1
|
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: 1.0] [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.
Collapse
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
| |
Collapse
|
2
|
Walugembe M, Bertolini F, Dematawewa CMB, Reis MP, Elbeltagy AR, Schmidt CJ, Lamont SJ, Rothschild MF. Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions. Front Genet 2019; 9:737. [PMID: 30693019 PMCID: PMC6339939 DOI: 10.3389/fgene.2018.00737] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022] Open
Abstract
Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal's immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of São Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix Axiom®600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments.
Collapse
Affiliation(s)
- Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | - Matheus P Reis
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil
| | - Ahmed R Elbeltagy
- Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt
| | - Carl J Schmidt
- Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
| |
Collapse
|
3
|
Wong J, de Bruyn J, Bagnol B, Grieve H, Li M, Pym R, Alders R. Small-scale poultry and food security in resource-poor settings: A review. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2017. [DOI: 10.1016/j.gfs.2017.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
4
|
Eltanany MA, Hemeda SA. Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis. J Adv Res 2016; 7:615-23. [PMID: 27489728 PMCID: PMC4949740 DOI: 10.1016/j.jare.2016.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 11/23/2022] Open
Abstract
This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC) using representative breeds: Sinai (North), Fayoumi (Middle) and Dandarawi (South) of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (F ST = 0.003). The unimodal mismatch distribution and negative values of Tajima's D (-0.659) and Fu's Fs (-0.157) indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.
Collapse
Affiliation(s)
- Marwa A. Eltanany
- Department for Animal Wealth Development, Faculty of Veterinary Medicine, Benha University, 13736 Moshtohor, Toukh, Egypt
| | - Shabaan A. Hemeda
- Department for Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Egypt
| |
Collapse
|
5
|
Osman SAM, Yonezawa T, Nishibori M. Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region. Poult Sci 2016; 95:1248-56. [PMID: 26994197 DOI: 10.3382/ps/pew029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/08/2016] [Indexed: 11/20/2022] Open
Abstract
Domestic chickens (Gallus gallus) play a significant role, ranging from food and entertainment to religion and ornamentation. However, the details on their domestication process are still controversial, especially the origin and evolution of African chickens. Egypt is thought to be important place for this event because of its geographic location as well as its long history of civilization. However, the genetic component and structure of Egyptian native chicken (ENC) have not been studied so far. The aim of this study is to clarify the origin and evolution of African chickens through assessing the genetic diversities and structure of five ENC breeds using the mitochondrial D-loop sequences. Our results suggest there is genetic differentiation between the pure native breeds and the improved native breeds. The latter breeds were established by the hybridization of the pure native and the exotic breeds. The pure native breeds were estimated to be established about 800 years ago. Subsequently, we extensively analyzed the D-loop sequences from the ENC as well as the globally collected chickens (2,010 individuals in total). Our phylogenetic tree among the regional populations shows African chickens can be separated to two distinct clades. The first clade consists of North African (Egypt), Central African (Sudan and Cameroon), European, and West (and Central) Asian chickens. The second clade consists of East African (Kenya, Malawi, and Zimbabwe) and Pacific chickens. It suggests the dual origins of African native chickens. The first group was probably originated from South Asia, and then migrated to West Asia, and finally arrived to Africa thorough Egypt. The second group migrated from Pacific to East Africa via Indian Ocean probably by Austronesian people. This dual origin hypothesis as well as estimated divergence times in this study is harmonious with the archaeological and historical evidences. Our migration analysis suggests there is limited gene flow within African continent. These obtained findings are important for the better understanding of the diversity and uniqueness of African native chickens.
Collapse
Affiliation(s)
- Sayed A-M Osman
- Laboratory of Animal Genetics, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan Department of Genetics, Faculty of Agriculture, Minia University, El Minia 61517, Egypt
| | - Takahiro Yonezawa
- School of Life Sciences, Fudan University, SongHu Rd. 2005, Shanghai 200438, China The Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa, Tokyo 190-8562, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
| |
Collapse
|
6
|
Hassaballah K, Zeuh V, A. Lawal R, Hanotte O, Sembene M. Diversity and Origin of Indigenous Village Chickens (<i>Gallus gallus</i>) from Chad, Central Africa. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/abb.2015.69062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|