzhen Xu
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Ailiang Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Xinyong You
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Yan Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Wenjing He
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Luyao Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China
| | - Shuming Yang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, China.
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Yue SJ, Zhao YQ, Gu XR, Yin B, Jiang YL, Wang ZH, Shi KR. A genome-wide association study suggests new candidate genes for milk production traits in Chinese Holstein cattle. Anim Genet 2017; 48:677-681. [PMID: 28857209 DOI: 10.1111/age.12593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2017] [Indexed: 11/27/2022]
Abstract
A genome-wide association study (GWAS) was conducted on 15 milk production traits in Chinese Holstein. The experimental population consisted of 445 cattle, each genotyped by the GGP (GeneSeek genomic profiling)-BovineLD V3 SNP chip, which had 26 151 public SNPs in its manifest file. After data cleaning, 20 326 SNPs were retained for the GWAS. The phenotypes were estimated breeding values of traits, provided by a public dairy herd improvement program center that had been collected once a month for 3 years. Two statistical models, a fixed-effect linear regression model and a mixed-effect linear model, were used to estimate the association effects of SNPs on each of the phenotypes. Genome-wide significant and suggestive thresholds were set at 2.46E-06 and 4.95E-05 respectively. The two statistical models concurrently identified two genome-wide significant (P < 0.05) SNPs on milk production traits in this Chinese Holstein population. The positional candidate genes, which were the ones closest to these two identified SNPs, were EEF2K (eukaryotic elongation factor 2 kinase) and KLHL1 (kelch like family member 1). These two genes could serve as new candidate genes for milk yield and lactation persistence, yet their roles need to be verified in further function studies.
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Affiliation(s)
- S J Yue
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Y Q Zhao
- State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - X R Gu
- State Key Laboratory for Agrobiotechnology, College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - B Yin
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Y L Jiang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Z H Wang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - K R Shi
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
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Martin P, Palhière I, Maroteau C, Bardou P, Canale-Tabet K, Sarry J, Woloszyn F, Bertrand-Michel J, Racke I, Besir H, Rupp R, Tosser-Klopp G. A genome scan for milk production traits in dairy goats reveals two new mutations in Dgat1 reducing milk fat content. Sci Rep 2017; 7:1872. [PMID: 28500343 PMCID: PMC5431851 DOI: 10.1038/s41598-017-02052-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/05/2017] [Indexed: 11/21/2022] Open
Abstract
The quantity of milk and milk fat and proteins are particularly important traits in dairy livestock. However, little is known about the regions of the genome that influence these traits in goats. We conducted a genome wide association study in French goats and identified 109 regions associated with dairy traits. For a major region on chromosome 14 closely associated with fat content, the Diacylglycerol O-Acyltransferase 1 (DGAT1) gene turned out to be a functional and positional candidate gene. The caprine reference sequence of this gene was completed and 29 polymorphisms were found in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substitutions in the protein sequence. The R251L mutation was found in the Saanen breed at a frequency of 3.5% and the R396W mutation both in the Saanen and Alpine breeds at a frequencies of 13% and 7% respectively. The R396W mutation explained 46% of the genetic variance of the trait, and the R251L mutation 6%. Both mutations were associated with a notable decrease in milk fat content. Their causality was then demonstrated by a functional test. These results provide new knowledge on the genetic basis of milk synthesis and will help improve the management of the French dairy goat breeding program.
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Affiliation(s)
- Pauline Martin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Cyrielle Maroteau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
- Division of Molecular and Clinical Medecine, School of Medecine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
- INRA, Sigenae, Castanet-Tolosan, France
| | - Kamila Canale-Tabet
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | | | - Ines Racke
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Hüseyin Besir
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
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Melo C, Gallardo D, Quintanilla R, Zidi A, Castelló A, Díaz I, Amills M, Pena R. An association analysis between polymorphisms of the pig solute carrier family 27A (SLC27A), member 1 and 4 genes and serum and muscle lipid traits. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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