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Ibrahim A, Baliarti E, Budisatria IGS, Artama WT, Widayanti R, Maharani D, Tavares L, Margawati ET. Genetic diversity and relationship among Indonesian local sheep breeds on Java Island based on mitochondrial cytochrome b gene sequences. J Genet Eng Biotechnol 2023; 21:34. [PMID: 36930372 PMCID: PMC10023820 DOI: 10.1186/s43141-023-00491-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND The cytochrome b (Cyt b) gene is one of the most studied mitochondrial DNA (mtDNA) genes to determine sheep's genetic profile. This study aimed to determine the genetic diversity and relationships of several Indonesian local sheep populations on Java Island, Indonesia, based on the mtDNA Cyt b gene sequences. Blood samples were collected from forty-one individual sheep in seven populations of Indonesia local sheep breeds on Java Island (Priangan = 6, Garut = 6, Batur = 7, Wonosobo = 5, Javanese Thin-Tailed/JTT = 7, Javanese Fat-Tailed/JFT = 5, and Sapudi = 5). DNA extraction was performed on blood samples, and the mtDNA Cyt b gene was amplified using specific primers (Alek-CBF: 5'-CAACCCCACCACTTACAA-3' and Alek-CBR: 5'-CCTTGAGTCTTAGGGAGGTT-3'). The polymerase chain reaction (PCR) products were then sequenced, and data were analyzed using the MEGA version 7.0, DNA SP version 6.0, and NTSYS-pc version 2.11 software. RESULTS A total of 1140 bp complete mtDNA Cyt b gene sequences in this study obtained 1134 monomorphic sites (I), six polymorphic sites (V), one segregation site (S), and five parsimony informative sites (P) with a nucleotide diversity (Pi), the average number of nucleotide differences (K), and sequence conservation (SC) were 0.00119, 1.35610, and 0.9947, respectively. There were six haplotypes consisting of two unique haplotypes and four shared haplotypes with a haplotype diversity (Hd) of 0.5415. The genetic distance within and between populations ranged from 0.0000 to 0.0016 and 0.0000 to 0.0020, respectively. Wonosobo, JFT, and Sapudi sheep have the closest relationship, and then these three breeds were close to JTT sheep, followed by Batur, Priangan, and Garut sheep. Two haplogroups have been found based on the Ovine haplogroup clustering. All Wonosobo, JTT, JFT, Sapudi sheep, and most Batur sheep were clustered into haplogroup B. In contrast, Garut sheep were mostly clustered into haplogroup A, while Priangan sheep were clustered into both haplogroups with the same percentage. CONCLUSION Seven Indonesian local sheep breeds on Java Island have a close relationship clustered into two haplogroups, namely haplogroups A and B. Most Indonesian local sheep breeds on Java Island in this study were clustered into haplogroup B, except for Garut and Priangan sheep.
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Affiliation(s)
- Alek Ibrahim
- Department of Animal Production, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia, 55281.,Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor, Indonesia, 16911
| | - Endang Baliarti
- Department of Animal Production, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia, 55281.
| | - I Gede Suparta Budisatria
- Department of Animal Production, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia, 55281
| | - Wayan Tunas Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia, 55281
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia, 55281
| | - Dyah Maharani
- Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, Indonesia, 55281
| | - Luis Tavares
- Department of Animal Science, Faculty of Agriculture, Universidade Nacional Timor Lorosa'e, Dili, Timor-Leste
| | - Endang Tri Margawati
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor, Indonesia, 16911
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Salim B, Alasmari S, Mohamed NS, Ahmed MKA, Nakao R, Hanotte O. Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages. BMC Genomics 2023; 24:118. [PMID: 36927331 PMCID: PMC10018940 DOI: 10.1186/s12864-023-09231-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D- loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.
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Affiliation(s)
- Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, P.O Box 32, Khartoum-North, Sudan.
| | - Saeed Alasmari
- Department of Biology, Faculty of Arts and Sciences, Najran University, 1988, Najran, Kingdom of Saudi Arabia
| | - Nouh Saad Mohamed
- Molecular Biology Unit, Sirius Training and Research Center, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.,LiveGene - CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
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