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Kang R, Lee H, Seon H, Park C, Song J, Park JK, Kim YK, Kim M, Park T. Effects of diets for three growing stages by rumen inocula donors on in vitro rumen fermentation and microbiome. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:523-542. [PMID: 38975572 PMCID: PMC11222118 DOI: 10.5187/jast.2023.e109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 07/09/2024]
Abstract
Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [Eubacterium] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation.
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Affiliation(s)
- Ryukseok Kang
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
| | - Huseong Lee
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
- Graduate School of Agricultural Science,
Tohoku University, Sendai 980-0845, Japan
| | - Hyeonsu Seon
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Cheolju Park
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | | | | | | | - Minseok Kim
- Division of Animal Science, Chonnam
National University, Gwangju 61186, Korea
| | - Tansol Park
- Department of Animal Science and
Technology, Chung-Ang University, Anseong 17546, Korea
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2
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Sambe BS, Diouf MN, Houaga I, Ndiaye B, Badji MN, Diop M, Sembene M. Genetic diversity of bovine populations raised in Senegal. Vet Med Sci 2022; 8:2173-2182. [PMID: 35781798 PMCID: PMC9514503 DOI: 10.1002/vms3.873] [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] [Indexed: 11/24/2022] Open
Abstract
Background The Gobra zebu and N'dama taurine cattle breeds are important genetic animal resources for Senegal. For several decades, genetic breeding programmes have been devoted to them at the Centre de Recherches Zootechniques de Dahra and Kolda. Since then, these animals have been subjected to mass selection, mainly in closed selection nuclei. Objective This study aims to assess the genetic diversity within these selection nuclei in order to orient future selection strategies. Material and methods The study was carried out on the Gobra zebu and N'dama taurine populations from selection nuclei of Dahra and Kolda respectively, which were compared to 5 other populations of the main cattle breeds in Senegal. One hundred eighty (180) animals were genotyped with 21 microsatellite markers recommended by the Food and Agriculture Organisation. Results All populations were found to be polymorphic with a PIC of over 55%. However, animals from the CRZ‐Dahra (indigenous) and CRZ‐Kolda stations had the lowest mean heterozygosity (0.643 and 0.591 respectively). The other populations had an average heterozygosity between 0.650 and 0.737. Conclusion The cattle populations maintained at the different CRZs show a lower genetic diversity than the other populations described in our study. The main reasons for this are reproductive isolation and selection pressure on these populations.
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Affiliation(s)
| | - Mame Nahé Diouf
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
| | - Isidore Houaga
- Centre International de Recherche‐Développement sur l'Elevage en zone Subhumide (CIRDES) Bobo‐Dioulasso Burkina Faso
| | - Bakary Ndiaye
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
- Département de Biologie Animale Université Cheikh Anta Diop (UCAD) Dakar Sénégal
| | - Marc Noël Badji
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
- Département de Biologie Animale Université Cheikh Anta Diop (UCAD) Dakar Sénégal
| | - Mamadou Diop
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
| | - Mbacké Sembene
- Département de Biologie Animale Université Cheikh Anta Diop (UCAD) Dakar Sénégal
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Ariyaraphong N, Laopichienpong N, Singchat W, Panthum T, Farhan Ahmad S, Jattawa D, Duengkae P, Muangmai N, Suwanasopee T, Koonawootrittriron S, Srikulnath K. High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing. Animals (Basel) 2021; 11:ani11061680. [PMID: 34199963 PMCID: PMC8227385 DOI: 10.3390/ani11061680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup "I", were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.
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Affiliation(s)
- Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Danai Jattawa
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok 10900, Thailand
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Thakor PB, Hinsu AT, Bhatia DR, Shah TM, Nayee N, Sudhakar A, Rank DN, Joshi CG. High-throughput genotype-based population structure analysis of selected buffalo breeds. Transl Anim Sci 2021; 5:txab033. [PMID: 33981962 PMCID: PMC8103726 DOI: 10.1093/tas/txab033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/01/2021] [Indexed: 11/29/2022] Open
Abstract
India is considered as the home tract of some of the best buffalo breeds. However, the genetic structure of the Indian river buffalo is poorly understood. Hence, there is a need to characterize the populations and understand the genetic structure of various buffalo breeds for selection and to design breeding strategies. In this study, we have analyzed genetic variability and population structure of seven buffalo breeds from their respective geographical regions using Axiom Buffalo Genotyping Array. Diversity, as measured by expected heterozygosity, ranged from 0.364 in Surti to 0.384 in Murrah breed, and pair-wise FST values revealed the lowest genetic distance between Murrah and Nili-Ravi (0.0022), while the highest between Surti and Pandharpuri (0.030). Principal component analysis and structure analysis unveiled the differentiation of Surti, Pandharpuri, and Jaffarabadi in first two principal components and at K = 4, respectively, while remaining breeds were grouped together as a separate single cluster and admixed. Murrah and Mehsana showed early linkage disequilibrium (LD) decay, while Surti breed showed late decay. In LD blocks to quantitative trait locis (QTLs) concordance analysis, 4.65% of concordance was observed with 873 LD blocks overlapped with 2,330 QTLs. Overall, total 4,090 markers were identified from all LD blocks for six types of traits. Results of this study indicated that these single-nucleotide polymorphism (SNP) markers could differentiate phenotypically distinct breeds like Surti, Pandharpuri, and Jaffarabadi but not others. So, there is a need to develop SNP chip based on SNP markers identified by sequence information of local breeds.
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Affiliation(s)
- Prakash B Thakor
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Ankit T Hinsu
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Dhruv R Bhatia
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Tejas M Shah
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Nilesh Nayee
- National Dairy Development Board, Anand 388001, India
| | - A Sudhakar
- National Dairy Development Board, Anand 388001, India
| | - Dharamshibhai N Rank
- Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agriculture University, Anand 388001, India.,Gujarat Biotechnology Research Centre, Gandhinagar 382017, India
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5
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Dar AH, Kumar S, Mukesh M, Ahmad SF, Singh DV, Sharma RK, Ghosh AK, Singh B, Rahman JU, Sodhi M. Genetic characterization and population structure of different coat colour variants of Badri cattle. Mol Biol Rep 2020; 47:8485-8497. [PMID: 33063149 DOI: 10.1007/s11033-020-05890-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/03/2020] [Indexed: 11/25/2022]
Abstract
The present study aimed to genetically characterize the Badri cattle and its three colour variants and assess their population structure using 24 microsatellite markers. Out of 96 animals analyzed, 32 each were collected from grey (GVBC), brown (BrVBC) and black (BVBC) colour variants of Badri cattle (BC). The genetic diversity parameters including allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Shannon's indices and F-statistics were estimated using POPGENE software. Bottleneck analysis was performed using both qualitative and quantitative approaches. A total of 274 alleles (50 private and 224 shared) were scored for BC, GVBC, BrVBC and BVBC with mean number of 11.417, 9.083, 9.125 and 9.083 alleles, respectively. All populations exhibited average heterozygosity estimate > 0.5 indicating existence of substantial genetic variability, concurrent with revelations from Shannon's indices. Observed mean PIC estimates (> 0.74) were indicative of optimum informativeness of used microsatellite markers. The mean inbreeding estimates (F) in GVBC, BrVBC and BVBC were 0.041, - 0.024 and 0.016, respectively. The pair wise genetic (> 0.91) pointed towards similarity between different colour variant populations. STRUCTURE analysis also revealed clear admixture for the three Badri colour variants indicating absence of genetic differentiation. The present study revealed first-hand information that populations of Badri cattle with different phenotypes with respect to coat colour are genetically related and can be considered as a single breed. The comprehensive knowledge generated for Badri cattle will help in designing breeding plan for its genetic improvement and deciding the conservation priorities.
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Affiliation(s)
- Aashaq Hussain Dar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Sanjay Kumar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, 132001, India
| | - Sheikh Firdous Ahmad
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Dev Vrat Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Rabendra Kumar Sharma
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Ashis Kumar Ghosh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Balwinder Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Javid Ur Rahman
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, 132001, India.
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6
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Gamarra D, Taniguchi M, Aldai N, Arakawa A, Lopez-Oceja A, de Pancorbo MM. Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes. Animals (Basel) 2020; 10:E1584. [PMID: 32899488 PMCID: PMC7552125 DOI: 10.3390/ani10091584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/23/2020] [Accepted: 09/03/2020] [Indexed: 11/26/2022] Open
Abstract
Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10-25 and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest FST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest FST markers is proposed for a confident parentage analysis and high traceability.
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Affiliation(s)
- David Gamarra
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (D.G.); (A.L.-O.)
| | - Masaaki Taniguchi
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan; (M.T.); (A.A.)
| | - Noelia Aldai
- Lactiker Research Group, Department of Pharmacy and Food Sciences, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain;
| | - Aisaku Arakawa
- Animal Genome Unit, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan; (M.T.); (A.A.)
| | - Andres Lopez-Oceja
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (D.G.); (A.L.-O.)
| | - Marian M. de Pancorbo
- Biomics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (D.G.); (A.L.-O.)
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7
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Svishcheva G, Babayan O, Lkhasaranov B, Tsendsuren A, Abdurasulov A, Stolpovsky Y. Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle. Animals (Basel) 2020; 10:E1493. [PMID: 32846979 PMCID: PMC7552156 DOI: 10.3390/ani10091493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/03/2022] Open
Abstract
We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.
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Affiliation(s)
- Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Babayan
- Gordiz Ltd., Skolkovo Innovation Centre, 121205 Moscow, Russia
| | | | - Ariuntuul Tsendsuren
- Institute of General and Experimental Biology, The Mongolian Academy of Sciences, Ulaanbaatar 210351, Mongolia
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500 Osh, Kyrgyzstan
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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8
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Edea Z, Jung KS, Shin SS, Yoo SW, Choi JW, Kim KS. Signatures of positive selection underlying beef production traits in Korean cattle breeds. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:293-305. [PMID: 32568261 PMCID: PMC7288235 DOI: 10.5187/jast.2020.62.3.293] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 01/01/2023]
Abstract
The difference in the breeding programs and population history may have diversely
shaped the genomes of Korean native cattle breeds. In the absence of phenotypic
data, comparisons of breeds that have been subjected to different selective
pressures can aid to identify genomic regions and genes controlling qualitative
and complex traits. In this study to decipher genetic variation and identify
evidence of divergent selection, 3 Korean cattle breeds were genotyped using the
recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array.
The three Korean cattle breeds clustered according to their coat color
phenotypes and breeding programs. The Heugu breed reliably showed smaller
effective population size at all generations considered. Across the autosomal
chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and
Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the
two pairwise comparisons. The most important signals of selection were detected
on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb),
containing genes related to body size, and coat color (XKR4,
LYN, PLAG1, SDR16C5,
TMEM68, CDH15, MC1R, and
GALNS). Some of the candidate genes are also associated
with meat quality traits (ACSF3, EIF2B1,
BANP, APCDD1, and GALM)
and harbor quantitative trait locus (QTL) for beef production traits. Further
functional analysis revealed that the candidate genes (DBI,
ACSF3, HINT2, GBA2,
AGPAT5, SCAP, ELP6,
APOB, and RBL1) were involved in gene
ontology (GO) terms relevant to meat quality including fatty acid oxidation,
biosynthesis, and lipid storage. Candidate genes previously known to affect beef
production and quality traits could be used in the beef cattle selection
strategies.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Sub Jung
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Sung-Sub Shin
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Song-Won Yoo
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Jae Won Choi
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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9
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Park B, Choi TJ, Park MN, Oh SH. Estimation of environmental effects and genetic parameters of carcass traits on Chikso (Korean brindle cattle). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:525-530. [PMID: 31480162 PMCID: PMC7054609 DOI: 10.5713/ajas.19.0136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 07/16/2019] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The purpose of this study was i) to identify the characteristics of carcass traits in Chikso by gender, region, age at slaughter, and coat color using the carcass data collected from the nationwide pedigree information and coat color investigation, and ii) to estimate genetic parameters for breed improvement. METHODS A linear model was used to analyze the environmental effects on the carcass traits and to estimate genetic parameters. Analysis of variance was performed using TYPE III sum of squares for the unbalanced data provided by the general linear model procedure. Variance components for genetic parameters was estimated using REMLF90 of the BLUPF90 family programs. RESULTS Phenotypic performance of carcass weight (CW), eye muscle area (EMA), and backfat thickness (BF) in Chikso were lower than those of Hanwoo. This is a natural outcome because Hanwoo have undergone significant efforts for improvement at the national level, a phenomenon not observed in Chikso. Another factor influencing the above outcome was the smaller population size of Chikso compared to that of Hanwoo's. The heritabilities of CW, EMA, BF, and marbling score in Chikso were estimated as 0.50, 0.37, 0.35, and 0.53, respectively, which were was higher than those of Hanwoo. CONCLUSION Based on the genetic parameters that were estimated in this study, it is expected that the carcass traits will improve when the livestock research institutes at each province conduct small-scale performance tests and the semen is provided to farmers after selecting proven bulls using the state-of-art selection technique such as genomic selection.
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Affiliation(s)
- Byoungho Park
- National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Tae Jeong Choi
- National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Mi Na Park
- National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Sang-Hyon Oh
- Department of Agriculture, Food, and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
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Asma B, Zhao F, Cai X, Luo X. Mining and Polymorphic Analysis of Di-Nucleotide Microsatellites from Yak Genome. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Sudrajad P, Seo DW, Choi TJ, Park BH, Roh SH, Jung WY, Lee SS, Lee JH, Kim S, Lee SH. Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds. Anim Genet 2016; 48:85-89. [PMID: 27642108 DOI: 10.1111/age.12488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 12/01/2022]
Abstract
The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (Ne ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and Ne in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small Ne values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and Ne for each breed reflect the breeding strategy applied. The Ne for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.
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Affiliation(s)
- P Sudrajad
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea.,Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jakarta, 12540, Indonesia
| | - D W Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea
| | - T J Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea
| | - B H Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea
| | - S H Roh
- Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea
| | - W Y Jung
- Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea
| | - S S Lee
- Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea
| | - J H Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea
| | - S Kim
- Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea
| | - S H Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea
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12
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Kim JH, Lee SS, Kim SC, Choi SB, Kim SH, Lee CW, Jung KS, Kim ES, Choi YS, Kim SB, Kim WH, Cho CY. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:624-30. [PMID: 26954229 PMCID: PMC4852222 DOI: 10.5713/ajas.15.0692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/23/2015] [Accepted: 01/05/2016] [Indexed: 11/27/2022]
Abstract
Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds.
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Affiliation(s)
- Jae-Hwan Kim
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Seong-Su Lee
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Seung Chang Kim
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Seong-Bok Choi
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
| | - Su-Hyun Kim
- Gyeonggi Livestock and Veterinary Service, Suwon 16381, Korea
| | - Chang Woo Lee
- Gangwon Provincial Livestock Research Center, Hoengseong 25266, Korea
| | - Kyoung-Sub Jung
- Chungbuk Institute of Livestock and Veterinary Research, Cheongwon 28153, Korea
| | - Eun Sung Kim
- Jeonbuk Institute of Livestock and Veterinary Research, Gimje 54324, Korea
| | - Young-Sun Choi
- Jeonnam Agricultural Research and Extension Services, Gangjin 59213, Korea
| | - Sung-Bok Kim
- Chungnam Institute of Livestock Experiment Research, Cheongyang 33350, Korea
| | - Woo Hyun Kim
- Gyeongbuk Livestock Research Institute, Yeongju 36052, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Research Center, NIAS, RDA, Namwon 55717, Korea
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Agung PP, Saputra F, Septian WA, Lusiana, Zein MSA, Sulandari S, Anwar S, Wulandari AS, Said S, Tappa B. Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:176-83. [PMID: 26732442 PMCID: PMC4698697 DOI: 10.5713/ajas.15.0155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 11/27/2022]
Abstract
A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.
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Affiliation(s)
- Paskah Partogi Agung
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ferdy Saputra
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Wike Andre Septian
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Lusiana
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Moch Syamsul Arifin Zein
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Sri Sulandari
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Saiful Anwar
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ari Sulistyo Wulandari
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Syahruddin Said
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Baharuddin Tappa
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
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Strucken EM, Lee SH, Jang GW, Porto-Neto LR, Gondro C. Towards breed formation by island model divergence in Korean cattle. BMC Evol Biol 2015; 15:284. [PMID: 26677975 PMCID: PMC4683938 DOI: 10.1186/s12862-015-0563-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/08/2015] [Indexed: 01/03/2023] Open
Abstract
Background The main cattle breed in Korea is the brown Hanwoo, which has been under artificial selection within a national breeding program for several decades. Varieties of the Hanwoo known as Jeju Black and Chikso were not included in the breeding program and remained isolated from the effects of recent artificial selection advancements. We analysed the Jeju Black and Chikso populations in regards to their genetic variability, state of inbreeding, as well as level of differentiation from the mainland Hanwoo population. Results Jeju Black and Chikso were found to have small estimated effective population sizes (Ne) of only 11 and 7, respectively. Despite a small Ne, higher than expected heterozygosity levels were observed (0.303 and 0.306), however, lower allelic richness was found for the two island populations (1.76 and 1.77) compared to the mainland population (1.81). The increase in heterozygosity could be due to environmental disease challenges that promoted maintenance of higher genetic variability; however, no direct proof exists. Increased heterozygosity due to a first generation crossing of genetically different populations is not recorded. The differentiation between the Korean populations had FST values between 0.014 and 0.036 which is not as high as the differentiation within European beef or dairy cattle breeds (0.047–0.111). This suggests that the three populations have not separated into independent breeds. Conclusion Results agree with an island model of speciation where the brown Hanwoo represents the ancestral breed, whilst the Jeju Black and Chikso diverge from this common ancestor, following different evolutionary trajectories. Nevertheless, differences are minor and whether Jeju Black and Chikso cattle will develop into discrete breeds or reintegrate with the main population has to be seen in the future and will largely depend on human management decisions. This offers a rare opportunity to accompany the development of new breeds but also poses challenges on how to preserve these incipient breeds and ensure their long term viability. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0563-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eva M Strucken
- University of New England, School of Environmental and Rural Science, Armidale, Australia.
| | - Seung H Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, Korea.
| | - Gul W Jang
- Rural Development Administration, National Institute of Animal Science, Wanju, Korea.
| | - Laercio R Porto-Neto
- Scientific and Industrial Research Organization, Agricultural Flagship, Brisbane, Australia.
| | - Cedric Gondro
- University of New England, School of Environmental and Rural Science, Armidale, Australia.
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15
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Associations between allelic polymorphism of the BMP Binding Endothelial Regulator and phenotypic variation of cattle. Mol Cell Probes 2015; 29:358-364. [DOI: 10.1016/j.mcp.2015.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 11/22/2022]
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16
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Wangkumhang P, Wilantho A, Shaw PJ, Flori L, Moazami-Goudarzi K, Gautier M, Duangjinda M, Assawamakin A, Tongsima S. Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry. PeerJ 2015; 3:e1318. [PMID: 26528405 PMCID: PMC4627918 DOI: 10.7717/peerj.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/22/2015] [Indexed: 12/20/2022] Open
Abstract
Cattle commonly raised in Thailand have characteristics of Bos indicus (zebu). We do not know when or how cattle domestication in Thailand occurred, and so questions remain regarding their origins and relationships to other breeds. We obtained genome-wide SNP genotypic data of 28 bovine individuals sampled from four regions: North (Kho-Khaolampoon), Northeast (Kho-Isaan), Central (Kho-Lan) and South (Kho-Chon) Thailand. These regional varieties have distinctive traits suggestive of breed-like genetic variations. From these data, we confirmed that all four Thai varieties are Bos indicus and that they are distinct from other indicine breeds. Among these Thai cattle, a distinctive ancestry pattern is apparent, which is the purest within Kho-Chon individuals. This ancestral component is only present outside of Thailand among other indicine breeds in Southeast Asia. From this pattern, we conclude that a unique Bos indicus ancestor originated in Southeast Asia, and native Kho-Chon Thai cattle retain the signal of this ancestry with limited admixture of other bovine ancestors.
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Affiliation(s)
- Pongsakorn Wangkumhang
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology , Pathum Thani , Thailand
| | - Alisa Wilantho
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology , Pathum Thani , Thailand
| | - Philip J Shaw
- Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology , Pathum Thani , Thailand
| | - Laurence Flori
- UMR INTERTRYP, CIRAD , Montpellier , France ; UMR 1313 GABI, INRA , Jouy-en-Josas , France
| | | | - Mathieu Gautier
- UMR CBGP (INRA/CIRAD/IRD/Supagro), INRA , Montferrier-sur-Lez , France
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University , Khon Kaen , Thailand
| | - Anunchai Assawamakin
- Department of Pharmacology, Faculty of Pharmacy, Mahidol University , Bangkok , Thailand
| | - Sissades Tongsima
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology , Pathum Thani , Thailand
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