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Zhang C, Asadollahpour Nanaei H, Jafarpour Negari N, Amiri Roudbar M, Amiri Ghanatsaman Z, Niyazbekova Z, Yang X. Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats. BMC Genomics 2024; 25:477. [PMID: 38745140 PMCID: PMC11094986 DOI: 10.1186/s12864-024-10387-y] [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: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Since domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate. RESULTS To explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (- 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds. CONCLUSIONS The results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions.
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Affiliation(s)
- Chenxi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hojjat Asadollahpour Nanaei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | | | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful 333, Iran
| | - Zeinab Amiri Ghanatsaman
- Animal Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [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: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
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Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
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Peng W, Zhang Y, Gao L, Shi W, Liu Z, Guo X, Zhang Y, Li B, Li G, Cao J, Yang M. Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds. BMC Genomics 2024; 25:420. [PMID: 38684985 PMCID: PMC11057119 DOI: 10.1186/s12864-024-10334-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: 11/29/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.
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Affiliation(s)
- Weifeng Peng
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.
| | - Yiyuan Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Wanlu Shi
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Zi Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Xinyu Guo
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Yunxia Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Bing Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Jingya Cao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.
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Liu Z, Jiang A, Lv X, Fan D, Chen Q, Wu Y, Zhou C, Tan Z. Combined Metabolomics and Biochemical Analyses of Serum and Milk Revealed Parity-Related Metabolic Differences in Sanhe Dairy Cattle. Metabolites 2024; 14:227. [PMID: 38668355 PMCID: PMC11052102 DOI: 10.3390/metabo14040227] [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: 02/27/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The production performance of dairy cattle is closely related to their metabolic state. This study aims to provide a comprehensive understanding of the production performance and metabolic features of Sanhe dairy cattle across different parities, with a specific focus on evaluating variations in milk traits and metabolites in both milk and serum. Sanhe dairy cattle from parities 1 to 4 (S1, n = 10; S2, n = 9; S3, n = 10; and S4, n = 10) at mid-lactation were maintained under the same feeding and management conditions. The milk traits, hydrolyzed milk amino acid levels, serum biochemical parameters, and serum free amino acid levels of the Sanhe dairy cattle were determined. Multiparous Sanhe dairy cattle (S2, S3, and S4) had a greater milk protein content, lower milk lactose content, and lower solids-not-fat content than primiparous Sanhe dairy cattle (S1). Moreover, S1 had a higher ratio of essential to total amino acids (EAAs/TAAs) in both the serum and milk. The serum biochemical results showed the lower glucose and total protein levels in S1 cattle were associated with milk quality. Furthermore, ultra-high-resolution high-performance liquid chromatography with tandem MS analysis (UPLC-MS/MS) identified 86 and 105 differential metabolites in the serum and milk, respectively, and these were mainly involved in amino acid, carbohydrate, and lipid metabolism. S1 and S2/S3/S4 had significantly different metabolic patterns in the serum and milk, and more vitamin B-related metabolites were significantly higher identified in S1 than in multiparous cattle. Among 36 shared differential metabolites in the serum and milk, 10 and 7 metabolites were significantly and strongly correlated with differential physiological indices, respectively. The differential metabolites identified were enriched in key metabolic pathways, illustrating the metabolic characteristics of the serum and milk from Sanhe dairy cattle of different parities. L-phenylalanine, dehydroepiandrosterone, and linoleic acid in the milk and N-acetylornithine in the serum could be used as potential marker metabolites to distinguish between Sanhe dairy cattle with parities of 1-4. In addition, a metabolic map of the serum and milk from the three aspects of carbohydrates, amino acids, and lipids was created for the further analysis and exploration of their relationships. These results reveal significant variations in milk traits and metabolites across different parities of Sanhe dairy cattle, highlighting the influence of parity on the metabolic profiles and production performance. Tailored nutritional strategies based on parity-specific metabolic profiles are recommended to optimize milk production and quality in Sanhe cattle.
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Affiliation(s)
- Zixin Liu
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Aoyu Jiang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaokang Lv
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
- College of Animal Science, Anhui Science and Technology University, Bengbu 233100, China
| | - Dingkun Fan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
| | - Qingqing Chen
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
| | - Yicheng Wu
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanshe Zhou
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiliang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (Z.L.); (A.J.); (X.L.); (D.F.); (Q.C.); (Y.W.); (Z.T.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
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5
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Rajawat D, Ghildiyal K, Sonejita Nayak S, Sharma A, Parida S, Kumar S, Ghosh AK, Singh U, Sivalingam J, Bhushan B, Dutt T, Panigrahi M. Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle. Gene 2024; 901:148178. [PMID: 38242377 DOI: 10.1016/j.gene.2024.148178] [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: 09/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Pharmacology & Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shive Kumar
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - A K Ghosh
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Umesh Singh
- ICAR Central Institute for Research on Cattle, Meerut, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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Ahmad HI, Mahmood S, Hassan M, Sajid M, Ahmed I, Shokrollahi B, Shahzad AH, Abbas S, Raza S, Khan K, Muhammad SA, Fouad D, Ataya FS, Li Z. Genomic insights into Yak (Bos grunniens) adaptations for nutrient assimilation in high-altitudes. Sci Rep 2024; 14:5650. [PMID: 38453987 PMCID: PMC10920680 DOI: 10.1038/s41598-024-55712-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
High-altitude environments present formidable challenges for survival and reproduction, with organisms facing limited oxygen availability and scarce nutrient resources. The yak (Bos grunniens), indigenous to the Tibetan Plateau, has notably adapted to these extreme conditions. This study delves into the genomic basis of the yak's adaptation, focusing on the positive selection acting on genes involved in nutrient assimilation pathways. Employing techniques in comparative genomics and molecular evolutionary analyses, we selected genes in the yak that show signs of positive selection associated with nutrient metabolism, absorption, and transport. Our findings reveal specific genetic adaptations related to nutrient metabolism in harsh climatic conditions. Notably, genes involved in energy metabolism, oxygen transport, and thermoregulation exhibited signs of positive selection, suggesting their crucial role in the yak's successful colonization of high-altitude regions. The study also sheds light on the yak's immune system adaptations, emphasizing genes involved in response to various stresses prevalent at elevated altitudes. Insights into the yak's genomic makeup provide valuable information for understanding the broader implications of high-altitude adaptations in mammalian evolution. They may contribute to efforts in enhancing livestock resilience to environmental challenges.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Sammina Mahmood
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Mubashar Hassan
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Muhammad Sajid
- Department of Pathobiology, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Irfan Ahmed
- Department of Animal Nutrition, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Borhan Shokrollahi
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, 25340, Korea
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Kurdistan, Iran
| | - Abid Hussain Shahzad
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Shaista Abbas
- Department of Physiology and Biochemistry, College of Veterinary and Animal Sciences, Jhang, 35200, Pakistan
| | - Sanan Raza
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Komal Khan
- Department of Basic Sciences, Anatomy Section, College of Veterinary and Animal Sciences, Jhang, 35200, Pakistan
| | - Sayyed Aun Muhammad
- Department of Clinical Sciences, College of Veterinary and Animal Sciences (Sub campus UVAS, Lahore), Jhang, 35200, Pakistan
| | - Dalia Fouad
- Department of Zoology, College of Science, King Saud University, PO Box 22452, Riyadh, 11495, Saudi Arabia
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11495, Riyadh, Saudi Arabia
| | - Zhengtian Li
- Qujing Normal University, College of Biological Resource and Food Engineering, 655011, Yunnan, China.
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7
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Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
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Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
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Wen H, Johnson JS, Freitas PHF, Maskal JM, Gloria LS, Araujo AC, Pedrosa VB, Tiezzi F, Maltecca C, Huang Y, Schinckel AP, Brito LF. Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models. Genet Sel Evol 2023; 55:95. [PMID: 38129768 PMCID: PMC10734178 DOI: 10.1186/s12711-023-00868-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Automatic and continuous recording of vaginal temperature (TV) using wearable sensors causes minimal disruptions to animal behavior and can generate data that enable the evaluation of temporal body temperature variation under heat stress (HS) conditions. However, the genetic basis of TV in lactating sows from a longitudinal perspective is still unknown. The objectives of this study were to define statistical models and estimate genetic parameters for TV in lactating sows using random regression models, and identify genomic regions and candidate genes associated with HS indicators derived from automatically-recorded TV. RESULTS Heritability estimates for TV ranged from 0.14 to 0.20 over time (throughout the day and measurement period) and from 0.09 to 0.18 along environmental gradients (EG, - 3.5 to 2.2, which correspond to dew point values from 14.87 to 28.19 ˚C). Repeatability estimates of TV over time and along EG ranged from 0.57 to 0.66 and from 0.54 to 0.77, respectively. TV measured from 12h00 to 16h00 had moderately high estimates of heritability (0.20) and repeatability (0.64), indicating that this period might be the most suitable for recording TV for genetic selection purposes. Significant genotype-by-environment interactions (GxE) were observed and the moderately high estimates of genetic correlations between pairs of extreme EG indicate potential re-ranking of selection candidates across EG. Two important genomic regions on chromosomes 10 (59.370-59.998 Mb) and16 (21.548-21.966 Mb) were identified. These regions harbor the genes CDC123, CAMK1d, SEC61A2, and NUDT5 that are associated with immunity, protein transport, and energy metabolism. Across the four time-periods, respectively 12, 13, 16, and 10 associated genomic regions across 14 chromosomes were identified for TV. For the three EG classes, respectively 18, 15, and 14 associated genomic windows were identified for TV, respectively. Each time-period and EG class had uniquely enriched genes with identified specific biological functions, including regulation of the nervous system, metabolism and hormone production. CONCLUSIONS TV is a heritable trait with substantial additive genetic variation and represents a promising indicator trait to select pigs for improved heat tolerance. Moderate GxE for TV exist, indicating potential re-ranking of selection candidates across EG. TV is a highly polygenic trait regulated by a complex interplay of physiological, cellular and behavioral mechanisms.
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Affiliation(s)
- Hui Wen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Jay S Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, IN, USA
| | - Pedro H F Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Jacob M Maskal
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | | | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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9
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Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [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: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
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Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
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10
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Worku D, Hussen J, De Matteis G, Schusser B, Alhussien MN. Candidate genes associated with heat stress and breeding strategies to relieve its effects in dairy cattle: a deeper insight into the genetic architecture and immune response to heat stress. Front Vet Sci 2023; 10:1151241. [PMID: 37771947 PMCID: PMC10527375 DOI: 10.3389/fvets.2023.1151241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023] Open
Abstract
The need for food products of animal origin is increasing worldwide. Satisfying these needs in a way that has minimal impact on the environment requires cutting-edge technologies and techniques to enhance the genetic quality of cattle. Heat stress (HS), in particular, is affecting dairy cattle with increasing frequency and severity. As future climatic challenges become more evident, identifying dairy cows that are more tolerant to HS will be important for breeding dairy herds that are better adapted to future environmental conditions and for supporting the sustainability of dairy farming. While research into the genetics of HS in the context of the effect of global warming on dairy cattle is gaining momentum, the specific genomic regions involved in heat tolerance are still not well documented. Advances in omics information, QTL mapping, transcriptome profiling and genome-wide association studies (GWAS) have identified genomic regions and variants associated with tolerance to HS. Such studies could provide deeper insights into the genetic basis for response to HS and make an important contribution to future breeding for heat tolerance, which will help to offset the adverse effects of HS in dairy cattle. Overall, there is a great interest in identifying candidate genes and the proportion of genetic variation associated with heat tolerance in dairy cattle, and this area of research is currently very active worldwide. This review provides comprehensive information pertaining to some of the notable recent studies on the genetic architecture of HS in dairy cattle, with particular emphasis on the identified candidate genes associated with heat tolerance in dairy cattle. Since effective breeding programs require optimal knowledge of the impaired immunity and associated health complications caused by HS, the underlying mechanisms by which HS modulates the immune response and renders animals susceptible to various health disorders are explained. In addition, future breeding strategies to relieve HS in dairy cattle and improve their welfare while maintaining milk production are discussed.
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Affiliation(s)
- Destaw Worku
- Department of Animal Science, College of Agriculture, Food and Climate Sciences, Injibara University, Injibara, Ethiopia
| | - Jamal Hussen
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Giovanna De Matteis
- Council for Agricultural Research and Economics, CREA Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Benjamin Schusser
- Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mohanned Naif Alhussien
- Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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11
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes. Animals (Basel) 2023; 13:2351. [PMID: 37508128 PMCID: PMC10376189 DOI: 10.3390/ani13142351] [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: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
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12
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Osei-Amponsah R, Dunshea FR, Leury BJ, Abhijith A, Chauhan SS. Association of Phenotypic Markers of Heat Tolerance with Australian Genomic Estimated Breeding Values and Dairy Cattle Selection Indices. Animals (Basel) 2023; 13:2259. [PMID: 37508037 PMCID: PMC10376013 DOI: 10.3390/ani13142259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/24/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Dairy cattle predicted by genomic breeding values to be heat tolerant are known to have less milk production decline and lower core body temperature increases in response to elevated temperatures. In a study conducted at the University of Melbourne's Dookie Robotic Dairy Farm during summer, we identified the 20 most heat-susceptible and heat-tolerant cows in a herd of 150 Holstein Friesian lactating cows based on their phenotypic responses (changes in respiration rate, surface body temperature, panting score, and milk production). Hair samples were collected from the tip of the cows' tails following standard genotyping protocols. The results indicated variation in feed saved and HT genomic estimated breeding values (GEBVs) (p ≤ 0.05) across age, indicating a potential for their selection. As expected, the thermotolerant group had higher GEBVs for HT and feed saved but lower values for milk production. In general, younger cows had superior GEBVs for the Balanced Performance Index (BPI) and Australian Selection Index (ASI), whilst older cows were superior in fertility, feed saved (FS), and HT. This study demonstrated highly significant (p ≤ 0.001) negative correlations (-0.28 to -0.74) between HT and GEBVs for current Australian dairy cattle selection indices (BPI, ASI, HWI) and significant (p ≤ 0.05) positive correlations between HT and GEBVs for traits like FS (0.45) and fertility (0.25). Genomic selection for HT will help improve cow efficiency and sustainability of dairy production under hot summer conditions. However, a more extensive study involving more lactating cows across multiple farms is recommended to confirm the associations between the phenotypic predictors of HT and GEBVs.
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Affiliation(s)
- Richard Osei-Amponsah
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne 3010, Australia
- Department of Animal Science, School of Agriculture, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 226, Ghana
| | - Frank R Dunshea
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne 3010, Australia
- Faculty of Biological Sciences, The University of Leeds, Leeds LS2 9JT, UK
| | - Brian J Leury
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne 3010, Australia
| | - Archana Abhijith
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne 3010, Australia
| | - Surinder S Chauhan
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Melbourne 3010, Australia
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Habimana V, Nguluma AS, Nziku ZC, Ekine-Dzivenu CC, Morota G, Mrode R, Chenyambuga SW. Heat stress effects on milk yield traits and metabolites and mitigation strategies for dairy cattle breeds reared in tropical and sub-tropical countries. Front Vet Sci 2023; 10:1121499. [PMID: 37483284 PMCID: PMC10361820 DOI: 10.3389/fvets.2023.1121499] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Heat stress is an important problem for dairy industry in many parts of the world owing to its adverse effects on productivity and profitability. Heat stress in dairy cattle is caused by an increase in core body temperature, which affects the fat production in the mammary gland. It reduces milk yield, dry matter intake, and alters the milk composition, such as fat, protein, lactose, and solids-not-fats percentages among others. Understanding the biological mechanisms of climatic adaptation, identifying and exploring signatures of selection, genomic diversity and identification of candidate genes for heat tolerance within indicine and taurine dairy breeds is an important progression toward breeding better dairy cattle adapted to changing climatic conditions of the tropics. Identifying breeds that are heat tolerant and their use in genetic improvement programs is crucial for improving dairy cattle productivity and profitability in the tropics. Genetic improvement for heat tolerance requires availability of genetic parameters, but these genetic parameters are currently missing in many tropical countries. In this article, we reviewed the HS effects on dairy cattle with regard to (1) physiological parameters; (2) milk yield and composition traits; and (3) milk and blood metabolites for dairy cattle reared in tropical countries. In addition, mitigation strategies such as physical modification of environment, nutritional, and genetic development of heat tolerant dairy cattle to prevent the adverse effects of HS on dairy cattle are discussed. In tropical climates, a more and cost-effective strategy to overcome HS effects is to genetically select more adaptable and heat tolerant breeds, use of crossbred animals for milk production, i.e., crosses between indicine breeds such as Gir, white fulani, N'Dama, Sahiwal or Boran to taurine breeds such as Holstein-Friesian, Jersey or Brown Swiss. The results of this review will contribute to policy formulations with regard to strategies for mitigating the effects of HS on dairy cattle in tropical countries.
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Affiliation(s)
- Vincent Habimana
- Department of Animal, Aquaculture, and Range Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Athumani Shabani Nguluma
- Department of Animal, Aquaculture, and Range Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | | | - Gota Morota
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Raphael Mrode
- International Livestock Research Institute (ILRI), Nairobi, Kenya
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14
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Huang N, Zhao L, Wang J, Jiang Q, Ju Z, Wang X, Yang C, Gao Y, Wei X, Zhang Y, Xiao Y, Liu W, Lu S, Huang J. Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate. J Anim Sci 2023; 101:skad006. [PMID: 36617259 PMCID: PMC9985157 DOI: 10.1093/jas/skad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 01/06/2023] [Indexed: 01/09/2023] Open
Abstract
Cold climate shapes the genome of animals and drives them to carry sufficient genetic variations to adapt to changes in temperature. However, limited information is available about the genome-wide pattern of adaptations to cold environments in cattle. In the present study, we used 777K SNP genotyping (15 Chinese cattle breeds, 198 individuals) and whole genome resequencing data (54 cattle breeds of the world, 432 individuals) to disentangle divergent selection signatures, especially between the cold-adapted (annual average temperature of habitat, 6.24 °C to 10.3 °C) and heat-adapted (20.2 °C to 24.73 °C) Chinese native cattle breeds. Genomic analyses revealed a set of candidate genes (e.g., UQCR11, DNAJC18, EGR1, and STING1) were functionally associated with thermogenesis and energy metabolism. We also characterized the adaptive loci of cattle exposed to cold temperatures. Our study finds new candidate genes and provides new insights into adaptations to cold climates in cattle.
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Affiliation(s)
- Ning Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, P. R. China
| | - Lihong Zhao
- Informatic Center, SAAMS, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Jinpeng Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Qiang Jiang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Zhihua Ju
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Xiuge Wang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Chunhong Yang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yaping Gao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiaochao Wei
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yaran Zhang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Yao Xiao
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Wenhao Liu
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
| | - Shaoxiong Lu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, P. R. China
| | - Jinming Huang
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Jinan, P. R. China
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15
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Kaur U, Malacco VMR, Bai H, Price TP, Datta A, Xin L, Sen S, Nawrocki RA, Chiu G, Sundaram S, Min BC, Daniels KM, White RR, Donkin SS, Brito LF, Voyles RM. Invited review: integration of technologies and systems for precision animal agriculture-a case study on precision dairy farming. J Anim Sci 2023; 101:skad206. [PMID: 37335911 PMCID: PMC10370899 DOI: 10.1093/jas/skad206] [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: 02/24/2023] [Accepted: 06/17/2023] [Indexed: 06/21/2023] Open
Abstract
Precision livestock farming (PLF) offers a strategic solution to enhance the management capacity of large animal groups, while simultaneously improving profitability, efficiency, and minimizing environmental impacts associated with livestock production systems. Additionally, PLF contributes to optimizing the ability to manage and monitor animal welfare while providing solutions to global grand challenges posed by the growing demand for animal products and ensuring global food security. By enabling a return to the "per animal" approach by harnessing technological advancements, PLF enables cost-effective, individualized care for animals through enhanced monitoring and control capabilities within complex farming systems. Meeting the nutritional requirements of a global population exponentially approaching ten billion people will likely require the density of animal proteins for decades to come. The development and application of digital technologies are critical to facilitate the responsible and sustainable intensification of livestock production over the next several decades to maximize the potential benefits of PLF. Real-time continuous monitoring of each animal is expected to enable more precise and accurate tracking and management of health and well-being. Importantly, the digitalization of agriculture is expected to provide collateral benefits of ensuring auditability in value chains while assuaging concerns associated with labor shortages. Despite notable advances in PLF technology adoption, a number of critical concerns currently limit the viability of these state-of-the-art technologies. The potential benefits of PLF for livestock management systems which are enabled by autonomous continuous monitoring and environmental control can be rapidly enhanced through an Internet of Things approach to monitoring and (where appropriate) closed-loop management. In this paper, we analyze the multilayered network of sensors, actuators, communication, networking, and analytics currently used in PLF, focusing on dairy farming as an illustrative example. We explore the current state-of-the-art, identify key shortcomings, and propose potential solutions to bridge the gap between technology and animal agriculture. Additionally, we examine the potential implications of advancements in communication, robotics, and artificial intelligence on the health, security, and welfare of animals.
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Affiliation(s)
- Upinder Kaur
- School of Engineering Technology, Purdue University, West Lafayette, IN, 47907, USA
| | - Victor M R Malacco
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Huiwen Bai
- School of Engineering Technology, Purdue University, West Lafayette, IN, 47907, USA
| | - Tanner P Price
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Arunashish Datta
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Lei Xin
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Shreyas Sen
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Robert A Nawrocki
- School of Engineering Technology, Purdue University, West Lafayette, IN, 47907, USA
| | - George Chiu
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Shreyas Sundaram
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Byung-Cheol Min
- Department of Computer and Information Technology, West Lafayette, IN, 47907, USA
| | - Kristy M Daniels
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Robin R White
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Shawn S Donkin
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Richard M Voyles
- School of Engineering Technology, Purdue University, West Lafayette, IN, 47907, USA
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16
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Elayadeth-Meethal M, Keambou Tiambo C, Poonkuzhi Naseef P, Saheer Kuruniyan M, K Maloney S. The profile of HSPA1A gene expression and its association with heat tolerance in crossbred cattle and the tropically adapted dwarf Vechur and Kasaragod. J Therm Biol 2023; 111:103426. [PMID: 36585090 DOI: 10.1016/j.jtherbio.2022.103426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Certain livestock breeds are adapted to hot and humid environments, and these breeds have genetics that could be useful in a changing climate. The expression of several genes has been identified as a useful biomarker for heat stress. In this study, the responses to heat exposure of heat-tolerant Vechur and Kasaragod cattle found in Kerala state in India (also known as dwarf Bos taurus indicus) were compared to crossbred cattle (crosses of Bos t. taurus with Bos t. indicus). At various time points during heat exposure, rectal temperature and the expression of HSPA1A were determined, and the relationship between them was characterized. We characterized HSPA1A mRNA in Vechur cattle and performed molecular clock analysis. The expression of HSPA1A between the lineages and at different temperature humidity index (THI) was significant. There were significant differences between the expression profiles of HSPA1A in Kasaragod and crossbred (p < 0.01) and Vechur and crossbred (p < 0.01) cattle, but no significant difference in expression was observed between Vechur and Kasaragod cattle. The genetic distance between Vechur, B. grunniens, B. t. taurus, and B. t. indicus was 0.0233, 0.0059, and 0.007, respectively. The genetic distance between Vechur and the Indian dwarf breed Malnad Gidda was 0.0081. A molecular clock analysis revealed divergent adaptive evolution of Vechur cattle to B. t. taurus, with adaptations to the high temperatures and humidity that are prevalent in their breeding tract in Kerala, India. These results could also prove useful in selecting heat-tolerant animals using HSPA1A as a marker.
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Affiliation(s)
- Muhammed Elayadeth-Meethal
- Department of Animal Breeding and Genetics, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad, Kerala, India.
| | - Christian Keambou Tiambo
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya.
| | | | - Mohamed Saheer Kuruniyan
- Department of Dental Technology, College of Applied Medical Sciences, King Khalid University, Abha, 61421, Saudi Arabia.
| | - Shane K Maloney
- School of Human Sciences, University of Western Australia, Crawley, Australia.
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17
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Assessing Genetic Diversity and Searching for Selection Signatures by Comparison between the Indigenous Livni and Duroc Breeds in Local Livestock of the Central Region of Russia. DIVERSITY 2022. [DOI: 10.3390/d14100859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Indigenous pig breeds are mainly associated with the adaptive capacity that is necessary to respond adequately to climate change, food security, and livelihood needs, and natural resources conservation. Livni pigs are an indigenous fat-type breed farmed in a single farm in the Orel region and located in the Central European part of the Russian Federation. To determine the genomic regions and genes that are affected by artificial selection, we conducted the comparative study of two pig breeds with different breeding histories and breeding objectives, i.e., the native fat-type Livni and meat-type Duroc breeds using the Porcine GGP HD BeadChip, which contains ~80,000 SNPs. To check the Livni pigs for possible admixture, the Landrace and the Large White breeds were included into the study of genetic diversity as these breeds participated in the formation of the Livni pigs. We observed the highest level of genetic diversity in Livni pigs compared to commercial breeds (UHE = 0.409 vs. 0.319–0.359, p < 0.001; AR = 1.995 vs. 1.894–1.964, p < 0.001). A slight excess of heterozygotes was found in all of the breeds. We identified 291 candidate genes, which were localized within the regions under putative selection, including 22 and 228 genes, which were specific for Livni and Duroc breeds, respectively, and 41 genes common for both breeds. A detailed analysis of the molecular functions identified the genes, which were related to the formation of meat and fat traits, and adaptation to environmental stress, including extreme temperatures, which were different between breeds. Our research results are useful for conservation and sustainable breeding of Livni breed, which shows a high level of genetic diversity. This makes Livni one of the valuable national pig genetic resources.
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18
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Paim TDP, Hay EH, Brito LF. Editorial: Genetic diversity and selection signatures in composite breeds. Front Genet 2022; 13:992609. [PMID: 36061174 PMCID: PMC9429830 DOI: 10.3389/fgene.2022.992609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Tiago do Prado Paim
- Instituto Federal Goiano, Rio Verde, GO, Brazil
- *Correspondence: Tiago do Prado Paim,
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, United States
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Vahedi SM, Salek Ardestani S, Pahlevan Afshari K, Ghoreishifar SM, Moghaddaszadeh-Ahrabi S, Banabazi MH, Brito LF. Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle. Front Genet 2022; 13:844653. [PMID: 35719394 PMCID: PMC9201998 DOI: 10.3389/fgene.2022.844653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic introgression from interbreeding hybridization of European Bos taurus taurus (EBT) and Indian Bos taurus indicus (IBI) cattle breeds have been widely used to combine the climatic resilience of the IBI cattle and the higher productivity of EBT when forming new composite beef cattle (CB) populations. The subsequent breeding strategies have shifted their initial genomic compositions. To uncover population structure, signatures of selection, and potential introgression events in CB populations, high-density genotypes [containing 492,954 single nucleotide polymorphisms (SNPs) after the quality control] of 486 individuals from 15 cattle breeds, including EBT, IBI, and CB populations, along with two Bos grunniens genotypes as outgroup were used in this study. Then, in-depth population genetics analyses were performed for three CB breeds of Beefmaster, Brangus, and Santa Gertrudis. Neighbor-joining, principal components, and admixture analyses confirmed the historical introgression of EBT and IBI haplotypes into CB breeds. The fdM statistics revealed that only 12.9% of CB populations' genetic components are of IBI origin. The results of signatures of selection analysis indicated different patterns of selection signals in the three CB breeds with primary pressure on pathways involved in protein processing and stress response in Beefmaster, cell proliferation regulation and immune response in Brangus, and amino acids and glucose metabolisms in Santa Gertrudis. An average of >90% of genomic regions underlying selection signatures were of EBT origin in the studied CB populations. Investigating the CB breeds' genome allows the estimation of EBT and IBI ancestral proportions and the locations within the genome where either taurine or indicine origin alleles are under selective pressure. Such findings highlight various opportunities to control the selection process more efficiently and explore complementarity at the genomic level in CB populations.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kian Pahlevan Afshari
- Department of Animal Sciences, Islamic Azad University, Varamin-Pishva Branch, Varamin, Iran
| | - Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Mohammad Hossein Banabazi
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Luiz Fernando Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Cheruiyot EK, Haile-Mariam M, Cocks BG, Pryce JE. Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions. Front Genet 2022; 13:894067. [PMID: 35769985 PMCID: PMC9234448 DOI: 10.3389/fgene.2022.894067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g., solar radiation). In this article, we focus on evidence from recent studies in Australia that leveraged large a dataset [∼40,000 animals with phenotypes and 15 million whole-genome sequence variants] to elucidate the genetic basis of thermal stress as a critical part of the strategy to breed cattle adapted to warmer environments. Genotype-by-environment interaction (i.e., G × E) due to temperature and humidity variation is increasing, meaning animals are becoming less adapted (i.e., more sensitive) to changing environments. There are opportunities to reverse this trend and accelerate adaptation to warming climate by 1) selecting robust or heat-resilient animals and 2) including resilience indicators in breeding goals. Candidate causal variants related to the nervous system and metabolic functions are relevant for heat tolerance and, therefore, key for improving this trait. This could include adding these variants in the custom SNP panels used for routine genomic evaluations or as the basis to design specific agonist or antagonist compounds for lowering core body temperature under heat stress conditions. Indeed, it was encouraging to see that adding prioritized functionally relevant variants into the 50k SNP panel (i.e., the industry panel used for genomic evaluation in Australia) increased the prediction accuracy of heat tolerance by up to 10% units. This gain in accuracy is critical because genetic improvement has a linear relationship with prediction accuracy. Overall, while this article used data mainly from Australia, this could benefit other countries that aim to develop breeding values for heat tolerance, considering that the warming climate is becoming a topical issue worldwide.
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Affiliation(s)
- Evans K. Cheruiyot
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Mekonnen Haile-Mariam
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
- *Correspondence: Mekonnen Haile-Mariam,
| | - Benjamin G. Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Jennie E. Pryce
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
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21
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Li G, Tang J, Huang J, Jiang Y, Fan Y, Wang X, Ren J. Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds. Front Genet 2022; 13:774196. [PMID: 35559012 PMCID: PMC9086400 DOI: 10.3389/fgene.2022.774196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
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Affiliation(s)
- Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.,Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Jinyan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang, China
| | - Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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22
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Narayan E, Sawyer G, Fox D, Smith R, Tilbrook A. Interplay Between Stress and Reproduction: Novel Epigenetic Markers in Response to Shearing Patterns in Australian Merino Sheep (Ovis aries). Front Vet Sci 2022; 9:830450. [PMID: 35464367 PMCID: PMC9021797 DOI: 10.3389/fvets.2022.830450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/15/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, we determined the effect(s) of early shearing on Australian Merino ewes (Ovis aries) and their lambs. To test this research question, we used a suite of field and laboratory methods including GPS collars, wool cortisol, and epigenetic change between ewes and lambs identified using Illumina NovaSeq RRBS. Once shorn ewes (n = 24) were kept on their full fleece throughout the entire gestation period, whereas twice (early) shorn ewes (n = 24) had their wool shorn pre-joining. Top-knot wool sample was taken from ewes during pre-joining, day 50 (mid-gestation), and day 90 (late gestation) for laboratory analysis. Ewes were pregnancy scanned at mid-gestation to determine whether they were early or late parturition (this confirmation is provided by the pregnancy scanner based on fetus size). Top-knot wool sample was also taken from the lambs at weaning for hormone and wool quality testing. Ear tissue was taken from ewes at day 50 (mid-gestation) and from lambs at lamb marking for DNA analysis. Results showed that twice or early shorn ewes grazed 10% higher and maintained stronger body condition than once shorn ewes. Wool cortisol levels were also significantly lower in the early shorn ewes between mid- and late gestation. Lambs bred from twice shorn ewes had on average better visual wool quality parameters in terms of micron, spin finesses, and curvature. For the DNA methylation results, when comparing a group of once sheared with twice sheared ewes, we have discovered one locus (Chr20:50404014) that was significantly differentially methylated [False Discovery Rate (FDR) = 0.005]. This locus is upstream of a protein-coding gene (ENSOARG00000002778.1), which shows similarities to the forkhead box C1 (FOXC1) mRNA using BLAST searches. To further our understanding of the potential interaction between pregnancy status and shearing frequency of the ewes, we performed further differential methylation analysis using a combination of shearing treatment and pregnancy scanning status. The comparisons (1) late pregnancy vs. early pregnancy for ewes with one shearing treatment and (2) late pregnancy vs. early pregnancy for sheep with two shearing treatments were carried out to identify associations between loci and pregnancy duration for sheep with either one or two shearing events. We discovered that 36 gene loci were significantly modulated either between different shearing treatments or late vs. early pregnancy status of ewes. This result suggests that maternal pregnancy and nutritional status during gestation influence DNA methylation. We further investigated DNA methylation in lambs and identified 16 annotated gene loci that showed epigenetic modulation as a result of being born from an early or late stage pregnancy. From the genomics data, we pointed out that ewes go through epigenetic modifications during gestation, and there is a degree of intra-individual variation in the reproductive performance of ewes, which could be due to combination of intrinsic (genetic and physiological) and extrinsic (management and climatic) factors. Collectively, this research provides novel dataset combining physiological, molecular epigenetics, and digital tracking indices that advances our understanding of how Merino ewes respond to shearing frequency, and this information could guide further research on Merino sheep breeding and welfare.
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Affiliation(s)
- Edward Narayan
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St.Lucia, QLD, Australia
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, QLD, Australia
- *Correspondence: Edward Narayan
| | - Gregory Sawyer
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Dylan Fox
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, St.Lucia, QLD, Australia
| | - Ryan Smith
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Alan Tilbrook
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St.Lucia, QLD, Australia
- School of Veterinary Science, Faculty of Science, The University of Queensland, St.Lucia, QLD, Australia
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23
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Wang X, Li G, Ruan D, Zhuang Z, Ding R, Quan J, Wang S, Jiang Y, Huang J, Gu T, Hong L, Zheng E, Li Z, Cai G, Wu Z, Yang J. Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines. Front Vet Sci 2022; 9:832633. [PMID: 35350434 PMCID: PMC8957889 DOI: 10.3389/fvets.2022.832633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/24/2022] [Indexed: 12/29/2022] Open
Abstract
Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.
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Affiliation(s)
- Xiaopeng Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Guixin Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Shiyuan Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jinyan Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
- *Correspondence: Zhenfang Wu
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
- Jie Yang
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24
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Gross JJ. Limiting factors for milk production in dairy cows: perspectives from physiology and nutrition. J Anim Sci 2022; 100:6528443. [PMID: 35157044 PMCID: PMC8919814 DOI: 10.1093/jas/skac044] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Milk production in dairy cows increases worldwide since many decades. With rising milk yields, however, potential limiting factors are increasingly discussed. Particularly, the availability of glucose and amino acids is crucial to maintain milk production as well as animal health. Limitations arise from feed sources, the rumen and digestive tract, tissue mobilization, intermediary metabolism and transport, and the uptake of circulating nutrients by the lactating mammary gland. The limiting character can change depending on the stage of lactation. Although physiological boundaries are prevalent throughout the gestation-lactation cycle, limitations are aggravated during the early lactation period when high milk production is accompanied by low feed intake and high mobilization of body reserves. The knowledge about physiological constraints may help to improve animal health and make milk production more sustainably. The scope of this review is to address contemporary factors related to production limits in dairy cows from a physiological perspective. Besides acknowledged physiological constraints, selected environmental and management-related factors affecting animal performance and physiology will be discussed. Potential solutions and strategies to overcome or to alleviate these constraints can only be presented briefly. Instead, they are thought to address existing shortcomings and to identify possibilities for optimization. Despite a scientific-based view on physiological limits, we should keep in mind that only healthy animals could use their genetic capacity and produce high amounts of milk.
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Affiliation(s)
- Josef J Gross
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, CH-3012 Bern, Switzerland,Corresponding author:
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25
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Kour A, Niranjan SK, Malayaperumal M, Surati U, Pukhrambam M, Sivalingam J, Kumar A, Sarkar M. Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak. Genes (Basel) 2022; 13:genes13020254. [PMID: 35205299 PMCID: PMC8872319 DOI: 10.3390/genes13020254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.
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Affiliation(s)
- Aneet Kour
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
- Correspondence:
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mohan Malayaperumal
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Utsav Surati
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Martina Pukhrambam
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mihir Sarkar
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
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26
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Cesarani A, Gaspa G, Correddu F, Dimauro C, Macciotta NPP. Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity. J Anim Breed Genet 2022; 139:292-306. [PMID: 34984736 DOI: 10.1111/jbg.12666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 02/04/2023]
Abstract
Natural adaptation and artificial selection have shaped the genome of modern livestock breeds. Among SNP-based metrics that are used to detect signatures of selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 Sarda breed ewes farmed at different levels of altitude are analysed to investigate the effect of the environment on the patterns of homozygosity. A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by both the altitude and temperature of the place where the flock was located. The highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest one for mountain. A total of 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. These markers mapped in eight chromosomes and they clustered into 17 ROH islands, where 80 candidate genes were mapped. Results of this study highlighted differences in the ROH distribution and features among sheep farmed in flocks located at different levels of altitude, confirming the role of environmental adaptability in shaping the genome of this breed.
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Affiliation(s)
- Alberto Cesarani
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Giustino Gaspa
- Department of Agricultural, Forestry and Alimentary Sciences, University of Torino, Grugliasco, Italy
| | - Fabio Correddu
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
| | - Corrado Dimauro
- Department of Agricultural Sciences, University of Sassari, Sassari, Italy
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27
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Trujano-Chavez MZ, Sánchez-Ramos R, Pérez-Rodríguez P, Ruíz-Flores A. Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle. Vet Sci 2021; 8:vetsci8120329. [PMID: 34941856 PMCID: PMC8707377 DOI: 10.3390/vetsci8120329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/05/2021] [Accepted: 12/12/2021] [Indexed: 11/18/2022] Open
Abstract
Mastitis is a disease that causes significant economic losses, since resistance to mastitis is a difficult trait to be improved due to its multifactorial occurrence. Therefore, our objective was to characterize a Mexican Braunvieh cattle population for genetic resistance and susceptibility to mastitis. We used 66 SNP markers for 45 candidate genes in 150 animals. The average heterozygosity was 0.445 ± 0.076, a value higher than those reported for some European breeds. The inbreeding coefficient was slightly negative for resistance to subclinical (−0.058 ± 0.055) and clinical (−0.034 ± 0.076) mastitis, possibly due to low selection for the immunological candidate genes that influence these traits. The genotypic profiles for the candidate loci per K-means group were obtained, as well as the group distribution through the graphics of the principal component analysis. The genotypic profiles showed high genetic diversity among groups. Resistance to clinical mastitis had the lowest presence of the heterozygous genotypes. Although the percentage of highly inbred animals (>50%) is up to 13.3%, there are highly heterozygous groups in terms of the studied traits, a favorable indicator of the presence of genetic diversity. The results of this study constitute evidence of the genetic potential of the Mexican Braunvieh population to improve mastitis-related traits.
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Affiliation(s)
- Mitzilin Zuleica Trujano-Chavez
- Posgrado en Producción Animal, Universidad Autónoma Chapingo, Carretera Federal México-Texcoco Km 38.5, Texcoco 56227, Estado de México, Mexico;
| | - Reyna Sánchez-Ramos
- Recursos Genéticos y Productividad, Colegio de Postgraduados, Carretera Federal México-Texcoco Km 36.5, Texcoco 56230, Estado de México, Mexico;
| | - Paulino Pérez-Rodríguez
- Socio Economía Estadística e Informática-Estadística, Colegio de Postgraduados, Carretera Federal México-Texcoco Km 36.5, Texcoco 56230, Estado de México, Mexico;
| | - Agustín Ruíz-Flores
- Posgrado en Producción Animal, Universidad Autónoma Chapingo, Carretera Federal México-Texcoco Km 38.5, Texcoco 56227, Estado de México, Mexico;
- Correspondence: ; Tel.: +52-595-952-1621
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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Ramón M, Carabaño MJ, Díaz C, Kapsona VV, Banos G, Sánchez-Molano E. Breeding Strategies for Weather Resilience in Small Ruminants in Atlantic and Mediterranean Climates. Front Genet 2021; 12:692121. [PMID: 34539734 PMCID: PMC8446191 DOI: 10.3389/fgene.2021.692121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Many efforts are being made to cope with negative consequences of climate change (CC) on livestock. Among them, selective breeding of resilient animals to CC is presented as an opportunity to maintain high levels of performance regardless of variation in weather. In the present work, we proposed a set of breeding strategies to improve weather resilience in dairy goats raised in north-western European Atlantic conditions and dairy sheep raised in Mediterranean conditions while improving production efficiency at the same time. Breeding strategies differed in the selection emphasis placed on resilience traits, ranging from 0 to 40% in the index. Simulations were carried out mimicking real breeding programs including: milk yield, length of productive life, age at first kidding and mastitis incidence in dairy goats and milk, fat and protein yields, and fertility for dairy sheep. Considering the particular climatic conditions in the two regions, the predicted future climate scenarios, and genetic correlations among breeding objectives, resilience was defined as stability to weather changes for dairy goats and as the ability to improve performance under heat stress for dairy sheep. A strategy giving a selection weight of 10 and 20% for goat and sheep resilience, respectively, resulted in the best overall genetic response in terms of both, production and resilience ability. Not considering resilience in breeding programs could lead to a major production loss in future climate scenarios, whereas putting too much emphasis on resilience would result in a limited progress in milk production.
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Affiliation(s)
- Manuel Ramón
- Centro Regional de Selección y Reproducción Animal, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal de Castilla-La Mancha, Valdepeñas, Spain
| | - María Jesús Carabaño
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agroalimentaria, Madrid, Spain
| | - Clara Díaz
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agroalimentaria, Madrid, Spain
| | - Vanessa Varvara Kapsona
- Scotland's Rural College, Easter Bush Campus - University of Edinburgh, Midlothian, United Kingdom
| | - Georgios Banos
- Scotland's Rural College, Easter Bush Campus - University of Edinburgh, Midlothian, United Kingdom
| | - Enrique Sánchez-Molano
- The Roslin Institute, Easter Bush Campus - University of Edinburgh, Midlothian, United Kingdom
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Igoshin A, Yudin N, Aitnazarov R, Yurchenko AA, Larkin DM. Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations. Life (Basel) 2021; 11:959. [PMID: 34575108 PMCID: PMC8467296 DOI: 10.3390/life11090959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/30/2022] Open
Abstract
Despite the economic importance of creating cold resilient cattle breeds, our knowledge of the genetic basis of adaptation to cold environments in cattle is still scarce compared to information on other economically important traits. Herein, using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress combined with the existing SNP (single nucleotide polymorphism) functional annotations, we report chromosomal regions and candidate SNPs controlling body temperature in the Siberian cattle populations. The SNP ranking procedure based on regional FST calculations, functional annotations, and the allele frequency difference between cold-tolerant and cold-sensitive groups of animals pointed to multiple candidate genes. Among these, GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2 were previously related to thermal adaptations in cattle. Other genes, for example KMT2D and SNRPA1, are known to be related to thermogenesis in mice and cold adaptation in common carp, respectively. This work could be useful for cattle breeding strategies in countries with harsh climates, including the Russian Federation.
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Affiliation(s)
- Alexander Igoshin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Nikolay Yudin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ruslan Aitnazarov
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Andrey A. Yurchenko
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
| | - Denis M. Larkin
- Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.); (N.Y.); (R.A.); (A.A.Y.)
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
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Hu L, Brito LF, Abbas Z, Sammad A, Kang L, Wang D, Wu H, Liu A, Qi G, Zhao M, Wang Y, Xu Q. Investigating the Short-Term Effects of Cold Stress on Metabolite Responses and Metabolic Pathways in Inner-Mongolia Sanhe Cattle. Animals (Basel) 2021; 11:ani11092493. [PMID: 34573458 PMCID: PMC8469163 DOI: 10.3390/ani11092493] [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: 07/20/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Cold stress is a major environmental stressor affecting cattle performance in temperate regions, which causes impaired welfare and economic losses to cattle producers. The identification of biological mechanisms associated with cold stress response is paramount for developing effective mitigation strategies, such as genomic selection. In this study, we assessed the short-term effects of hyper-cold stress on metabolite responses and metabolic pathways in the serum of Inner-Mongolia Sanhe cattle. Moreover, 19 differential metabolites were found, mainly involved in amino acid metabolism. A further integration of metabolome results and gene expression highlighted the regulation of metabolic changes and related pathways in severe cold exposure, such as “aminoacyl-tRNA biosynthesis” and “valine, leucine, and isoleucine degradation”. In summary, we presented new insights on the short-term effects of severe cold stress as well as metabolites and metabolic pathways associated with cold stress response in Inner-Mongolia Sanhe cattle. Abstract Inner-Mongolia Sanhe cattle are well-adapted to low-temperature conditions, but the metabolic mechanisms underlying their climatic resilience are still unknown. Based on the 1H Nuclear Magnetic Resonance platform, 41 metabolites were identified and quantified in the serum of 10 heifers under thermal neutrality (5 °C), and subsequent exposure to hyper-cold temperature (−32 °C) for 3 h. Subsequently, 28 metabolites were pre-filtrated, and they provided better performance in multivariate analysis than that of using 41 metabolites. This indicated the need for pre-filtering of the metabolome data in a paired experimental design. In response to the cold exposure challenge, 19 metabolites associated with cold stress response were identified, mainly enriched in “aminoacyl-tRNA biosynthesis” and “valine, leucine, and isoleucine degradation”. A further integration of metabolome and gene expression highlighted the functional roles of the DLD (dihydrolipoamide dehydrogenase), WARS (tryptophanyl-tRNA synthetase), and RARS (arginyl-tRNA synthetase) genes in metabolic pathways of valine and leucine. Furthermore, the essential regulations of SLC30A6 (solute carrier family 30 (zinc transporter), member 6) in metabolic transportation for propionate, acetate, valine, and leucine under severe cold exposure were observed. Our findings presented a comprehensive characterization of the serum metabolome of Inner-Mongolia Sanhe cattle, and contributed to a better understanding of the crucial roles of regulations in metabolites and metabolic pathways during cold stress events in cattle.
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Affiliation(s)
- Lirong Hu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China; (L.H.); (Z.A.); (L.K.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA;
| | - Zaheer Abbas
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China; (L.H.); (Z.A.); (L.K.)
| | - Abdul Sammad
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
| | - Ling Kang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China; (L.H.); (Z.A.); (L.K.)
| | - Dongsheng Wang
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Hulunbuir 021012, China; (D.W.); (H.W.); (A.L.); (G.Q.); (M.Z.)
| | - Hongjun Wu
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Hulunbuir 021012, China; (D.W.); (H.W.); (A.L.); (G.Q.); (M.Z.)
| | - Airong Liu
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Hulunbuir 021012, China; (D.W.); (H.W.); (A.L.); (G.Q.); (M.Z.)
| | - Guiqiang Qi
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Hulunbuir 021012, China; (D.W.); (H.W.); (A.L.); (G.Q.); (M.Z.)
| | - Man Zhao
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Hulunbuir 021012, China; (D.W.); (H.W.); (A.L.); (G.Q.); (M.Z.)
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
- Correspondence: (Y.W.); (Q.X.)
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China; (L.H.); (Z.A.); (L.K.)
- Correspondence: (Y.W.); (Q.X.)
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Cheruiyot EK, Haile-Mariam M, Cocks BG, MacLeod IM, Xiang R, Pryce JE. New loci and neuronal pathways for resilience to heat stress in cattle. Sci Rep 2021; 11:16619. [PMID: 34404823 PMCID: PMC8371109 DOI: 10.1038/s41598-021-95816-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
While understanding the genetic basis of heat tolerance is crucial in the context of global warming's effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual's heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.
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Affiliation(s)
- Evans K. Cheruiyot
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Mekonnen Haile-Mariam
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Benjamin G. Cocks
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Iona M. MacLeod
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Ruidong Xiang
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia ,grid.1008.90000 0001 2179 088XFaculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Jennie E. Pryce
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
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