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Bhowmik N, Seaborn T, Ringwall KA, Dahlen CR, Swanson KC, Hulsman Hanna LL. Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States. Genes (Basel) 2023; 14:1842. [PMID: 37895190 PMCID: PMC10606367 DOI: 10.3390/genes14101842] [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: 08/11/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.
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Affiliation(s)
- Nayan Bhowmik
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Travis Seaborn
- School of Natural Resource Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Kris A. Ringwall
- Dickinson Research Extension Center, North Dakota State University, Dickinson, ND 58601, USA
| | - Carl R. Dahlen
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Kendall C. Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58108, USA
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Schmidt PI, Mota LFM, Fonseca LFS, Dos Santos Silva DB, Frezarim GB, Arikawa LM, de Abreu Santos DJ, Magalhães AFB, Cole JB, Carvalheiro R, de Oliveira HN, Null DJ, VanRaden P, Ma L, de Albuquerque LG. Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle. Sci Rep 2023; 13:10399. [PMID: 37369809 DOI: 10.1038/s41598-023-37586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
The wide use of genomic information has enabled the identification of lethal recessive alleles that are the major genetic causes of reduced conception rates, longer calving intervals, or lower survival for live-born animals. This study was carried out to screen the Nellore cattle genome for lethal recessive haplotypes based on deviation from the expected population homozygosity, and to test SNP markers surrounding the lethal haplotypes region for association with heifer rebreeding (HR), post-natal mortality (PNM) and stayability (STAY). This approach requires genotypes only from apparently normal individuals and not from affected embryos. A total of 62,022 animals were genotyped and imputed to a high-density panel (777,962 SNP markers). Expected numbers of homozygous individuals were calculated, and the probabilities of observing 0 homozygotes was obtained. Deregressed genomic breeding values [(G)EBVs] were used in a GWAS to identify candidate genes and biological mechanisms affecting HR, STAY and PNM. In the functional analyses, genes within 100 kb down and upstream of each significant SNP marker, were researched. Thirty haplotypes had high expected frequency, while no homozygotes were observed. Most of the alleles present in these haplotypes had a negative mean effect for PNM, HR and STAY. The GWAS revealed significant SNP markers involved in different physiological mechanisms, leading to harmful effect on the three traits. The functional analysis revealed 26 genes enriched for 19 GO terms. Most of the GO terms found for biological processes, molecular functions and pathways were related to tissue development and the immune system. More phenotypes underlying these putative regions in this population could be the subject of future investigation. Tests to find putative lethal haplotype carriers could help breeders to eliminate them from the population or manage matings in order to avoid homozygous.
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Affiliation(s)
- Patrícia Iana Schmidt
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Danielly Beraldo Dos Santos Silva
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Leonardo Machestropa Arikawa
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Jordan de Abreu Santos
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - John Bruce Cole
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Roberto Carvalheiro
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Henrique Nunes de Oliveira
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Jacob Null
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Paul VanRaden
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, 20742, USA
| | - Lucia Galvão de Albuquerque
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil.
- National Council for Scientific and Technological Development (CNPq), Brasília, Brazil.
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Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers. Animals (Basel) 2022; 12:ani12223214. [PMID: 36428441 PMCID: PMC9686749 DOI: 10.3390/ani12223214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.
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Mam S, Tep B, Rin S, Uenoyama Y, Matsuyama S, Ohkura S, Murase T, Nunome M, Morita Y. A Survey of Genome-Wide Genetic Characterizations of Crossbred Dairy Cattle in Local Farms in Cambodia. Animals (Basel) 2022; 12:ani12162072. [PMID: 36009661 PMCID: PMC9405130 DOI: 10.3390/ani12162072] [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: 06/27/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The Cambodian dairy sector collapsed due to the civil war. Thereby, the Cambodia dairy sector has not obtained basic information, such as cattle breed and milk production. To encourage the recovery of the Cambodian dairy sector, the present study aimed to reveal the genetic variation and the milk production in Cambodian crossbred dairy cattle. Initially, we conducted interviews to understand the breeding background and milk production of two local farms (Farm R and Farm M) in Cambodia. The percentage (%) of milk fat content in Farm R was higher than that in Farm M. A genome-wide analysis of the genetic characterization for 75 cows in the two dairy farms implies that some cows in Farm R are genetically far from other crossbred cattle and retain a higher proportion of genetic background derived from Cambodian-native cattle. The present study indicated genetic characteristics and milk composition in Cambodian crossbred cattle. Gene character in Cambodian local crossbred cattle could contribute to milk production in the Cambodian dairy system. Thus, our basic genetic study could provide a new breeding strategy by using local Cambodian crossbred dairy cattle to establish an adequate dairy strain. Abstract To improve the dairy sector in Cambodia in the future, we aimed to reveal the genetic variation and the milk production in Cambodian crossbred dairy cattle. We calculated the percent (%) milk fat content and the average milk yield per cow (L/day) for two farms (Farm R and M) based on the farmers’ records and interviews. The crossbred cows originated from Cambodian local farmers and Thailand breeders in Farm R, whereas the crossbred cows originated in Thailand breeders in Farm M. Then, we performed genetic characterization for 75 individuals from the two farms and an individual Japanese pure Holstein-Friesian cow based on 133,705 single nucleotide polymorphisms (SNPs) obtained by the GRAS-Di method. The milk fat contents in the bulk milk in the dry season and the average milk yield per cow on Farm R were 3.77 ± 0.98% and 7.81 ± 2.66 L/day, respectively, and were higher than those on Farm M (3.35 ± 0.54% and 6.5–7.5 L/day). Cattle originating in Cambodia in Farm R possessed a unique genetic character different from cattle from Thailand in Farm M. The present study suggests that the differences in milk fat content between the two farms might be explained by the genetic differences in crossbred cows.
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Affiliation(s)
- Somony Mam
- Asian Satellite Campus in Cambodia, Nagoya University, c/o Royal University of Agriculture, Phnom Penh P.O. Box 2696, Cambodia
- Department of Animal Health and Veterinary Public Health, General Directorate of Animal Health and Production, Phnom Penh P.O. Box 12352, Cambodia
| | - Bengthay Tep
- Department of Animal Health and Veterinary Public Health, General Directorate of Animal Health and Production, Phnom Penh P.O. Box 12352, Cambodia
| | - Soriya Rin
- Asian Satellite Campus in Cambodia, Nagoya University, c/o Royal University of Agriculture, Phnom Penh P.O. Box 2696, Cambodia
| | - Yoshihisa Uenoyama
- Laboratory of Animal Reproduction, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Shuichi Matsuyama
- Laboratory of Animal Production Science, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Satoshi Ohkura
- Laboratory of Animal Production Science, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Tetsuma Murase
- Laboratory of Veterinary Theriogenology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Mitsuo Nunome
- Laboratory of Animal Genetics, Department of Zoology, Faculty of Science, Okayama University of Science, Okayama 700-0005, Japan
- Correspondence: (M.N.); (Y.M.); Tel.: +81-86-256-946 (M.N.); +81-155-49-5375 (Y.M.)
| | - Yasuhiro Morita
- Laboratory of Animal Production Science, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
- Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan
- Department of Clinical Veterinary Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
- Correspondence: (M.N.); (Y.M.); Tel.: +81-86-256-946 (M.N.); +81-155-49-5375 (Y.M.)
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Qi A, Yan J, Yang Y, Tang J, Ru W, Jiang X, Lei C, Sun X, Chen H. SNP within the bovine ASB-3 gene and their association analysis with stature traits in three Chinese cattle breeds. Gene 2022; 838:146700. [PMID: 35772652 DOI: 10.1016/j.gene.2022.146700] [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: 08/11/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022]
Abstract
ASB-3 is one of the 18 members of ASB gene family. As a special negative regulation factor of TNF-R2, ASB-3 inhibits the signal transduction of JNK-TNF-R2 and JNK-STAT signaling pathway by TNF-R2 protein. In this study, the genetic polymorphisms of ASB-3 were detected in total of 637 from Qinchuan, Jinnan and Xianan cattle using the sequence of mixed DNA pool, Tetra-primer ARMS-PCR and PCR-RFLP methods. Four mutation sites were detected including the g.C41255T, g.G74754A, and g.T75438C were synonymous mutation, whereas the g.C115213T was missense mutation (Pro > Ser). The associated analysis of four polymorphic loci of ASB-3 gene respectively with growth traits in the three cattle breeds. The result showed that SNP1 site was significantly related with Qinchuan cattle height and TT was the dominant genotype; SNP2 had a significant relationship with body length of Xianan cattle and cross department height of Qinchuan cattle, AA was the dominant genotype; SNP3 was significantly related to cross height of Xianan cattle, TT was the dominant genotype; SNP4 site was significantly correlated with body height of Xianan cattle and cross height of Jinnan cattle. Genotype combinations were only significantly correlated with the hucklebone width in the adult Qinchuan cattle. The combination genotype CTAGCTCC was outperformed other combination genotypes of Qinchuan cattle. The results showed that ASB-3 could be an important candidate gene and the four SNPs in ASB-3 can be used for molecular marker-assisted selection of four beef cattle breeds.
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Affiliation(s)
- Ao Qi
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Jianyu Yan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Yu Yang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Jia Tang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Wenxiu Ru
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xiaojun Jiang
- Shaanxi Agricultural and Animal Husbandry Good Seed Farm, Fufeng, Shaanxi 722203, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xiuzhu Sun
- College of Grassland Agriculrure, Northwest A&F University, Shaanxi 712100, China.
| | - Hong Chen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China; College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
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6
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Kawaguchi F, Nakamura M, Kobayashi E, Yonezawa T, Sasazaki S, Mannen H. Comprehensive assessment of genetic diversity, structure, and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis. Anim Sci J 2022; 93:e13770. [PMID: 36210484 DOI: 10.1111/asj.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022]
Abstract
There are four unique cattle breeds in Japan: Japanese Black, Japanese Brown, Japanese Polled, and Japanese Shorthorn. The objective of this study was to comprehensively assess the genetic diversity, structure, relationship, and the degree of influence from foreign breeds (Angus, Simmental, Hanwoo, Shorthorn, Ayrshire, Brown Swiss, and Devon) in the Japanese cattle breeds using Illumina 50 K SNP array. In principal component analysis, each Japanese breed was separately clustered except for Japanese Shorthorn and Shorthorn. Japanese cattle breeds also showed different genetic components from each other at K ≥ 5 in population structure analysis. Japanese Shorthorn, on the other hand, had a very similar structure to Shorthorn at K ≤ 9, and Japanese Polled had a partially similar component with Angus at K = 3-7. Such close relationships were also observed in the phylogenetic tree. These findings imply that Japanese cattle breeds share genetic components with European cattle breeds to some extent while they have been almost differentiated. In population structure analysis, Japanese Black cattle shared little genetic component (3.5%) with European breeds. This is the first study to determine the extent to which European breeds impact Japanese breeds.
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Affiliation(s)
- Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science Kobe University Kobe Japan
| | - Mitsuki Nakamura
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science Kobe University Kobe Japan
| | - Eiji Kobayashi
- National Agriculture and Food Research Organization (NARO) Institute of Livestock and Grassland Science Tsukuba Japan
| | - Takahiro Yonezawa
- Laboratory of Animal Genetics, Faculty of Agriculture Tokyo University of Agriculture Atsugi Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science Kobe University Kobe Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science Kobe University Kobe Japan
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Ma MT, Jennings MR, Blazeck J, Lieberman RL. Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation. Acta Crystallogr D Struct Biol 2022; 78:91-103. [PMID: 34981765 PMCID: PMC8725166 DOI: 10.1107/s2059798321011785] [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: 09/12/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023] Open
Abstract
Homo sapiens adenosine deaminase 1 (HsADA1; UniProt P00813) is an immunologically relevant enzyme with roles in T-cell activation and modulation of adenosine metabolism and signaling. Patients with genetic deficiency in HsADA1 suffer from severe combined immunodeficiency, and HsADA1 is a therapeutic target in hairy cell leukemias. Historically, insights into the catalytic mechanism and the structural attributes of HsADA1 have been derived from studies of its homologs from Bos taurus (BtADA) and Mus musculus (MmADA). Here, the structure of holo HsADA1 is presented, as well as biochemical characterization that confirms its high activity and shows that it is active across a broad pH range. Structurally, holo HsADA1 adopts a closed conformation distinct from the open conformation of holo BtADA. Comparison of holo HsADA1 and MmADA reveals that MmADA also adopts a closed conformation. These findings challenge previous assumptions gleaned from BtADA regarding the conformation of HsADA1 that may be relevant to its immunological interactions, particularly its ability to bind adenosine receptors. From a broader perspective, the structural analysis of HsADA1 presents a cautionary tale for reliance on homologs to make structural inferences relevant to applications such as protein engineering or drug development.
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Affiliation(s)
- Minh Thu Ma
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
| | - Maria Rain Jennings
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
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Dixit SP, Bhatia AK, Ganguly I, Singh S, Dash S, Sharma A, Anandkumar N, Dang AK, Jayakumar S. Genome analyses revealed genetic admixture and selection signatures in Bos indicus. Sci Rep 2021; 11:21924. [PMID: 34753978 PMCID: PMC8578574 DOI: 10.1038/s41598-021-01144-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.
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Affiliation(s)
- S P Dixit
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
| | - A K Bhatia
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Indrajit Ganguly
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Sanjeev Singh
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Soumya Dash
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anurodh Sharma
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - N Anandkumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - A K Dang
- ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S Jayakumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
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Elayadeth-Meethal M, Thazhathu Veettil A, Asaf M, Pramod S, Maloney SK, Martin GB, Rivero MJ, Sejian V, Naseef PP, Kuruniyan MS, Lee MRF. Comparative Expression Profiling and Sequence Characterization of ATP1A1 Gene Associated with Heat Tolerance in Tropically Adapted Cattle. Animals (Basel) 2021; 11:2368. [PMID: 34438824 PMCID: PMC8388727 DOI: 10.3390/ani11082368] [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: 07/23/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/20/2022] Open
Abstract
Climate change is an imminent threat to livestock production. One adaptation strategy is selection for heat tolerance. While it is established that the ATP1A1 gene and its product play an important role in the response to many stressors, there has been no attempt to characterize the sequence or to perform expression profiling of the gene in production animals. We undertook a field experiment to compare the expression profiles of ATP1A1 in heat-tolerant Vechur and Kasaragod cattle (Bos taurus indicus) with the profile of a heat-susceptible crossbreed (B. t. taurus × B. t. indicus). The cattle were exposed to heat stress while on pasture in the hot summer season. The environmental stress was quantified using the temperature humidity index (THI), while the heat tolerance of each breed was assessed using a heat tolerance coefficient (HTC). The ATP1A1 mRNA of Vechur cattle was amplified from cDNA and sequenced. The HTC varied significantly between the breeds and with time-of-day (p < 0.01). The breed-time-of-day interaction was also significant (p < 0.01). The relative expression of ATP1A1 differed between heat-tolerant and heat-susceptible breeds (p = 0.02). The expression of ATP1A1 at 08:00, 10:00 and 12:00, and the breed-time-of-day interaction, were not significant. The nucleotide sequence of Vechur ATP1A1 showed 99% homology with the B. t. taurus sequence. The protein sequence showed 98% homology with B. t. taurus cattle and with B. grunniens (yak) and 97.7% homology with Ovis aries (sheep). A molecular clock analysis revealed evidence of divergent adaptive evolution of the ATP1A1 gene favoring climate resilience in Vechur cattle. These findings further our knowledge of the relationship between the ATP1A1 gene and heat tolerance in phenotypically incongruent animals. We propose that ATP1A1 could be used in marker assisted selection (MAS) for heat tolerance.
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Affiliation(s)
- Muhammed Elayadeth-Meethal
- Department of Animal Breeding and Genetics, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad 673576, Kerala, India;
- Livestock Research Station, Thiruvazhamkunnu, Palakkad 678601, Kerala, India;
- UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009, Australia;
| | - Aravindakshan Thazhathu Veettil
- Centre for Advanced Studies in Animal Genetics and Breeding, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad 680651, Kerala, India;
| | - Muhasin Asaf
- Department of Animal Breeding and Genetics, Kerala Veterinary and Animal Sciences University, Pookode, Wayanad 673576, Kerala, India;
| | | | - Shane K. Maloney
- School of Human Sciences, University of Western Australia, Crawley, WA 6009, Australia;
| | - Graeme B. Martin
- UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009, Australia;
| | | | - Veerasamy Sejian
- ICAR-National Institute of Animal Nutrition and Physiology, Adugodi 560030, Bangalore, India;
| | | | - Mohamed Saheer Kuruniyan
- Department of Dental Technology, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia;
| | - Michael R. F. Lee
- School of Sustainable Food and Farming, Harper Adams University, Edgmond, Newport TF10 8NB, UK;
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10
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Chawala AR, Sanchez-Molano E, Dewhurst RJ, Peters A, Chagunda MGG, Banos G. Breeding strategies for improving smallholder dairy cattle productivity in Sub-Saharan Africa. J Anim Breed Genet 2021; 138:668-687. [PMID: 34076907 DOI: 10.1111/jbg.12556] [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] [Received: 01/17/2021] [Revised: 04/20/2021] [Accepted: 05/13/2021] [Indexed: 11/28/2022]
Abstract
Breeding strategies for smallholder dairy farming systems in Sub-Saharan Africa (SSA) were simulated and evaluated considering cow traits identified as priorities by farmers in different agro-ecological zones. These traits were related to cow milk yield, fertility, temperament, feed intake and disease resistance. The first breeding strategy was based on continuous importation of genetically superior exotic dairy sire semen to SSA and crossing with local females leading to a gradual upgrade of the indigenous population. The second strategy assumed that semen from elite exotic bulls would be imported to SSA and used on indigenous cows to produce F1 animals. Thereafter, elite animals would be selected from within the F1 and each subsequent generation to establish a new synthetic breed. The third strategy was to improve the indigenous population by genetically selecting the best sires available domestically. Results showed positive genetic progress for all breeding goal traits. After 15 generations of selection, the genetic response of the importation strategy exceeded the corresponding genetic response of the synthetic breed strategy by 20%-60%. The former also exceeded the genetic response of the indigenous breed improvement strategy by 43%-75%. Potentially there is an opportunity for breeders to choose an appropriate breeding strategy that fits a specific need of smallholder dairy farmers.
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Affiliation(s)
- Aluna R Chawala
- Tanzania Livestock Research Institute (TALIRI), Mpwapwa, Tanzania.,Scotland's Rural College (SRUC) Research, Edinburgh, UK
| | | | | | - Andrew Peters
- Supporting Evidence Based Interventions, University of Edinburgh, Midlothian, UK
| | - Mizeck G G Chagunda
- Animal Breeding and Husbandry in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
| | - Georgios Banos
- Scotland's Rural College (SRUC) Research, Edinburgh, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, UK
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11
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Strucken EM, Gebrehiwot NZ, Swaminathan M, Joshi S, Al Kalaldeh M, Gibson JP. Genetic diversity and effective population sizes of thirteen Indian cattle breeds. Genet Sel Evol 2021; 53:47. [PMID: 34074236 PMCID: PMC8170732 DOI: 10.1186/s12711-021-00640-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/19/2021] [Indexed: 11/25/2022] Open
Abstract
Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00640-3.
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Affiliation(s)
- Eva M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
| | - Netsanet Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | | | - Sachin Joshi
- BAIF Development Research Foundation, Pune, India
| | - Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - John P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
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12
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Mandefro A, Sisay T, Kim KS, Edea Z, Konwarh R, Dadi H. Single nucleotide polymorphisms of leptin gene in five Ethiopian indigenous cattle breeds and the Korean Hanwoo breed. Trop Anim Health Prod 2021; 53:202. [PMID: 33694014 DOI: 10.1007/s11250-021-02642-1] [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] [Received: 11/13/2020] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Considering the escalating number of scientific reports on the association between the leptin gene and diverse physiological traits and performance of cattle populations, this study was directed towards identifying SNPs in the leptin gene among five indigenous cattle breeds of Ethiopia. DNA samples were extracted from the nasal swabs of the Ethiopian indigenous cattle breeds: Arsi (n = 18), Horro (n = 20), Begait (n = 21), Boran (n = 19), and Fogera (n = 17) and the Korean Hanwoo (a representative taurine breed) (n = 20), followed by PCR amplification of exon 2 and exon 3 regions of the leptin gene and sequence analysis of the PCR products. Five SNPs, two (generating missense mutations) on exon 2 and three (generating silent mutations) on exon 3 regions, were explicated in this study. Allele frequency and genotype frequency distribution pertaining to the SNPs were recorded for the studied cattle breeds besides the minor allele frequency and deviation from the Hardy-Weinberg equilibrium. Positive FIS index values were recorded for all the markers except SNP2, illustrative of heterozygote deficiency. MEGA X software-based evolutionary divergence analysis of the phylogenetic tree based on the SNP data revealed that the large-sized breeds, Hanwoo, Begait, Boran, and Fogera, were more closely clustered compared to the small-sized Arsi breed. Among the seven haplotypes documented from the various breeds, sequence analysis was suggestive of haplotypes 1 and 2 to be ancestral haplotypes for the leptin gene. This study is envisaged to accelerate molecular breeding programs for the genetic improvement of the Ethiopian cattle breeds.
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Affiliation(s)
- Ayele Mandefro
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia.,Institute of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Tesfaye Sisay
- Institute of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Kwan-Suk Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungbuk, 361-763, South Korea
| | - Zewdu Edea
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungbuk, 361-763, South Korea
| | - Rocktotpal Konwarh
- Department of Biotechnology, Addis Ababa Science and Technology University, P.O. Box 16417, Addis Ababa, Ethiopia.,Division of Nanobiomaterials and Nanomedicine, Uniglobe Scientific Pvt. Ltd., 7/9, Kishan Garh, Vasant Kunj, New Delhi, 110070, India
| | - Hailu Dadi
- Ethiopian Biotechnology Institute, P.O. Box 2490, Addis Ababa, Ethiopia.
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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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Ramírez-Ayala LC, Rocha D, Ramos-Onsins SE, Leno-Colorado J, Charles M, Bouchez O, Rodríguez-Valera Y, Pérez-Enciso M, Ramayo-Caldas Y. Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. Genet Sel Evol 2021; 53:3. [PMID: 33397281 PMCID: PMC7784321 DOI: 10.1186/s12711-020-00597-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/11/2020] [Indexed: 02/01/2023] Open
Abstract
Background In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. Results In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Conclusions Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle.
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Affiliation(s)
- Lino C Ramírez-Ayala
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Dominique Rocha
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France
| | - Sebas E Ramos-Onsins
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Jordi Leno-Colorado
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Mathieu Charles
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France.,INRAE, SIGENAE, Jouy-En-Josas, 78350, France
| | - Olivier Bouchez
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, US, 1426, France
| | | | - Miguel Pérez-Enciso
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain.,Institut Català de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes De Montbui, 08140, Spain.
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15
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Alam MZ, Lee YM, Son HJ, Hanna LH, Riley DG, Mannen H, Sasazaki S, Park SP, Kim JJ. Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms. Anim Biosci 2020; 34:789-800. [PMID: 32882779 PMCID: PMC8100474 DOI: 10.5713/ajas.19.0888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/29/2020] [Indexed: 11/27/2022] Open
Abstract
Objective Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei’s genetic distance and Weir and Cockerham’s FST. Results Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was −0.076 for Jeju Black, while −0.018 to −0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.
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Affiliation(s)
- M Zahangir Alam
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Hyo-Jung Son
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Lauren H Hanna
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58105, USA
| | - David G Riley
- Department of Animal Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Shinji Sasazaki
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Se Pill Park
- Faculty of Biotechnology, Jeju National University, Jeju 13557, Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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16
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Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes Genomics 2019; 42:203-215. [DOI: 10.1007/s13258-019-00888-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
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17
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Ahmad SF, Panigrahi M, Chhotaray S, Pal D, Parida S, Bhushan B, Gaur GK, Mishra BP, Singh RK. Revelation of genomic breed composition in a crossbred cattle of India with the help of Bovine50K BeadChip. Genomics 2019; 112:1531-1535. [PMID: 31472242 DOI: 10.1016/j.ygeno.2019.08.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/22/2019] [Accepted: 08/27/2019] [Indexed: 01/24/2023]
Abstract
The aim of the present study was to assess the population structure and admixture levels in the Vrindavani composite population in India by using Bovine50KSNP BeadChip data. Genotypic data were generated for randomly selected animals (n = 72) of Vrindavani population and the data for parental breeds i.e., Hariana (n = 10), Holstein-Friesian (n = 63), Jersey (n = 28) and Brown Swiss (n = 22) were retrieved from a public repository. The indices of population structure were calculated using PLINK software and R-program. The merged dataset was analysed for assessing admixture levels and population stratification using three different approaches i.e., principal component analysis (PCA), multi-dimensional scaling (MDS) approach and the model-based approach in STRUCTURE software. The average minor allele frequency (MAF) value for Vrindavani population was estimated to be 0.235. Vrindavani population was found to possess an average ancestry of 39.5, 22.9, 26.9, and 10.7% inheritance levels from Holstein Friesian, Jersey, Hariana and Brown Swiss cattle breeds, respectively.
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Affiliation(s)
- Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Supriya Chhotaray
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Dhan Pal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B P Mishra
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - R K Singh
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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18
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Saravanan K, Panigrahi M, Kumar H, Bhushan B. Advanced software programs for the analysis of genetic diversity in livestock genomics: a mini review. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1642650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K.A. Saravanan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR - Indian Veterinary Research Institute, Bareilly, India
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19
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Hanif Q, Farooq M, Amin I, Mansoor S, Zhang Y, Khan QM. In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. PLoS One 2018; 13:e0206154. [PMID: 30365525 PMCID: PMC6203363 DOI: 10.1371/journal.pone.0206154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/08/2018] [Indexed: 12/28/2022] Open
Abstract
The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes' miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.
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Affiliation(s)
- Quratulain Hanif
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, PK
| | - Muhammad Farooq
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Imran Amin
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Shahid Mansoor
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Yi Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qaiser Mahmood Khan
- Environmental Toxicology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
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20
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Polymorphisms in toll-like receptor (TLR) 1, 4, 9 and SLC11A1 genes and their association with paratuberculosis susceptibility in Holstein and indigenous crossbred cattle in Turkey. J Genet 2018. [DOI: 10.1007/s12041-018-1008-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Lwin M, Mon SLY, Yamanaka H, Nagano Y, Mannen H, Faruque MO, Kawabe K, Okamoto S, Shimogiri T. Genetic diversities and population structures of four popular Myanmar local cattle breeds. Anim Sci J 2018; 89:1648-1655. [PMID: 30318818 DOI: 10.1111/asj.13112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 11/30/2022]
Abstract
Local cattle breeds are popular in Myanmar because they make excellent draught animals, so it is of fundamental importance that their genetic diversities and population structures are elucidated for breeding and conservation purposes. In this study, we characterized the genetic diversities and population structures of four popular Myanmar local cattle breeds and five native cattle populations from neighboring countries (Bangladesh, Laos, Cambodia, and Vietnam) using the GGP Bovine 50K array. The mean observed and expected heterozygosity estimates using pruned datasets ranged from 0.317 and 0.322, respectively, in Cambodia to 0.448 and 0.421, respectively, in Vietnam South. The four Myanmar local breeds exhibited similar levels of genetic diversity. However, AMOVA revealed significant genetic differentiation among the nine populations (p < 0.00001), and Neighbor-Net analysis showed that Shan Ngwar Pu was distinct from the other Myanmar local breeds. Furthermore, PCA and population structure analyses revealed that the native cattle from neighboring countries genetically influenced the Myanmar local breeds to some extent and that the genetic origins could also be observed in the local breeds. These findings highlight the importance of Myanmar local breeds as genetic resources and provide useful information for the future development of breeding strategies and conservation management plans.
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Affiliation(s)
- Moe Lwin
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Su Lai Y Mon
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Hayate Yamanaka
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Analytical Research Center for Experimental Sciences, Saga University, Honjo, Saga, Japan
| | - Hideyuki Mannen
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | | | - Kotaro Kawabe
- Education Center, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan.,Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan
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22
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Sermyagin AA, Dotsev AV, Gladyr EA, Traspov AA, Deniskova TE, Kostyunina OV, Reyer H, Wimmers K, Barbato M, Paronyan IA, Plemyashov KV, Sölkner J, Popov RG, Brem G, Zinovieva NA. Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds. Genet Sel Evol 2018; 50:37. [PMID: 29996786 PMCID: PMC6042431 DOI: 10.1186/s12711-018-0408-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/01/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references. RESULTS The observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337-0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource. CONCLUSIONS Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.
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Affiliation(s)
- Alexander A Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Elena A Gladyr
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Alexey A Traspov
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Olga V Kostyunina
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, Piacenza, Italy
| | - Ivan A Paronyan
- Russian Research Institute of Farm Animal Genetics and Breeding, Moskovskoe shosse 55a, St. Petersburg-Pushkin, Russia, 196601
| | - Kirill V Plemyashov
- Russian Research Institute of Farm Animal Genetics and Breeding, Moskovskoe shosse 55a, St. Petersburg-Pushkin, Russia, 196601
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Ruslan G Popov
- Yakut Scientific Research Institute of Agriculture, 23/1, ul. Bestuzheva-Marlynskogo, Yakutsk, Sakha Republic, Russia, 677001
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy 60, Podolsk, Moscow, Russia, 142132.
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23
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Mukherjee A, Mukherjee S, Dhakal R, Mech M, Longkumer I, Haque N, Vupru K, Khate K, Jamir IY, Pongen P, Rajkhowa C, Mitra A, Guldbrandtsen B, Sahana G. High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis). Sci Rep 2018; 8:10316. [PMID: 29985484 PMCID: PMC6037757 DOI: 10.1038/s41598-018-28718-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/20/2018] [Indexed: 12/20/2022] Open
Abstract
The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.
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Affiliation(s)
- Anupama Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India.,Dairy Cattle Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Sabyasachi Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India.
| | - Rajan Dhakal
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Moonmoon Mech
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Imsusosang Longkumer
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Nazrul Haque
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Kezhavituo Vupru
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Kobu Khate
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - I Yanger Jamir
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Pursenla Pongen
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Chandan Rajkhowa
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Abhijit Mitra
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland, 797106, India
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
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Selvam R, Murali N, Thiruvenkadan AK, Saravanakumar R, Ponnudurai G, Jawahar TP. Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds. Vet World 2017; 10:549-555. [PMID: 28620261 PMCID: PMC5465771 DOI: 10.14202/vetworld.2017.549-555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/04/2017] [Indexed: 11/16/2022] Open
Abstract
AIM The present study was thus undertaken to analyze the genetic diversity of Kilakarsal and Vembur sheep breeds using single-nucleotide polymorphism (SNP) markers within Toll-like receptor (TLR) 3, 5, 6, 9, and 10 genes. MATERIALS AND METHODS Competitive allele-specific polymerase chain reaction (PCR)-based end-point genotyping was performed using real-time PCR to type the SNPs. Allele discrimination module implemented in real-time PCR was utilized to call the genotypes based on fluorescence intensity recorded for each of the two alleles. Basic diversity indices, namely, gene frequencies, observed heterozygosity, expected heterozygosity, and inbreeding coefficient (FIS), and testing for Hardy-Weinberg equilibrium (HWE) were estimated using package for elementary analysis of SNP data software program. RESULTS Of the 25 SNPs, 22 were found to be polymorphic, whereas two SNPs, namely, TLR3_1081_AC and TLR9_2036_CT, were monomorphic in both Kilakarsal and Vembur sheep populations. The SNP TLR10_1180_AG was monomorphic in Kilakarsal but polymorphic in Vembur sheep. The observed heterozygosities were estimated as 0.289 and 0.309 in Kilakarsal and Vembur sheep, respectively, whereas the expected heterozygosity values were 0.305 and 0.309 in the two breeds, respectively. The overall mean FIS was 0.107 ranging from -0.005 to 0.241 in Kilakarsal sheep and -0.047 ranging from -0.005 to 0.255 in Vembur sheep. In Kilakarsal sheep, the test for HWE revealed TLR9_1308_GC SNP locus with significant deviation (p<0.05) due to heterozygosity deficit. In Vembur sheep, TLR10_82_CT and TLR10_292_CG loci showed significant deviation (p<0.05) due to heterozygosity excess. Other SNP loci did not deviate from HWE (p>0.05) revealing that the population was in HWE proportions. CONCLUSIONS The SNP markers within five TLR genes (TLR3, TLR5, TLR6, TLR9, and TLR10) utilized for genotyping in this study were highly polymorphic in Kilakarsal and Vembur breeds of sheep. This study on the genetic diversity analysis of the Kilakarsal and Vembur sheep breeds revealed considerable genetic variation within the breeds and it can be utilized to improve desirable traits.
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Affiliation(s)
- Rathinasamy Selvam
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India
| | - Nagarajan Murali
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India
| | - A Kannan Thiruvenkadan
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India
| | - Ramesh Saravanakumar
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India
| | - Gurusamy Ponnudurai
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India
| | - Thilak Pon Jawahar
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India
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25
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Blackburn HD, Krehbiel B, Ericsson SA, Wilson C, Caetano AR, Paiva SR. A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford). PLoS One 2017; 12:e0176474. [PMID: 28459870 PMCID: PMC5411102 DOI: 10.1371/journal.pone.0176474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/11/2017] [Indexed: 01/30/2023] Open
Abstract
Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.
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Affiliation(s)
- H. D. Blackburn
- National Animal Germplasm Program, Agricultural Research Service, USDA Fort Collins, CO, United States of America
- * E-mail:
| | - B. Krehbiel
- National Animal Germplasm Program, Agricultural Research Service, USDA Fort Collins, CO, United States of America
- Department of Animal Science Colorado State University, Fort Collins, CO, United States of America
| | - S. A. Ericsson
- Sul Ross University, Alpine, TX, United States of America
| | - C. Wilson
- National Animal Germplasm Program, Agricultural Research Service, USDA Fort Collins, CO, United States of America
| | - A. R. Caetano
- EMBRAPA—–Recursos Geneticos e Biotechnologia Brasilia, BR
- CNPq Fellow, EMBRAPA LABEX, Fort Collins, CO, United States of America
| | - S. R. Paiva
- EMBRAPA—–Recursos Geneticos e Biotechnologia Brasilia, BR
- CNPq Fellow, EMBRAPA LABEX, Fort Collins, CO, United States of America
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26
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Msalya G, Kim ES, Laisser ELK, Kipanyula MJ, Karimuribo ED, Kusiluka LJM, Chenyambuga SW, Rothschild MF. Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses. PLoS One 2017; 12:e0171088. [PMID: 28129396 PMCID: PMC5271371 DOI: 10.1371/journal.pone.0171088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/16/2017] [Indexed: 11/29/2022] Open
Abstract
Background More than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them. Methodology/Principal findings The Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain. Conclusions Population admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle.
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Affiliation(s)
- George Msalya
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
- * E-mail:
| | - Eui-Soo Kim
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Emmanuel L. K. Laisser
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
- Ministry of Education and Vocational Training, Inspectorate Department Eastern Zone, Morogoro, Tanzania
| | | | - Esron D. Karimuribo
- Department of Veterinary Medicine and Public Health, SUA, Morogoro, Tanzania
| | - Lughano J. M. Kusiluka
- Department of Veterinary Medicine and Public Health, SUA, Morogoro, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Sebastian W. Chenyambuga
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture (SUA), Morogoro, Tanzania
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
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27
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Karimi K, Strucken EM, Moghaddar N, Ferdosi MH, Esmailizadeh A, Gondro C. Local and global patterns of admixture and population structure in Iranian native cattle. BMC Genet 2016; 17:108. [PMID: 27418004 PMCID: PMC4946207 DOI: 10.1186/s12863-016-0416-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/08/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Two separate domestication events gave rise to humped zebu cattle in India and humpless taurine cattle in the Fertile Crescent of the Near and Middle East. Iran covers the Eastern side of the Fertile Crescent and exhibits a variety of native cattle breeds, however, only little is known about the admixture patterns of Iranian cattle and their contribution to the formation of modern cattle breeds. RESULTS Genome-wide data (700 k chip) of eight Iranian cattle breeds (Sarabi N = 19, Kurdi N = 7, Taleshi N = 7, Mazandarani N = 10, Najdi N = 7, Pars N = 7, Kermani N = 9, and Sistani N = 9) were collected from across Iran. For a local assessment, taurine (Holstein and Jersey) and indicine (Brahman) outgroup samples were used. For the global perspective, 134 world-wide cattle breeds were included. Between breed variation amongst Iranian cattle explained 60 % (p < 0.001) of the total molecular variation and 82.88 % (p < 0.001) when outgroups were included. Several migration edges were observed within the Iranian cattle breeds. The highest indicine proportion was found in Sistani. All Iranian breeds with higher indicine ancestry were more admixed with a complex migration pattern. Nineteen founder populations most accurately explained the admixture of 44 selected representative cattle breeds (standard error 0.4617). Low levels of African ancestry were identified in Iranian cattle breeds (on average 7.5 %); however, the signal did not persist through all analyses. Admixture and migration analyses revealed minimal introgression from Iranian cattle into other taurine cattle (Holstein, Hanwoo, Anatolian breeds). CONCLUSION The eight Iranian cattle breeds feature a discrete genetic composition which should be considered in conservation programs aimed at preserving unique species and genetic diversity. Despite a complex admixture pattern among Iranian cattle breeds, there was no strong introgression from other world-wide cattle breeds into Iranian cattle and vice versa. Considering Iran's central location of cattle domestication, Iranian cattle might represent a local domestication event that remained contained and did not contribute to the formation of modern breeds, or genetics of the ancestral population that gave rise to modern cattle is too diluted to be linked directly to any current cattle breeds.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran.
| | - Eva M Strucken
- School of Environmental and Rural Science, University of New England, Armidale, 2351, NSW, Australia
| | - Nasir Moghaddar
- School of Environmental and Rural Science, University of New England, Armidale, 2351, NSW, Australia
| | | | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB, 76169-133, Iran.,State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, 2351, NSW, Australia
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28
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Jiang J, Yu J, Li J, Li P, Fan Z, Niu L, Deng J, Yue B, Li J. Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques. PLoS One 2016; 11:e0154665. [PMID: 27135608 PMCID: PMC4852913 DOI: 10.1371/journal.pone.0154665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/18/2016] [Indexed: 01/20/2023] Open
Abstract
The evolutionary history of macaques, genus Macaca, has been under debate due to the short times of divergence. In this study, maternal, paternal, and biparental genetic systems were applied to infer phylogenetic relationships among macaques and to trace ancient hybridization events in their evolutionary history. Using a PCR display method, 17 newly phylogenetically informative Alu insertions were identified from M. assamensis. We combined presence/absence analysis of 84 Alu elements with mitochondrial genomes as well as nuclear sequences (five autosomal genes, two Y chromosomal genes, and one X chromosomal fragment) to reconstruct a robust macaque phylogeny. Topologies generated from different inherited markers were similar supporting six well defined species groups and a close relationship of M. assamensis and M. thibetana, but differed in the placing of M. arctoides. Both Alu elements and nuclear genes supported that M. arctoides was close to the sinica group, whereas the mitochondrial data clustered it into the fascicularis/mulatta lineage. Our results reveal that a sex-biased hybridization most likely occurred in the evolutionary history of M. arctoides, and suggest an introgressive pattern of male-mediated gene flow from the ancestors of M. arctoides to the M. mulatta population followed by nuclear swamping. According to the estimation of divergence dates, the hybridization occurred around 0.88~1.77 mya (nuclear data) or 1.38~2.56 mya (mitochondrial data). In general, our study indicates that a combination of various molecular markers could help explain complicated evolutionary relationships. Our results have provided new insights into the evolutionary history of macaques and emphasize that hybridization might play an important role in macaque evolution.
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Affiliation(s)
- Juan Jiang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Jianqiu Yu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Peng Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Lili Niu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jiabo Deng
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
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Al-Mamun HA, Clark SA, Kwan P, Gondro C. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol 2015; 47:90. [PMID: 26602211 PMCID: PMC4659207 DOI: 10.1186/s12711-015-0169-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 11/02/2015] [Indexed: 01/23/2023] Open
Abstract
Background Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (Ne), heterozygosity, fixation index (FST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. Methods In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r2 and D′), Ne, heterozygosity, FST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Results Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller Ne than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest FST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. Conclusions This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Samuel A Clark
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - Paul Kwan
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia.
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
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Dalirsefat SB, Dong X, Deng X. Molecular phylogenetic analysis of Chinese indigenous blue-shelled chickens inferred from whole genomic region of the SLCO1B3 gene. Poult Sci 2015; 94:1776-86. [PMID: 26069255 DOI: 10.3382/ps/pev146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2015] [Indexed: 11/20/2022] Open
Abstract
In total, 246 individuals from 8 Chinese indigenous blue- and brown-shelled chicken populations (Yimeng Blue, Wulong Blue, Lindian Blue, Dongxiang Blue, Lushi Blue, Jingmen Blue, Dongxiang Brown, and Lushi Brown) were genotyped for 21 SNP markers from the SLCO1B3 gene to evaluate phylogenetic relationships. As a representative of nonblue-shelled breeds, White Leghorn was included in the study for reference. A high proportion of SNP polymorphism was observed in Chinese chicken populations, ranging from 89% in Jingmen Blue to 100% in most populations, with a mean of 95% across all populations. The White Leghorn breed showed the lowest polymorphism, accounting for 43% of total SNPs. The mean expected heterozygosity varied from 0.11 in Dongxiang Blue to 0.46 in Yimeng Blue. Analysis of molecular variation (AMOVA) for 2 groups of Chinese chickens based on eggshell color type revealed 52% within-group and 43% between-group variations of the total genetic variation. As expected, FST and Reynolds' genetic distance were greatest between White Leghorn and Chinese chicken populations, with average values of 0.40 and 0.55, respectively. The first and second principal coordinates explained approximately 92% of the total variation and supported the clustering of the populations according to their eggshell color type and historical origins. STRUCTURE analysis showed a considerable source of variation among populations for the clustering into blue-shelled and nonblue-shelled chicken populations. The low estimation of genetic differentiation (FST) between Chinese chicken populations is possibly due to a common historical origin and high gene flow. Remarkably similar population classifications were obtained with all methods used in the study. Aligning endogenous avian retroviral (EAV)-HP insertion sequences showed no difference among the blue-shelled chickens.
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Affiliation(s)
- Seyed Benyamin Dalirsefat
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing 100193, China
| | - Xianggui Dong
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing 100193, China
| | - Xuemei Deng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing 100193, China
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Makina SO, Muchadeyi FC, van Marle-Köster E, MacNeil MD, Maiwashe A. Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel. Front Genet 2014; 5:333. [PMID: 25295053 PMCID: PMC4170099 DOI: 10.3389/fgene.2014.00333] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/04/2014] [Indexed: 11/22/2022] Open
Abstract
Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.
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Affiliation(s)
- Sithembile O. Makina
- Agricultural Research Council-Animal Production InstituteIrene, South Africa
- Department of Animal and Wildlife Sciences, University of PretoriaHatfield, South Africa
| | - Farai C. Muchadeyi
- Agricultural Research Council-Biotechnology PlatformOnderstepoort, South Africa
| | - Este van Marle-Köster
- Department of Animal and Wildlife Sciences, University of PretoriaHatfield, South Africa
| | - Michael D. MacNeil
- Agricultural Research Council-Animal Production InstituteIrene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of Free StateBloemfontein, South Africa
- Delta G, Miles CityMT, USA
| | - Azwihangwisi Maiwashe
- Agricultural Research Council-Animal Production InstituteIrene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of Free StateBloemfontein, South Africa
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Uzzaman MR, Edea Z, Bhuiyan MSA, Walker J, Bhuiyan AKFH, Kim KS. Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1381-6. [PMID: 25178287 PMCID: PMC4150168 DOI: 10.5713/ajas.2014.14160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/23/2014] [Accepted: 06/09/2014] [Indexed: 11/27/2022]
Abstract
In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.
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Affiliation(s)
- Md Rasel Uzzaman
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Zewdu Edea
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Shamsul Alam Bhuiyan
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jeremy Walker
- GeneSeek, Neogen Corporation, Lincoln, NE 68521, USA
| | - A K F H Bhuiyan
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kwan-Suk Kim
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Nishimaki T, Ibi T, Tanabe Y, Miyazaki Y, Kobayashi N, Matsuhashi T, Akiyama T, Yoshida E, Imai K, Matsui M, Uemura K, Watanabe N, Fujita T, Saito Y, Komatsu T, Yamada T, Mannen H, Sasazaki S, Kunieda T. The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers. Anim Sci J 2013; 84:585-91. [PMID: 23607656 DOI: 10.1111/asj.12045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/07/2013] [Indexed: 11/28/2022]
Abstract
Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise FST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.
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Affiliation(s)
- Takahiro Nishimaki
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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Edea Z, Dadi H, Kim SW, Dessie T, Lee T, Kim H, Kim JJ, Kim KS. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Front Genet 2013; 4:35. [PMID: 23518904 PMCID: PMC3604626 DOI: 10.3389/fgene.2013.00035] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/01/2013] [Indexed: 11/16/2022] Open
Abstract
In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed.
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Affiliation(s)
- Zewdu Edea
- International Livestock Research Institute Addis Ababa, Ethiopia ; Department of Animal Science, Chungbuk National University Cheongju, Korea
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Woelders H, Windig J, Hiemstra SJ. How developments in cryobiology, reproductive technologies and conservation genomics could shape gene banking strategies for (farm) animals. Reprod Domest Anim 2013; 47 Suppl 4:264-73. [PMID: 22827380 DOI: 10.1111/j.1439-0531.2012.02085.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many local breeds are currently at risk because of replacement by a limited number of specialized commercial breeds. Concurrently, for many breeds, allelic diversity within breeds declines because of inbreeding. Gene banking of germplasm may serve to secure the breeds and the alleles for any future use, for instance to recover a lost breed, to address new breeding goals, to support breeding schemes in small populations to minimize inbreeding, and for conservation genetics and genomics research. Developments in cryobiology and reproductive technology have generated several possibilities for preserving germplasm in farm animals. Furthermore, in some mammalian and bird species, gene banking of material is difficult or impossible, requiring development of new alternative methods or improvement of existing methods. Depending on the species, there are interesting possibilities or research developments in the use of epididymal spermatozoa, oocytes and embryos, ovarian and testicular tissue, primordial germ cells, and somatic cells for the conservation of genetic diversity in farm- and other animal species. Rapid developments in genomics research also provide new opportunities to optimize conservation and sampling strategies and to characterize genome-wide genetic variation. With regard to gene banks for farm animals, collaboration between European countries is being developed through a number of organizations, aimed at sharing knowledge and expertise between national programmes. It would be useful to explore further collaboration between countries, within the framework of a European gene banking strategy that should minimize costs of conservation and maximize opportunities for exploitation and sustainable use of genetic diversity.
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Affiliation(s)
- H Woelders
- Wageningen UR, Centre for Genetic Resources, CGN, Wageningen, The Netherlands.
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Edea Z, Dadi H, Kim SW, Dessie T, Kim KS. Comparison of SNP variation and distribution in indigenous ethiopian and korean cattle (hanwoo) populations. Genomics Inform 2012; 10:200-5. [PMID: 23166531 PMCID: PMC3492656 DOI: 10.5808/gi.2012.10.3.200] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/25/2022] Open
Abstract
Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals, representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3 zebu (Borana, Arsi and Ambo), and 1 zebu × Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p < 0.001). Across the Ethiopian cattle populations, a common variant MAF (≥0.10 and ≤0.5) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.
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Affiliation(s)
- Zewdu Edea
- International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia. ; Chungbuk National University, Cheongju 361-763, Korea
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Aslam ML, Bastiaansen JWM, Elferink MG, Megens HJ, Crooijmans RPMA, Blomberg LA, Fleischer RC, Van Tassell CP, Sonstegard TS, Schroeder SG, Groenen MAM, Long JA. Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo). BMC Genomics 2012; 13:391. [PMID: 22891612 PMCID: PMC3496629 DOI: 10.1186/1471-2164-13-391] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/09/2012] [Indexed: 11/23/2022] Open
Abstract
Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD Wageningen, The Netherlands.
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