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Budi T, Kumnan N, Singchat W, Chalermwong P, Thong T, Wongloet W, Faniriharisoa Maxime Toky R, Pathomvanich P, Panthum T, Wattanadilokchatkun P, Farhan Ahmad S, Tanglertpaibul N, Vangnai K, Chaiyes A, Yokthongwattana C, Sinthuvanich C, Han K, Muangmai N, Koga A, Nunome M, Sawatdichaikul O, Duengkae P, Matsuda Y, Srikulnath K. Weak purifying selection in allelic diversity of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand. Gene 2024; 923:148587. [PMID: 38768877 DOI: 10.1016/j.gene.2024.148587] [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: 01/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
High levels of purine and uric acid, which are associated with health issues such as gout and cardiovascular disease, are found in the meat of fast-growing broiler chickens, which raises concerns about the quality of chicken meat and the health of the consumers who consume it. High genetic homogeneity and uniformity, particularly in genes involved in the synthesis of inosine monophosphate (IMP) and subsequent process of purine synthesis, which are associated with the meat quality, are exhibited in commercial broiler chickens owing to intensive inbreeding programs. Adenosine succinate lyase (ADSL) is a key enzyme involved in de novo purine biosynthetic pathway and its genetic polymorphisms affect IMP metabolism and purine content. In this study, we investigated the polymorphism of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand, using metabarcoding and genetic diversity analyses. Five alleles with 73 single nucleotide polymorphisms in exon 2, including missense and silent mutations, which may act on the synthesis efficiency of IMP and purine. Their protein structures revealed changes in amino acid composition that may affect ADSL enzyme activity. Weak purifying selection in these ADSL alleles was observed in the chicken population studied, implying that the variants have minor fitness impacts and a greater probability of fixation of beneficial mutations than strong purifying selection. A potential selective sweep was observed in Mae Hong Son chickens, whose purine content was lower than that in other breeds. This suggests a potential correlation between variations of the ADSL gene and reduced purine content and an impact of ADSL expression on the quality of chicken meat. However, further studies are required to validate its potential availability as a genetic marker for selecting useful traits that are beneficial to human health and well-being.
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Affiliation(s)
- Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), 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
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), 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
| | - Rajaonarison Faniriharisoa Maxime Toky
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Prangyapawn Pathomvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, 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
| | - Nivit Tanglertpaibul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kanithaporn Vangnai
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Chomdao Sinthuvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea; Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama City, Okayama 700-0005, Japan
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), 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
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, 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; Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
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2
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Deng C, Li M, Wang T, Duan W, Guo A, Ma G, Yang F, Dai F, Li Q. Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken. Br Poult Sci 2024:1-13. [PMID: 38922310 DOI: 10.1080/00071668.2024.2367228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.
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Affiliation(s)
- C Deng
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, China
| | - T Wang
- School of Pharmacy, Chengdu University, Chengdu, China
| | - W Duan
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - A Guo
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - G Ma
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Yang
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Q Li
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
- Kunming Xianghao Technology Co. Ltd., Kunming, China
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3
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Bahbahani H, Alfoudari A, Al-Ateeqi A, Al Abri M, Almathen F. Positive selection footprints and haplotype distribution in the genome of dromedary camels. Animal 2024; 18:101098. [PMID: 38377812 DOI: 10.1016/j.animal.2024.101098] [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: 10/09/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.
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Affiliation(s)
- H Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait.
| | - A Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - A Al-Ateeqi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - M Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - F Almathen
- Department of Public Health, King Faisal University, 400 Al-Ahsa, Kingdom of Saudi Arabia; Camel Research Center, King Faisal University, 400 Al-Ahsa, Saudi Arabia
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4
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Bendesky A, Brew J, Francis KX, Tello Corbetto EF, González Ariza A, Nogales Baena S, Shimmura T. The main genetic locus associated with the evolution of gamecocks is centered on ISPD. G3 (BETHESDA, MD.) 2024; 14:jkad267. [PMID: 37991999 PMCID: PMC10849328 DOI: 10.1093/g3journal/jkad267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, with 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with nongame chickens. Particularly noteworthy is a variant in an intron of the isoprenoid synthase domain containing gene (ISPD), an extreme outlier present at a frequency of 89% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.
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Affiliation(s)
- Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | - Joseph Brew
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | - Kerel X Francis
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027-2325, USA
| | | | - Antonio González Ariza
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain
- Diputación Provincial de Córdoba, Agropecuary Provincial Centre, 14014 Córdoba, Spain
| | - Sergio Nogales Baena
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain
| | - Tsuyoshi Shimmura
- Department of Biological Production, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
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5
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Tan X, Zhang J, Dong J, Huang M, Li Q, Wang H, Bai L, Cui M, Zhou Z, Yang S, Wang D. Whole-genome variants dataset of 209 local chickens from China. Sci Data 2024; 11:169. [PMID: 38316816 PMCID: PMC10844214 DOI: 10.1038/s41597-024-02995-w] [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: 03/24/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024] Open
Abstract
Compared to commercial chickens, local breeds exhibit better in meat quality and flavour, but the productivity (e.g., growth rate, body weight) of local chicken breeds is rather low. Genetic analysis based on whole-genome sequencing contributes to elucidating the genetic markers or putative candidate genes related to some economic traits, facilitating the improvement of production performance, the acceleration of breeding progress, and the conservation of genetic resources. Here, a total of 209 local chickens from 13 breeds were investigated, and the observation of approximately 91.4% high-quality sequences (Q30 > 90%) and a mapping rate over 99% for each individual indicated good results of this study, as confirmed by a genome coverage of 97.6%. Over 19 million single nucleotide polymorphisms (SNPs) and 1.98 million insertion-deletions (InDels) were identified using the reference genome (GRCg7b), further contributing to the public database. This dataset provides valuable resources for studying genetic diversity and adaptation and for the cultivation of new chicken breeds/lines.
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Affiliation(s)
- Xiaodong Tan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiawen Zhang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghai Li
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Huanhuan Wang
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Lijuan Bai
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Ming Cui
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Zhenzhen Zhou
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shuyuan Yang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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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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Kambal S, Tijjani A, Ibrahim SAE, Ahmed MKA, Mwacharo JM, Hanotte O. Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review. Anim Genet 2023; 54:689-708. [PMID: 37697736 DOI: 10.1111/age.13353] [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: 07/28/2023] [Revised: 07/28/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.
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Affiliation(s)
- Sumaya Kambal
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Sabah A E Ibrahim
- Department of Bioinformatics and Biostatistics, National University, Khartoum, Sudan
| | - Mohamed-Khair A Ahmed
- Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Khartoum, Sudan
| | - Joram M Mwacharo
- Scotland's Rural College and Centre for Tropical Livestock Genetics and Health, Edinburgh, UK
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Livestock Genetics, International Livestock Research Institute, Addis Ababa, Ethiopia
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
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8
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Bendesky A, Brew J, Francis KX, Tello Corbetto EF, González Ariza A, Nogales Baena S, Shimmura T. Noncoding genetic variation in ISPD distinguishes gamecocks from nongame chickens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553562. [PMID: 37662209 PMCID: PMC10473654 DOI: 10.1101/2023.08.16.553562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and of 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, at 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with, nongame chickens. Particularly noteworthy is a variant in an intron of ISPD, an extreme outlier present at a frequency of 90% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance.
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Affiliation(s)
- Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Joseph Brew
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kerel X. Francis
- Department of Ecology, Evolution and Environmental Biology and Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Antonio González Ariza
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
- Agropecuary Provincial Centre, Diputación Provincial de Córdoba, Córdoba, Spain
| | - Sergio Nogales Baena
- PAIDI AGR-218 Research Group, Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | - Tsuyoshi Shimmura
- Department of Agriculture, Tokyo University of Agriculture and Technology, Japan
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Wongloet W, Singchat W, Chaiyes A, Ali H, Piangporntip S, Ariyaraphong N, Budi T, Thienpreecha W, Wannakan W, Mungmee A, Jaisamut K, Thong T, Panthum T, Ahmad SF, Lisachov A, Suksavate W, Muangmai N, Chuenka R, Nunome M, Chamchumroon W, Han K, Nuangmek A, Matsuda Y, Duengkae P, Srikulnath K. Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken. Animals (Basel) 2023; 13:1949. [PMID: 37370459 PMCID: PMC10295432 DOI: 10.3390/ani13121949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.
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Affiliation(s)
- Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- 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 Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand;
| | - Hina Ali
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Surachai Piangporntip
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- School of Integrated Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Bureau of Conservation and Research, Zoological Park Organization of Thailand, Bangkok 10300, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Worawit Thienpreecha
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Wannapa Wannakan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Autchariyapron Mungmee
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Kittipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- 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 Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Warong Suksavate
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | | | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama 700-0005, Japan;
| | - Wiyada Chamchumroon
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand;
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Aniroot Nuangmek
- Mae Hong Son Provincial Livestock Office, Department of Livestock Development, Ministry of Agriculture and Cooperatives, Mae Hong Son 58000, Thailand;
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (W.W.); (W.S.); (H.A.); (S.P.); (N.A.); (T.B.); (W.T.); (W.W.); (A.M.); (K.J.); (T.T.); (T.P.); (S.F.A.); (A.L.); (W.S.); (N.M.); (K.H.); (Y.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- School of Integrated 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, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
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10
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Discovering novel clues of natural selection on four worldwide goat breeds. Sci Rep 2023; 13:2110. [PMID: 36747064 PMCID: PMC9902602 DOI: 10.1038/s41598-023-27490-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/03/2023] [Indexed: 02/08/2023] Open
Abstract
In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose. However, and despite the intensity of artificial selection, natural selection continues acting, possibly leaving a more diluted contribution over time, whose traces may be more difficult to capture. In order to explore selection footprints as response of environmental adaptation, we analysed a total of 993 goats from four transboundary goats breeds (Angora, Boer, Nubian and Saanen) genotyped with the SNP chip 50 K using outlier detection, runs of homozygosity and haplotype-based detection methods. Our results showed that all methods identified footprints on chromosome 6 (from 30 to 49 Mb) for two specific populations of Nubian goats sampled in Egypt. In Angora and Saanen breeds, we detected two selective sweeps using HapFLK, on chromosome 21 (from 52 to 55 Mb) and chromosome 25 (from 1 to 5 Mb) respectively. The analysis of runs of homozygosity showed some hotspots in all breeds. The overall investigation of the selected regions detected combining the different approaches and the gene ontology exploration revealed both novel and well-known loci related to adaptation, especially for heat stress. Our findings can help to better understand the balance between the two selective pressures in commercial goat breeds providing new insights on the molecular mechanisms of adaptation.
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11
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Zhao Y, Hu J, Wu J, Li Z. ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis. Front Genet 2023; 14:1108104. [PMID: 36911387 PMCID: PMC9996634 DOI: 10.3389/fgene.2023.1108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in invasive species, leaving the regulatory landscape of histone modifications in invasive species unclear. Methods: Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by the occupancy of H3K4me3, H3K27me3 or bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, where the average enrichment was almost constant. Transcriptomic analysis indicated that H3K4me3 is associated with active gene transcription, and H3K27me3 is mostly associated with transcriptional repression. Importantly, we identified genes and putative motifs modified by distinct histone modification patterns that may possibly regulate flight activity. Discussion: These findings provide the first evidence of histone modification signature in B. dorsalis, and will be useful for future studies of epigenetic signature in other invasive insect species.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiajiao Wu
- Technology Center of Guangzhou Customs, Guangzhou, China
| | - Zhihong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
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12
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Gut Microbiota, Intestinal Morphometric Characteristics, and Gene Expression in Relation to the Growth Performance of Chickens. Animals (Basel) 2022; 12:ani12243474. [PMID: 36552394 PMCID: PMC9774407 DOI: 10.3390/ani12243474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/04/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
this study aimed to investigate the growth mechanism in a local breed of chickens by comparing the highest weight (HW) and the lowest weight in their microbiota, histological characteristics, and gene expression. Golden Montazah chickens, an Egyptian breed, were reared until they were 49 days old. All of the birds were fed ad libitum by a starter diet from day 1 until day 21, followed by a grower diet from day 21 to the end of the study. At 49 days old, the forty-eight birds with the heaviest body weight (HW) and the lightest body weight (LW) were chosen. Blood biochemical and histological morphometric parameters, electron microscopy, and intestinal nutrient transporter gene expression were studied in the sampled jejunum. The microbial composition and functions of the content and mucosa in HW and LW chickens were studied using 16S rRNA gene sequencing. The histological morphometric parameters were all more significantly (p < 0.05) increased in the HW chickens than in the LW chickens. Total protein, albumin, and triglycerides in serum were significantly higher (p < 0.05) in the HW chickens than in the LW chickens. The microbiome profile in the gut showed that Microbacterium and Sphingomonas were positively correlated with the body weights. In the local breed, there were significant differences in the intestinal microstructure which could enhance the growth mechanism and body weight. Our findings showed that some microbial components were significantly associated with body weight and their interactions with the host could be inferred to explain why these interactions might alter the host’s metabolic responses. Further investigation into combining bioinformatics with lab experiments in chickens will help us to understand how gut bacteria can change the host’s metabolism by special metabolic features in the gastrointestinal system.
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13
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Jones HE, Wilson PB. Progress and opportunities through use of genomics in animal production. Trends Genet 2022; 38:1228-1252. [PMID: 35945076 DOI: 10.1016/j.tig.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
Abstract
The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.
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Affiliation(s)
- Huw E Jones
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK.
| | - Philippe B Wilson
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK
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14
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Striving to be resilient: the role of crop-poultry integrated systems as a climate change adaptation strategy in semiarid eastern Kenya. Heliyon 2022; 8:e11579. [DOI: 10.1016/j.heliyon.2022.e11579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/21/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
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15
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Zhao X, Zhang J, Wang H, Li H, Qu C, Wen J, Zhang X, Zhu T, Nie C, Li X, Muhatai G, Wang L, Lv X, Yang W, Zhao C, Bao H, Li J, Zhu B, Cao G, Xiong W, Ning Z, Qu L. Genomic and transcriptomic analyses reveal genetic adaptation to cold conditions in the chickens. Genomics 2022; 114:110485. [PMID: 36126832 DOI: 10.1016/j.ygeno.2022.110485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/27/2022] [Accepted: 09/16/2022] [Indexed: 01/14/2023]
Abstract
Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.
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Affiliation(s)
- Xiurong Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Jinxin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Huie Wang
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830000, China.
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui 236037, China.
| | - Junhui Wen
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinye Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Xinghua Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Gemingguli Muhatai
- Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang 843300, China.
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - XueZe Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China.
| | - Chunjiang Zhao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haigang Bao
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Junying Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Bo Zhu
- Animal Health Supervision Institute of Zhuozhou, Hebei Province 072750, China.
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Guangxi Province 538001, China.
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Guangxi Province 538001, China.
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Gebru G, Belay G, Vallejo-Trujillo A, Dessie T, Gheyas A, Hanotte O. Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia). Front Genet 2022; 13:968961. [PMID: 36246589 PMCID: PMC9561088 DOI: 10.3389/fgene.2022.968961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The Tigray region is an ancient entry route for the domestic chickens into Africa. The oldest African chicken bones were found in this region at Mezber, a pre-Aksumite rural farming settlement. They were dated to around 800–400 BCE. Since then, the farming communities of the region have integrated chicken into their livelihoods. The region is also recognised for its high chicken-to-human population ratio and diverse and complex geography, ranging from 500 to 4,000 m above sea level (m.a.s.l.). More than 15 agro-ecological zones have been described. Following exotic chicken introductions, the proportion of indigenous chicken is now 70% only in the region. It calls for the characterisation of indigenous Tigrayan chicken ecotypes and their habitats. This study reports an Ecological Niche Modelling using MaxEnt to characterise the habitats of 16 indigenous village chicken populations of Tigray. A total of 34 ecological and landscape variables: climatic (22), soil (eight), vegetation, and land cover (four), were included. We applied Principal Component Analysis correlation, and MaxentVariableSelection procedures to select the most contributing and uncorrelated variables. The selected variables were three climatic (bio5 = maximum temperature of the warmest month, bio8 = mean temperature of the wettest quarter, bio13 = precipitation of the wettest month), three vegetation and land cover (grassland, forest land, and cultivated land proportional areas), and one soil (clay content). Following our analysis, we identified four main chicken agro-ecologies defining four candidates indigenous Tigrayan chicken ecotypes. The study provides baseline information for phenotypic and genetic characterisation as well as conservation interventions of indigenous Tigrayan chickens.
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Affiliation(s)
- Gebreslassie Gebru
- Tigray Agricultural Research Institute, Mekelle, Ethiopia
- Addis Ababa University, College of Natural and Computational Science, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- *Correspondence: Gebreslassie Gebru, ; Olivier Hanotte,
| | - Gurja Belay
- Addis Ababa University, College of Natural and Computational Science, Department of Microbial, Cellular and Molecular Biology, Addis Ababa, Ethiopia
| | | | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Almas Gheyas
- Centre for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), the Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Gebreslassie Gebru, ; Olivier Hanotte,
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Sjodin BMF, Russello MA. Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika ( Ochotona princeps). G3 GENES|GENOMES|GENETICS 2022; 12:6695220. [PMID: 36087005 PMCID: PMC9635661 DOI: 10.1093/g3journal/jkac241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/07/2022] [Indexed: 11/30/2022]
Abstract
High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, University of British Columbia, Okanagan Campus , Kelowna, V1V 1V7 BC, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus , Kelowna, V1V 1V7 BC, Canada
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18
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Ahbara AM, Musa HH, Robert C, Abebe A, Al-Jumaili AS, Kebede A, Latairish S, Agoub MO, Clark E, Hanotte O, Mwacharo JM. Natural adaptation and human selection of northeast African sheep genomes. Genomics 2022; 114:110448. [PMID: 35964803 DOI: 10.1016/j.ygeno.2022.110448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/25/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.
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Affiliation(s)
- Abulgasim M Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya; School of Life Sciences, University of Nottingham, University Park, Nottingham, UK; Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia; LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia; Animal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, UK.
| | - Hassan H Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan
| | - Christelle Robert
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, UK
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Ahmed S Al-Jumaili
- Department of Medical Laboratory Techniques, Al-Maarif University College, Ramadi, Anbar, Iraq
| | - Adebabay Kebede
- LiveGene-CTLGH, International Livestock Research Institute (ILRI) Ethiopia, Addis Ababa, Ethiopia; Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
| | - Suliman Latairish
- Department of Animal Production, Faculty of Agriculture, Misurata University, Misurata, Libya
| | | | - Emily Clark
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK; LiveGene-CTLGH, International Livestock Research Institute (ILRI) Ethiopia, Addis Ababa, Ethiopia.
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia; Animal and Veterinary Sciences, SRUC, The Roslin Institute Building, Midlothian, Edinburgh, UK; Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, UK.
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Vallejo-Trujillo A, Kebede A, Lozano-Jaramillo M, Dessie T, Smith J, Hanotte O, Gheyas AA. Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions.
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Antibiotic Resistance of Bacterial Isolates from Smallholder Poultry Droppings in the Guinea Savanna Zone of Nigeria. Antibiotics (Basel) 2022; 11:antibiotics11070973. [PMID: 35884227 PMCID: PMC9311501 DOI: 10.3390/antibiotics11070973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/15/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
There is a growing risk of antibiotic resistance (AR) in smallholder poultry (SP). This study, therefore, aimed to investigate AR pattern of bacterial isolates from SP in the Guinea Savanna agro-ecological zone of Nigeria. A total of 120 fresh poultry droppings were aseptically collected, randomly, from two tropically adapted (FUNAAB Alpha and Noiler) and local chickens. The chickens were raised either using ethnoveterinary medicines (n = 60) or antibiotics (n = 60). Bacterial isolates were characterized and analyzed using standard protocols, and appropriate statistical tools. Compared to Pseudomonas spp. (2.5%) and Klebsiella spp. (5.8%), Salmonella spp. (57.5%) and Escherichia coli (34.2%) were the most prevalent (χ2 = 96.67; p < 0.001). Prevalence of bacterial species was significantly (p = 0.024; Odds Ratio = 2.552) influenced by antibiotics usage. All four species were multi-drug resistant. In total, 30% of the isolates had a multiple AR index ≥ 0.2. Bacterial isolates from FUNAAB Alpha (58.0%) and Noiler (44.0%) were highly resistant to quinolones, while isolates from the local chickens (22.6%) were most resistant to aminoglycosides. Bacterial species isolated from FUNAAB Alpha and local chickens exhibited the lowest and highest percentage of AR, respectively. Clustering of isolates with similar antibiogram revealed inter-species dependence with possibility for inter-species gene transfer. These findings provide a background to investigate the metagenomics of local and improved chickens for AR.
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21
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Tijjani A, Salim B, da Silva MVB, Eltahir HA, Musa TH, Marshall K, Hanotte O, Musa HH. Genomic signatures for drylands adaptation at gene-rich regions in African zebu cattle. Genomics 2022; 114:110423. [PMID: 35803449 PMCID: PMC9388378 DOI: 10.1016/j.ygeno.2022.110423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022]
Abstract
Background Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector disease challenges. Here, we sequenced 60 indigenous Sudanese cattle from six indigenous breeds and analysed the data using three genomic scan approaches to unravel cattle adaptation to the African dryland region. Results We identified a set of gene-rich selective sweep regions, detected mostly on chromosomes 5, 7 and 19, shared across African and Gir zebu. These include genes involved in immune response, body size and conformation, and heat stress response. We also identified selective sweep regions unique to Sudanese zebu. Of these, a 250 kb selective sweep on chromosome 16 spans seven genes, including PLCH2, PEX10, PRKCZ, and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Conclusions Our results suggest that environmental adaptation may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control, in zebu cattle. Sudanese cattle thrive in the harshest environments of the African drylands. Bos indicus shared selected genes are involved in immune response, conformation, and heat stress response. Sudanese zebu-specific sweep includes genes involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Environmental adaptation in zebu cattle may involve recent and ancient selection at gene-rich regions, which might be under a common regulatory genetic control.
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Affiliation(s)
- Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), PO 5689, Addis Ababa, Ethiopia; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, PO Box 5689, Addis Ababa, Ethiopia; Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, United Kingdom.
| | - Bashir Salim
- Faculty of Veterinary Medicine, University of Khartoum, Sudan
| | | | | | - Taha H Musa
- Biomedical Research Institute, Darfur College, Sudan
| | - Karen Marshall
- International Livestock Research Institute (ILRI), PO Box 30709, Nairobi 00100, Kenya; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi 00100, Kenya
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), PO 5689, Addis Ababa, Ethiopia; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, PO Box 5689, Addis Ababa, Ethiopia; Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, United Kingdom.
| | - Hassan H Musa
- Institute of Molecular Biology, University of Nyala, Sudan; Faculty of Medical Laboratory Sciences, University of Khartoum, Sudan.
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22
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Atassi L, Haile A, Solomon D, Demissie T, Rischkowsky B, Biradar C, Mwacharo J. Environment Suitability Mapping of Livestock: A Case Study of Ethiopian Indigenous Sheep and Goats. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Chebo C, Betsha S, Melesse A. Chicken genetic diversity, improvement strategies and impacts on egg productivity in Ethiopia: a review. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2067020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chencha Chebo
- Department of Animal Science, Arba Minch University, College of Agricultural Sciences, Arba Minch, Ethiopia
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Simret Betsha
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Aberra Melesse
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
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25
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Gheyas A, Vallejo-Trujillo A, Kebede A, Dessie T, Hanotte O, Smith J. Whole genome sequences of 234 indigenous African chickens from Ethiopia. Sci Data 2022; 9:53. [PMID: 35165296 PMCID: PMC8844291 DOI: 10.1038/s41597-022-01129-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/15/2021] [Indexed: 11/15/2022] Open
Abstract
Indigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes. Measurement(s) | genome | Technology Type(s) | DNA sequencing | Factor Type(s) | animal population | Sample Characteristic - Organism | Gallus gallus | Sample Characteristic - Location | Ethiopia |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.16999891
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Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Ghanatsaman Z, Babenko O, Stavetska R, Kalashnik O, Kucher D, Kochuk-Yashchenko O, Asadollahpour Nanaei H. Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 2021; 17:369. [PMID: 34861880 PMCID: PMC8641187 DOI: 10.1186/s12917-021-03077-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. RESULTS To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20-2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. CONCLUSIONS We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.
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Affiliation(s)
| | | | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz, Iran
| | - Olena Babenko
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Ruslana Stavetska
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Oleksandr Kalashnik
- Department of Animal Science, Sumy National Agrarian University, Sumy, Ukraine
| | - Dmytro Kucher
- Department of Breeding, Animal Genetics and Biotechnology, Polissia National University, Zhytomyr, Ukraine
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Goto T, Ohya K, Takaya M. Genotype affects free amino acids of egg yolk and albumen in Japanese indigenous breeds and commercial Brown layer chickens. Poult Sci 2021; 101:101582. [PMID: 34890945 PMCID: PMC8665412 DOI: 10.1016/j.psj.2021.101582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/09/2021] [Accepted: 10/24/2021] [Indexed: 11/03/2022] Open
Abstract
Using a variety of genetic resources, the aim of this study is to see how genetic background affects egg traits in chickens. Three different chicken genotypes (a commercial Brown layer, BOR; 2 Japanese indigenous breeds, NGY and YKD) were investigated effects on genotype in 10 external and internal egg quality traits along with 20 yolk and albumen free amino acid traits. Significant effects on genotype in 10 external and internal egg quality traits and 18 yolk and 17 albumen amino acid traits were found (P < 0.05). In sizes and weights of egg and eggshell redness, there were significant differences among all combinations of genotype (BOR > NGY > YKD). In 14 yolk (Asn, Ser, Gln, Gly, His, Arg, Ala, Pro, Tyr, Val, Met, Leu, Phe, and Lys) and 8 albumen amino acid traits (Gln, Gly, His, Arg, Val, Ile, Leu, and Lys), BOR was significantly higher than NGY and YKD, while the opposite relations were seen in 2 amino acid traits (Cys and GABA). Moreover, phenotypic correlation analyses revealed that positive correlations among amino acid traits within each yolk and albumen were broadly seen (0.30 < r < 0.98, P < 0.05). However, there are almost no phenotypic correlations in amino acids between yolk and albumen in BOR and NGY, but negative correlations in YKD, which implying a potential use of untapped genetic resources for modifying amino acid balance. These results indicate genetic background affects not only sizes and weights of egg but also amino acid contents and their balance of yolk and albumen.
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Affiliation(s)
- Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan; Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
| | - Kosei Ohya
- Mie Prefecture Livestock Research Institute, Matsusaka, Mie 515-2324, Japan
| | - Masahiro Takaya
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan; Hokkaido Tokachi Area Regional Food Processing Technology Center, Tokachi Foundation, Obihiro, Hokkaido 080-2462, Japan
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Kebede FG, Komen H, Dessie T, Alemu SW, Hanotte O, Bastiaansen JWM. Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens. Front Genet 2021; 12:723360. [PMID: 34567075 PMCID: PMC8456010 DOI: 10.3389/fgene.2021.723360] [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: 06/10/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes.
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Affiliation(s)
- Fasil Getachew Kebede
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Hans Komen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Tadelle Dessie
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | | | - Olivier Hanotte
- International Livestock Research Institute, Addis Ababa, Ethiopia
- Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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Overview of Poultry Management as a Key Factor for Solving Food and Nutritional Security with a Special Focus on Chicken Breeding in East African Countries. BIOLOGY 2021; 10:biology10080810. [PMID: 34440042 PMCID: PMC8389547 DOI: 10.3390/biology10080810] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary The poultry sector in most developing countries is largely based on traditional production systems, which are based on indigenous breeds. Beyond economical, nutritional, socio-cultural, and religious functions, the inherent adaptability of indigenous birds to diverse environmental conditions also provides a unique genetic resource critical for addressing the global challenges of food security in this world impacted by climatic change and human population growth. Nevertheless, until recently, the potential of the indigenous chicken remained largely untapped for no strong reason. In this review, we offer an overview of food and nutritional security with a special focus on chicken breeding in East Africa. We highlighted and combined confirming evidence of production performance, phenotypic variability, and genetic diversity of East African indigenous chicken using both morphological and molecular tools. Previous attempts to improve the productivity of indigenous chicken are highlighted, and possible future breeding plans and areas of immediate research are suggested. Considering how indigenous chicken strongly affects the livelihood of the majority of households, and since the poultry sector is likely to be strongly affected by climate change, we recommended that the prospects of chicken breeding in Africa should create a permanent balance between the competing needs of genetic improvement and the genetic diversity of indigenous chickens. Abstract The focus of this review is to offer an overview of food and nutritional security, to identify associated constraints, and propose possible alternative solutions for improving the East African poultry sub-sector in the pursuit of food security, focusing on chicken breeding. To better understand the prospects of the poultry industry, we highlighted and combined confirming evidence of the phenotypic variability and genetic diversity of East African chicken genetic resources using both morphological and molecular tools, as well as performance traits. Furthermore, this work gives a detailed indication of what would be lost if indigenous chicken populations are left to suffer the ongoing massive genetic erosions due to various factors, not limited to indiscriminate crossbreeding. Previous and recent attempts to improve the productivity of indigenous chicken are highlighted, and possible future breeding plans and areas of immediate research are suggested as well. This review concludes that under the prevailing conditions, the village chicken production system appears to be the most imperious production system that needs to be extensively developed ; however, for the sustainability of the industry, the proposed improvement strategies should create a permanent balance between the competing needs of genetic improvement and the genetic diversity of the indigenous chicken genetic resource.
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Lawal RA, Hanotte O. Domestic chicken diversity: Origin, distribution, and adaptation. Anim Genet 2021; 52:385-394. [PMID: 34060099 DOI: 10.1111/age.13091] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.
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Affiliation(s)
- R A Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
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- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.,LiveGene, International Livestock Research Institute (ILRI), P.O. 5689, Addis Ababa, Ethiopia
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