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Rachman MP, Bamidele O, Dessie T, Smith J, Hanotte O, Gheyas AA. Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress. Sci Rep 2024; 14:2209. [PMID: 38278850 PMCID: PMC10817956 DOI: 10.1038/s41598-024-52569-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.
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Affiliation(s)
- Mifta P Rachman
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.
| | - Oladeji Bamidele
- African Chicken Genetic Gains (ACGG), Department of Animal Sciences, Obafemi Awolowo University, Ile Ife, 220282, Nigeria
| | - Tadelle Dessie
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia
| | - Jacqueline Smith
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Olivier Hanotte
- LiveGene-CTLGH, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Almas A Gheyas
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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Mon SLY, Lwin M, Maw AA, Htun LL, Bawm S, Kawabe K, Wada Y, Okamoto S, Shimogiri T. Phylogenetic analysis of Myanmar indigenous chickens using mitochondrial D-loop sequence reveals their characteristics as a genetic resource. Anim Sci J 2021; 92:e13647. [PMID: 34647390 DOI: 10.1111/asj.13647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 01/16/2023]
Abstract
Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D-loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty-four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star-like median-joining network of 37 F-haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources.
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Affiliation(s)
- Su Lai Yee Mon
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Moe Lwin
- Research and Development Division, Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Aye Aye Maw
- Department of Genetics and Animal Breeding, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Saw Bawm
- Department of International Relations and Information Technology, University of Veterinary Science, Nay Pyi Taw, Myanmar
| | - Kotaro Kawabe
- Education Center, Kagoshima University, Kagoshima, Japan
| | - Yasuhiko Wada
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Faculty of Agriculture, Saga University, Saga, Japan
| | - Shin Okamoto
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Takeshi Shimogiri
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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Lasagna E, Ceccobelli S, Cardinali I, Perini F, Bhadra U, Thangaraj K, Dababani RC, Rai N, Sarti FM, Lancioni H, Ige AO. Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria. Poult Sci 2020; 99:2852-2860. [PMID: 32475418 PMCID: PMC7597645 DOI: 10.1016/j.psj.2019.12.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/05/2019] [Accepted: 12/31/2019] [Indexed: 11/07/2022] Open
Abstract
Poultry are the most widely distributed type of livestock in Nigeria. Indigenous chickens are extremely common throughout the country. Indeed, approximately 83 million chickens are raised in extensive systems and 60 million in semi-intensive systems. To provide the first comprehensive overview of the maternal lineages in Southwest Nigeria, we analyzed 96 mitochondrial DNA control region sequences from 2 indigenous chicken ecotypes: Fulani and Yoruba. All samples belonged to the most frequent haplogroup (E) in Africa and Europe and showed noticeably low haplotype diversity. Although only 11 different haplotypes were detected, with 2 of them never found before in Nigeria, the presence of unique sequences among our indigenous samples testified to their status as an important genetic resource to be preserved. Furthermore, a total of 7,868 published sequences were included in the comparative analysis, which revealed an east-west geographic pattern of haplogroup distribution and led to the conclusion that the gene flow from Southeastern Asia mainly involved one mitochondrial clade. Moreover, owing to the extensive genetic intermixing among Nigerian chickens, conservation efforts are required to safeguard the extant mitochondrial variability in these indigenous ecotypes and establish future improvement and selection programs.
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Affiliation(s)
- E Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy.
| | - S Ceccobelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - I Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - F Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Agripolis Campus, University of Padova, 35020 Padova, Italy
| | - U Bhadra
- Centre for Cellular and Molecular Biology (CSIR), 500007 Hyderabad, India
| | - K Thangaraj
- Centre for Cellular and Molecular Biology (CSIR), 500007 Hyderabad, India
| | - R C Dababani
- Centre for Cellular and Molecular Biology (CSIR), 500007 Hyderabad, India
| | - N Rai
- Centre for Cellular and Molecular Biology (CSIR), 500007 Hyderabad, India
| | - F M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - H Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - A O Ige
- Department of Animal Nutrition and Biotechnology, Ladoke Akintola University of Technology, Ogbomoso Oyo, Nigeria
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