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Laodim T, Koonawootrittriron S, Elzo MA, Suwanasopee T, Jattawa D, Sarakul M. Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations. Anim Biosci 2024; 37:576-590. [PMID: 37946425 PMCID: PMC10915225 DOI: 10.5713/ab.23.0246] [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: 07/04/2023] [Revised: 08/27/2023] [Accepted: 10/01/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. METHODS A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-yearseason, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. RESULTS A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. CONCLUSION Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.
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Affiliation(s)
- Thawee Laodim
- Department of Animal Science, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140,
Thailand
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, 10900,
Thailand
| | - Mauricio A. Elzo
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Sciences, University of Florida, Gainesville, 32611-0910, FL,
USA
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, 10900,
Thailand
| | - Danai Jattawa
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, 10900,
Thailand
| | - Mattaneeya Sarakul
- Tropical Animal Genetic Special Research Unit (TAGU), Kasetsart University, Bangkok, 10900,
Thailand
- Department of Animal Science, Faculty of Agriculture and Technology, Nakhon Phanom University, Nakhon Phanom, 48000,
Thailand
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Lyu Y, Guan X, Xu X, Wang P, Li Q, Panigrahi M, Zhang J, Chen N, Huang B, Lei C. A whole genome scan reveals distinct features of selection in Zhaotong cattle of Yunnan province. Anim Genet 2023; 54:731-742. [PMID: 37796667 DOI: 10.1111/age.13363] [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: 03/20/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 10/07/2023]
Abstract
Over the years, indigenous cattle have not only played an essential role in securing primary food sources but have also been utilized for labor by humans, making them invaluable genetic resources. The Zhaotong cattle, a native Chinese breed from the Yunnan province, possess excellent meat quality and resistance to heat and humidity. Here we used whole genome sequencing data of 104 animals to delve into the population structure, genomic diversity and potential positive selection signals in Zhaotong cattle. The findings of this study demonstrate that the genetic composition of Zhaotong cattle was primarily derived from Chinese indicine cattle and East Asian cattle. The nucleotide diversity of Zhaotong cattle was only lower than that of Chinese indicine cattle, which was much higher than that of other taurine cattle. Genome-wide selection scans detected a series of positive candidate regions containing multiple key genes related to bone development and metabolism (CA10, GABRG3, GLDN and NOTUM), meat quality traits (ALG8, LINGO2, MYO5B, PRKG1 and GABRB1), immune response (ADA2, BMF, LEF1 and PAK6) and heat resistance (EIF2AK4 and LEF1). In summary, this study supplies essential genetic insights into the genome diversity within Zhaotong cattle and provides a foundational framework for comprehending the genetic basis of indigenous cattle breeds.
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Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinglong Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiaoxian Li
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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3
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Abstract
Heat stress is described as the cumulative detrimental effect caused by an imbalance between heat production within the body and heat dissipation. When cattle are exposed to heat stress with skin surface temperatures exceeding 35 °C, gene networks within and across cells respond to environmental heat loads with both intra and extracellular signals that coordinate cellular and whole-animal metabolism changes to store heat and rapidly increase evaporative heat loss. In this study, we examined evidence from genes known to be associated with heat tolerance (Hsp70, HSF1, HspB8, SOD1, PRLH, ATP1A1, MTOR, and EIF2AK4). This information could serve as valuable resource material for breeding programs aimed at increasing the thermotolerance of cattle.
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Affiliation(s)
- LuLan Zeng
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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4
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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: 0] [Impact Index Per Article: 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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5
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Li S, Lei H, Li J, Sun A, Ahmed Z, Duan H, Chen L, Zhang B, Lei C, Yi K. Analysis of genetic diversity and selection signals in Chaling cattle of southern China using whole-genome scan. Anim Genet 2023; 54:284-294. [PMID: 36864643 DOI: 10.1111/age.13305] [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: 10/12/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 03/04/2023]
Abstract
China has diversified resources of indigenous cattle, which are classified into Northern, Central, and Southern groups according to their geographical distribution. Chaling cattle belong to Southern group. This breed is famous for the production of good quality meat with elite meat grades. To analyze the genetic diversity of Chaling cattle, 20 samples were sequenced using whole-genome resequencing technology, along with 138 published whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle as control. It was found that Chaling cattle originated from Chinese indicine cattle. The genetic diversity of Chaling cattle is higher than that of Indian indicine cattle, East Asian taurine cattle, Eurasian taurine cattle, and European taurine cattle, but lower than that of Chinese indicine cattle and Xiangxi cattle. Annotating the selection signals obtained by composite likelihood ratio, θπ, FST , π-ratio, and XP-EHH methods, several genes associated with immunity, heat tolerance, reproduction, growth, and meat quality showed strong selection signals. In general, this study provides a theoretical basis for analyzing the genetic mechanism of Chaling cattle with excellent adaptability, rough feeding tolerance, good immune performance, and good meat quality. This work lays a foundation for genetic breeding of Chaling cattle in future.
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Affiliation(s)
- Shuang Li
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Lei
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Ao Sun
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Science, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Hongfeng Duan
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Lin Chen
- Chaling County Agricultural Development Corporation Ltd, Chaling, Hunan, China
| | - Baizhong Zhang
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
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6
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Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle). DIVERSITY 2022. [DOI: 10.3390/d14100828] [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
Evolutionary mechanisms have shaped the genomic architecture of Colombian Creole cattle breeds. The mating and selection processes have impacted several traits, promoting differences within and between populations. Studies of population structure and selection signatures in Colombian Creole breeds are scarce, and need more attention to better understand genetic differentiation, gene flow, and genetic distance. This study aimed to analyze the population structure and identify selection imprints in the Criollo Caqueteño (CAQ) population. It used 127 CAQ animals genotyped with Chip HD 777,000 SNPs. The population structure analyses used discriminant principal component analysis (DAPC), integrated haplotype scoring (iHS), and index-fixing (Fst) methodologies to detect selection signals. We can highlight SNP regions on the genes TMPRSS15, PGAM2, and EGFR, identified by the Fst method. Additionally, the iHS regions for cluster 1 identified candidate genes on BTA 3 (CMPK1 and FOXD2), BTA 11 (RCAN1), and BTA 22 (ARPP21). In group 2, we can highlight the genes on BTA 4 (SLC13A4, BRAF), BTA 9 (ULBP), BTA 14 (CSMD3) and BTA 19 (KRTAP9-2). These candidate genes have been associated with fertility traits, precocity, growth, and environmental and disease resistance, indicating a genetic potential in CAQ animals. All this promotes a better understanding of the diversity and genetic structure in the CAQ population. Based on that, our study can significantly assist the sustainable development and conservation of the breed in the Colombian Amazon.
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7
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Sun L, Qu K, Ma X, Hanif Q, Zhang J, Liu J, Chen N, Suolang Q, Lei C, Huang B. Whole-Genome Analyses Reveal Genomic Characteristics and Selection Signatures of Lincang Humped Cattle at the China-Myanmar Border. Front Genet 2022; 13:833503. [PMID: 35391795 PMCID: PMC8981028 DOI: 10.3389/fgene.2022.833503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
The location on the Yunnan border with Myanmar and its unique cultural landscape has shaped Lincang humped cattle over time. In the current study, we investigated the genetic characteristics of 22 Lincang humped cattle using whole-genome resequencing data. We found that Lincang humped cattle derived from both Indian indicine and Chinese indicine cattle depicted higher levels of genomic diversity. Based on genome-wide scans, candidate genomic regions were identified that were potentially involved in local thermal and humid environmental adaptions, including genes associated with the body size (TCF12, SENP2, KIF1C, and PFN1), immunity (LIPH, IRAK3, GZMM, and ELANE), and heat tolerance (MED16, DNAJC8, HSPA4, FILIP1L, HELB, BCL2L1, and TPX2). Missense mutations were detected in candidate genes IRAK3, HSPA4, and HELB. Interestingly, eight missense mutations observed in the HELB gene were specific to the indicine cattle pedigree. These mutations may reveal differences between indicine and taurine cattle adapted to variable climatic conditions. Our research provides new insights into the genetic characteristics of Lincang humped cattle representing Lincang and Pu'er areas as an important channel for the migration of Indian indicine from domestication centers toward southwestern China.
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Affiliation(s)
- Luyang Sun
- Yunnan Academy of Grassland and Animal Science, Kunming, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, China
| | - Xiaohui Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quji Suolang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
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8
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Mulim HA, Brito LF, Pinto LFB, Ferraz JBS, Grigoletto L, Silva MR, Pedrosa VB. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics 2022; 23:209. [PMID: 35291953 PMCID: PMC8925140 DOI: 10.1186/s12864-022-08384-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023] Open
Abstract
Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08384-0.
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Affiliation(s)
| | - Luiz F Brito
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA
| | | | - José Bento Sterman Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Lais Grigoletto
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA.,Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Bahia, Brazil. .,Department of Animal Science, State University of Ponta Grossa, Av. General Carlos Cavalcanti, 4748 - Uvaranas, Ponta Grossa, PR, 84030-900, Brazil.
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Balbi M, Bonamy M, Fernandez ME, Cecco P, Vaca RJA, Rogberg Muñoz A, Peral Gacía P, Prando AJ, Giovambattista G. Coat score. A possible explanation for the zebuine selective sweep located on bovine chromosome 5: 47,670,001-48,100,000 bp. Anim Biotechnol 2022:1-7. [PMID: 35130466 DOI: 10.1080/10495398.2022.2029464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Over 65% of the world's cattle population resides in warm areas where heat stress conditions limit the breed of European taurine cattle. Composite breeds were developed to retain the main traits of both parental breeds. The skin plays a central role in animal response to heat stress. Research on the genetic architecture of skin traits has identified genes and regions related to warm resistance skin features. The aim of this study was to determine whether the indicine proportion accounted for coat type or whether there were genes of large effect segregating in Brangus. Bulls (n = 108) were genotyped using microarrays and their coat score and hair length were evaluated. Indicine-taurine genome-wide composition was estimated and GWAS was performed. Although significant correlations between indicine proportion and traits were not observed, four windows of SNPs on BTA4 and BTA5 explained more than 2% of the trait variance. The GWAS for coat score in summer showed the main peak on BTA5:46,941,446-48,030,219 bp, accounting for 4.65% of the variance. Our results suggest that the variation in coat score and undercoat hair length in Argentinian Brangus bulls is associated with the presence of some particular gene variants, rather than with the whole indicine genetic content.
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Affiliation(s)
- Marianela Balbi
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Martín Bonamy
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Elena Fernandez
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Paulo Cecco
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Roberto J A Vaca
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina.,Facultad de Agronomía, INPA-Instituto de Producción Animal UBA-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pilar Peral Gacía
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Alberto J Prando
- Cátedra de Producción Bovina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Guillermo Giovambattista
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Noel Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
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Vijayakumar P, Singaravadivelan A, Mishra A, Jagadeesan K, Bakyaraj S, Suresh R, Sivakumar T. Whole-Genome comparative analysis reveals genetic mechanisms of disease resistance and heat tolerance of tropical Bos indicus cattle breeds. Genome 2021; 65:241-254. [PMID: 34914549 DOI: 10.1139/gen-2021-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Bos indicus cattle breeds have been naturally selected over thousands of years for disease resistance and thermo-tolerance. However, a genetic mechanism of these specific inherited characteristics needs to be discovered. Hence, in this study, the whole-genome comparative analysis of Bos indicus cattle breeds of Kangayam, Tharparkar, Sahiwal, Red Sindhi, and Hariana of the Indian subcontinent was conducted. The genetic variants identification analysis revealed a total of 15,58,51,012 SNPs and 1,00,62,805 InDels in the mapped reads across all Bos indicus cattle breeds. The functional annotation of 17,252 genes that comprised both, SNPs and InDels, of high functional impact on proteins, has been carried out. The functional annotation results revealed the pathways that were involved in the innate immune response including toll-like receptors, a retinoic acid-inducible gene I like receptors, NOD-like receptors, Jak-STAT signaling pathways, and the non-synonymous variants in the candidate immune genes. Further, we also identified several pathways involved in heat shock response, hair and skin properties, oxidative stress response, osmotic stress response, thermal sweating, feed intake, metabolism, and the non-synonymous variants in the candidate thermo-tolerant genes. These pathways and genes were directly or indirectly contributing to the disease resistance and thermo-tolerance adaptations of Bos indicus cattle breeds.
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Affiliation(s)
- Periyasamy Vijayakumar
- Veterinary College and Research Institute, TANUVAS, Animal Genetics and Breeding, Livestock Farm Comlex, Orathanadu, Tamil Nadu, India, 6145 625;
| | - Arunasalam Singaravadivelan
- Veterinary College and Research Institute, TANUVAS, Livestock Production Management, VCRI, Orathanadu, Orathanadu, Tamil Nadu, India, 614 625;
| | - Anamika Mishra
- High Security Animal Disease laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal, Madhya Pradesh, India, 462021;
| | - Krishnan Jagadeesan
- University Training and Research Centre, Pillayarpatty - 613 403, , Animal Genetics and Breeding, Thanjavur, Tamil Nadu, India;
| | - Sanniyasi Bakyaraj
- College of Poultry Production and Management, TANUVAS, Hosur, Tamil nadu, India;
| | - Ramalingam Suresh
- Veterinary College and Research Institute, TANUVAS, Animal Genetics and Breeding, VETERINARY COLLEGE AND RESEARCH INSTITUTE, Orathanadu, Tamil Nadu, India, 243122.,Indian Veterinary Research Institute, 30072, 117, Salihothra Hostel (4th hostel), IVRI, BAREILLY, Izatnagar, UTTAR PRADESH, India, 243122;
| | - Thiagarajan Sivakumar
- Veterinary College and Research Institute, TANUVAS, Livestock Production Management, Orathanadu, Tamil Nadu, India;
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11
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Cortellari M, Bionda A, Negro A, Frattini S, Mastrangelo S, Somenzi E, Lasagna E, Sarti FM, Ciani E, Ciampolini R, Marletta D, Liotta L, Ajmone Marsan P, Pilla F, Colli L, Talenti A, Crepaldi P. Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems. Genet Sel Evol 2021; 53:92. [PMID: 34895134 PMCID: PMC8666052 DOI: 10.1186/s12711-021-00685-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00685-4.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Elisa Somenzi
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | | | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
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12
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Overlapping haplotype blocks indicate shared genomic regions between a composite beef cattle breed and its founder breeds. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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14
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Cao Y, Jia P, Wu Z, Huang M, Chen S, Zhang J, Huang B, Lei C. A novel SNP of MYO1A gene associated with heat-tolerance in Chinese cattle. Anim Biotechnol 2020; 33:810-815. [PMID: 33146068 DOI: 10.1080/10495398.2020.1837147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With the advent of global climate change, heat-tolerance is becoming more and more important to the sustainability of animal husbandry production systems. Previous studies have shown that MYO1A gene associated with pigmentation may be closely related to heat-tolerance in cattle. In this study, a novel missense mutation (NC_037332.1 g.56390345 A > G) was first detected in MYO1A in 891 individuals of 35 cattle breeds, which transformed the amino acid isoleucine into valine. The purpose of this study was to determine the allele frequencies distribution of this locus in Chinese indigenous cattle and to analyze the relationship between this locus and heat-tolerance. Further analysis showed that frequency of wild allele A decreased gradually from northern cattle to southern cattle, whereas frequency of mutant type allele G showed the opposite pattern, which was consistent with the distribution of various climatic conditions of China. Additionally, association analysis was carried out between genotypes and four climatic conditions (annual mean temperature (T), relative humidity (H), temperature-humidity index (THI) and average annual sunshine hours (100-cloudiness) (SR)). Analysis results showed that genotypes were significantly correlated with climatic conditions. Therefore, our results suggest that the novel SNP (rs209559414) is related to heat-tolerance trait of Chinese indigenous cattle.
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Affiliation(s)
- Yanhong Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Peng Jia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuyue Wu
- The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Mingguang Huang
- The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shaomei Chen
- The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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15
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Svishcheva G, Babayan O, Lkhasaranov B, Tsendsuren A, Abdurasulov A, Stolpovsky Y. Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle. Animals (Basel) 2020; 10:E1493. [PMID: 32846979 PMCID: PMC7552156 DOI: 10.3390/ani10091493] [Citation(s) in RCA: 5] [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: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/03/2022] Open
Abstract
We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.
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Affiliation(s)
- Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Babayan
- Gordiz Ltd., Skolkovo Innovation Centre, 121205 Moscow, Russia
| | | | - Ariuntuul Tsendsuren
- Institute of General and Experimental Biology, The Mongolian Academy of Sciences, Ulaanbaatar 210351, Mongolia
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500 Osh, Kyrgyzstan
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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16
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Cardoso DF, Fernandes Júnior GA, Scalez DCB, Alves AAC, Magalhães AFB, Bresolin T, Ventura RV, Li C, de Sena Oliveira MC, Porto-Neto LR, Carvalheiro R, de Oliveira HN, Tonhati H, Albuquerque LG. Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle. Sci Rep 2020; 10:8770. [PMID: 32471998 PMCID: PMC7260210 DOI: 10.1038/s41598-020-65565-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/04/2020] [Indexed: 11/09/2022] Open
Abstract
Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77-65.25 Mb) and 14 (22.81-23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.
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Affiliation(s)
- Diercles Francisco Cardoso
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
| | - Gerardo Alves Fernandes Júnior
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Daiane Cristina Becker Scalez
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Anderson Antonio Carvalho Alves
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Ana Fabrícia Braga Magalhães
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Tiago Bresolin
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Ricardo Vieira Ventura
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science (FMVZ), University of Sao Paulo (USP), Pirassununga, SP, Brazil
| | - Changxi Li
- Department of Agricultural Food and Nutritional Science, Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | | | | | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil
| | - Henrique Nunes de Oliveira
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil
| | - Humberto Tonhati
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil
| | - Lucia Galvão Albuquerque
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
- National Council for Science and Technological Development, Brasília, Distrito Federal, Brazil.
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17
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Naval-Sánchez M, Porto-Neto LR, Cardoso DF, Hayes BJ, Daetwyler HD, Kijas J, Reverter A. Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genet Sel Evol 2020; 52:27. [PMID: 32460767 PMCID: PMC7251699 DOI: 10.1186/s12711-020-00546-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
Background Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. Results We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. Conclusions Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.
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Affiliation(s)
- Marina Naval-Sánchez
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia. .,Institute of Molecular Biosciences, The University of Queensland, 306 Carmody Road, St. Lucia, Brisbane, QLD, 4067, Australia.
| | - Laercio R Porto-Neto
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Diercles F Cardoso
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia.,Department of Animal Science, School of Agricultural and Veterinarian Sciences, Sao Paulo State University (UNESP), Jaboticabal, SP, Brazil.,Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - James Kijas
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
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18
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Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, Khansefid M. Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis. BMC Genet 2020; 21:16. [PMID: 32041535 PMCID: PMC7011551 DOI: 10.1186/s12863-020-0824-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Background Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.
| | - Mohammad Hossein Fallahi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Ali Jalil Sarghale
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Rostam Abdollahi-Arpanahi
- Departments of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, 33916-53755, Iran
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
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19
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Li R, Li C, Chen H, Li R, Chong Q, Xiao H, Chen S. Genome-wide scan of selection signatures in Dehong humped cattle for heat tolerance and disease resistance. Anim Genet 2019; 51:292-299. [PMID: 31887783 DOI: 10.1111/age.12896] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2019] [Indexed: 01/11/2023]
Abstract
Dehong humped cattle (DHH) is an indigenous zebu breed from southwestern China that possesses characteristics of heat tolerance and strong disease resistance and adapts well to the local tropical and subtropical climatic conditions. However, information on selection signatures of DHH is scarce. Herein, we compared the genomes of DHH and each of Diqing and Zhaotong cattle breeds using the population differentiation index (FST ), cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR) methods to explore the genomic signatures of heat tolerance and disease resistance in DHH. Several pathways and genes carried selection signatures, including thermal sweating (calcium signaling pathway), heat shock (HSF1) and oxidative stress response (PLCB1, PLCB4), coat color (RAB31), feed intake (ATP8A1, SHC3) and reproduction (TP63, MAP3K13, PTPN4, PPP3CC, ADAMTSL1, SS18L1, OSBPL2, TOX, RREB1, GRK2). These identified pathways and genes may contribute to heat tolerance in DHH. Simultaneously, we also identified LIPH, TP63 and CBFA2T3 genes under positive selection that were associated with immunity.
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Affiliation(s)
- R Li
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - C Li
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China.,National Demonstration Center for Experimental Life Sciences Education, Yunnan University, Kunming, Yunnan, 650500, China
| | - H Chen
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - R Li
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - Q Chong
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - H Xiao
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China
| | - S Chen
- School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, China.,National Demonstration Center for Experimental Life Sciences Education, Yunnan University, Kunming, Yunnan, 650500, China
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Jia P, Cai C, Qu K, Chen N, Jia Y, Hanif Q, Liu J, Zhang J, Chen H, Huang B, Lei C. Four Novel SNPs of MYO1A Gene Associated with Heat-Tolerance in Chinese Cattle. Animals (Basel) 2019; 9:E964. [PMID: 31766183 PMCID: PMC6912737 DOI: 10.3390/ani9110964] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 01/07/2023] Open
Abstract
Based on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a (MYO1A) gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. In our study, four novel candidate SNPs highly conserved in B. indicus breeds but barely existed in B. taurus were identified in MYO1A gene according to Bovine Genome Variation Database and Selective Signatures (BGVD). PCR and DNA sequencing were used to genotype 1072 individuals including 34 Chinese indigenous cattle breeds as well as Angus and Indian zebu. Two synonymous mutations (rs208210464 and rs110123931), one missense mutation (rs209999142; Phe172Ser), and one intron mutation (rs135771836) were detected. The frequencies of mutant alleles of the four SNPs gradually increased from northern groups to southern groups of Chinese cattle, which was consistent with the distribution of various climatic conditions of China. Additionally, four SNPs were significantly associated with four climatic conditions including annual mean temperature (T), relative humidity (H), temperature-humidity index (THI), and average annual sunshine hours (100-cloudiness) (SR). Among these, rs209999142 and Hap 1/1 had better performance than others. Our results suggested that rs209999142 was associated with heat-tolerance trait and rs208210464, rs110123931, and rs135771836 showed high phenotypic effect on heat-tolerance trait because of the strong linkage with rs209999142. These SNPs could be used as candidates for marker-assisted selection (MAS) in cattle breeding.
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Affiliation(s)
- Peng Jia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.J.); (C.C.); (N.C.); (H.C.)
| | - Cuicui Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.J.); (C.C.); (N.C.); (H.C.)
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China; (K.Q.); (J.L.); (J.Z.)
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.J.); (C.C.); (N.C.); (H.C.)
| | - Yutang Jia
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agriculture Science, Hefei 230001, China;
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad 577, Pakistan;
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China; (K.Q.); (J.L.); (J.Z.)
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China; (K.Q.); (J.L.); (J.Z.)
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.J.); (C.C.); (N.C.); (H.C.)
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China; (K.Q.); (J.L.); (J.Z.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (P.J.); (C.C.); (N.C.); (H.C.)
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A Novel SNP in EIF2AK4 Gene Is Associated with Thermal Tolerance Traits in Chinese Cattle. Animals (Basel) 2019; 9:ani9060375. [PMID: 31248194 PMCID: PMC6617145 DOI: 10.3390/ani9060375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 12/05/2022] Open
Abstract
Simple Summary China harbors two lineages of cattle (Bos taurus and Bos indicus) that display pronounced geographical distribution differences. Northern Chinese cattle predominantly belong to B. taurus and southern Chinese cattle belong to B. indicus. Both B. taurus and B. indicus contribute to the admixture of cattle in central China. Thermal stress induces oxidative stress and DNA damage in mammals. In general, B. indicus are more resistant to thermal stress than B. taurus. Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4), which pertains to the family of serine–threonine kinase, is a candidate gene for thermal stress. However, the effects of the bovine EIF2AK4 gene on the thermal tolerance traits of Chinese cattle breeds remain unknown. Our results suggest that a variant of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle. Abstract Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4, also known as GCN2), which pertains to the family of serine–threonine kinase, is involved in oxidative stress and DNA damage repair. A missense single-nucleotide polymorphism (SNP) (NC_037337.1 g.35615224 T > G) in exon 6 of the EIF2AK4 gene which encodes a p.Ile205Ser substitution was observed in the Bovine Genome Variation Database and Selective Signatures (BGVD). The purpose of the current study is to determine the allelic frequency distribution of the locus and analyze its association with thermal tolerance in Chinese indigenous cattle. In our study, the allelic frequency distribution of the missense mutation (NC_037337.1 g.35615224 T > G) in Chinese cattle was analyzed by sequencing 1105 individuals of 37 breeds including 35 Chinese indigenous cattle breeds and two exotic breeds. In particular, association analysis was carried out between the genotypes and three environmental parameters including annual mean temperature (T), relative humidity (RH), and temperature–humidity index (THI). The frequency of the mutant allele G (NC_037337.1 g.35615224 T > G) gradually decreased from the southern cattle groups to the northern cattle groups, whereas the frequency of the wild-type allele T showed an opposite pattern, consistent with the distribution of indicine and taurine cattle in China. In accordance with the association analysis, genotypes were significantly associated with T (P < 0.01), RH (P < 0.01), and THI (P < 0.01), suggesting that the cattle with genotype GG were found in regions with higher T, RH, and THI. Thus, our results suggest that the mutation (NC_037337.1 g.35615224 T > G) of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.
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