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Le SV, de Las Heras-Saldana S, Alexandri P, Olmo L, Walkden-Brown SW, van der Werf JHJ. Genetic diversity, population structure and origin of the native goats in Central Laos. J Anim Breed Genet 2024; 141:531-549. [PMID: 38520124 DOI: 10.1111/jbg.12862] [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: 11/15/2023] [Revised: 02/14/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024]
Abstract
Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.
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Affiliation(s)
- Sang V Le
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Sara de Las Heras-Saldana
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Panoraia Alexandri
- AGBU, a Joint Venture of the NSW Department of Primary Industries and the University of New England, Armidale, New South Wales, Australia
| | - Luisa Olmo
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W Walkden-Brown
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
| | - Julius H J van der Werf
- School of Rural & Environmental Science, University of New England, Armidale, New South Wales, Australia
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Kichamu N, Wanjala G, Cziszter LT, Strausz P, Astuti PK, Bagi Z, Kusza S. Assessing the population structure and genetic variability of Kenyan native goats under extensive production system. Sci Rep 2024; 14:16342. [PMID: 39014189 PMCID: PMC11252283 DOI: 10.1038/s41598-024-67374-2] [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: 08/28/2023] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval (GI) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders (fa/fe) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size (Ne) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.
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Affiliation(s)
- Nelly Kichamu
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
- Ministry of Agriculture Livestock, Fisheries and Cooperatives, Directorate of Livestock Development, Naivasha Sheep and Goats Breeding Station, P.O. Box 2238-20117, Naivasha, Kenya
| | - George Wanjala
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
- Ministry of Agriculture, Livestock, Fisheries, Cooperatives and Irrigation, Directorate of Livestock Production, P.O. Box 437-50200, Bungoma, Kenya
| | - Ludovic Toma Cziszter
- Faculty of Bioengineering of Animal Resources, University of Life Sciences "King Mihai I" From Timișoara, 300645, Timișoara, Romania
| | - Péter Strausz
- Institute of Strategy and Management, Department of Management, Corvinus University of Budapest, Budapest, 1093, Hungary
| | - Putri Kusuma Astuti
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
- Doctoral School of Animal Science, University of Debrecen, Debrecen, 4032, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, 4032, Hungary.
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Nantongo Z, Birungi J, Opiyo SO, Shirima G, Mugerwa S, Mutai C, Kyalo M, Munishi L, Agaba M, Mrode R. Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda's indigenous goat populations. Front Genet 2024; 15:1385611. [PMID: 38873114 PMCID: PMC11169577 DOI: 10.3389/fgene.2024.1385611] [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: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda's indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda's indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda's goat genetic resources.
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Affiliation(s)
- Ziwena Nantongo
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Consortium of International Agricultural Research Centers (CGIAR), Nairobi, Kenya
- School of Life Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- National Livestock Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
| | - Josephine Birungi
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Consortium of International Agricultural Research Centers (CGIAR), Nairobi, Kenya
| | - Stephen Obol Opiyo
- Molecular and Cellular Imaging Center, The Ohio State University, Columbus, OH, United States
- Patira Data Science, Kampala, Uganda
| | - Gabriel Shirima
- School of Life Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Swidiq Mugerwa
- National Livestock Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
| | - Collins Mutai
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Consortium of International Agricultural Research Centers (CGIAR), Nairobi, Kenya
| | - Martina Kyalo
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Consortium of International Agricultural Research Centers (CGIAR), Nairobi, Kenya
| | - Linus Munishi
- School of Life Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Morris Agaba
- School of Life Sciences, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Raphael Mrode
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Consortium of International Agricultural Research Centers (CGIAR), Nairobi, Kenya
- Scotland Rural College, Edinburgh, United Kingdom
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Zhong T, Wang X, Huang C, Yang L, Zhao Q, Chen X, Freitas-de-Melo A, Zhan S, Wang L, Dai D, Cao J, Guo J, Li L, Zhang H, Niu L. A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array. Animal 2023; 17:100706. [PMID: 36758301 DOI: 10.1016/j.animal.2023.100706] [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: 08/27/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5-10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.
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Affiliation(s)
- Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinlu Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunhua Huang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Liu Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaoyong Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Aline Freitas-de-Melo
- Departamento de Biociencias Veterinarias, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dinghui Dai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Baenyi Simon P, Owino Junga J, Tarekegn GM, Machuka E, Tiambo CK, Kabange D, Musale M Dieudinné K, Vumilia Kizungu R, Ochieng JW, Pelle R. Haplotype analysis of the mitochondrial DNA d-loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo. Ecol Evol 2022; 12:e8713. [PMID: 35342608 PMCID: PMC8928878 DOI: 10.1002/ece3.8713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/10/2021] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d‐loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d‐loop region (1169 bp d‐loop). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor‐joining (NJ) tree and median‐joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis (FST) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant (p‐value <.05) values for Fu's Fs (−20.418) and Tajima's (−2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long‐term conservation of indigenous goats in DRC.
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Affiliation(s)
- Patrick Baenyi Simon
- Department of Animal Production Université Evangélique en Afrique Bukavu Democratic Republic of Congo.,Department of Animal Production University of Nairobi Nairobi Kenya.,Institut National d'Etudes et des Recherches Agronomiques INERA Mulungu Bukavu Democratic Republic of Congo
| | | | - Getinet Mekuriaw Tarekegn
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya.,Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Uppsala Sweden.,Department of Animal Production and Technology Bahir Dar University Bahir Dar Ethiopia
| | - Eunice Machuka
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya
| | | | - Dorine Kabange
- Department of Veterinary Medicine Université de Lubumbashi Lubumbashi Democratic Republic of Congo
| | - Katunga Musale M Dieudinné
- Institut National d'Etudes et des Recherches Agronomiques INERA Mulungu Bukavu Democratic Republic of Congo
| | - Roger Vumilia Kizungu
- Institut National d'Etudes et des Recherches Agronomiques INERA, Gombe Kinshasa Kinshasa Democratic Republic of Congo
| | | | - Roger Pelle
- Bioscience Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub Nairobi Kenya
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