1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Vostry L, Vostra-Vydrova H, Moravcikova N, Kasarda R, Margetin M, Rychtarova J, Drzaic I, Shihabi M, Cubric-Curik V, Sölkner J, Curik I. Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds. J Dairy Sci 2024:S0022-0302(24)00937-8. [PMID: 38908686 DOI: 10.3168/jds.2023-24607] [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: 12/23/2023] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.
Collapse
Affiliation(s)
- Lubos Vostry
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
| | - Hana Vostra-Vydrova
- Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Nina Moravcikova
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Radovan Kasarda
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Milan Margetin
- Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovak Republic
| | - Jana Rychtarova
- Institute of Animal Science, Přátelství 815, 104 00 Prague, Czech Republic
| | - Ivana Drzaic
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Mario Shihabi
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Vlatka Cubric-Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Johan Sölkner
- University of Natural Resources & Life Sciences Vienna, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Ino Curik
- University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000 Zagreb, Croatia; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
| |
Collapse
|
3
|
An ZX, Shi LG, Hou GY, Zhou HL, Xun WJ. Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data. Animal 2024; 18:101147. [PMID: 38843669 DOI: 10.1016/j.animal.2024.101147] [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: 10/30/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 06/22/2024] Open
Abstract
Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed of south China's tropical island province of Hainan, possess distinctive traits such as black hair, a moderate growth rate, good meat quality, and small body size. However, they exhibit exceptional resilience to rough feeding conditions, possess high-quality meat, and show remarkable resistance to stress and heat. In this study, we resequenced the whole genome of Hainan black goats to study the economic traits and genetic basis of these goats, we leveraged whole-genome sequencing data from 33 Hainan black goats to analyze single nucleotide polymorphism (SNP) density, Runs of homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) and selection characteristics. Our findings revealed that Hainan black goats harbor a substantial degree of genetic variation, with a total of 23 608 983 SNPs identified. Analysis of ROHs identified 53 710 segments, predominantly composed of short fragments, with inbreeding events mainly occurring in ancient ancestors, the estimates of inbreeding based on ROH in Hainan black goats typically exhibit moderate values ranging from 0.107 to 0.186. This is primarily attributed to significant declines in the effective population size over recent generations. Moreover, we identified 921 candidate genes within the intersection candidate region of ROH and iHS. Several of these genes are associated with crucial traits such as immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE and PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 and LEPR), meat quality (ACOX1, SSTR1, CAMK2B, PPP2CA and PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 and CDK19), and stress resistance (TLR2, IFI44, ENPP1, STK3 and NFATC1). The presence of these genes may be attributed to the genetic adaptation of Hainan black goats to local climate conditions. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of Hainan black goats and their valuable genetic resources.
Collapse
Affiliation(s)
- Z X An
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - L G Shi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - G Y Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - H L Zhou
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - W J Xun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| |
Collapse
|
4
|
Feng H, Cao F, Jin T, Wang L. Forest fragmentation causes an isolated population of the golden takin (Budorcas taxicolor bedfordi Thomas, 1911) (Artiodactyla: Bovidae) in the Qinling Mountains (China). BMC ZOOL 2024; 9:2. [PMID: 38287429 PMCID: PMC10826085 DOI: 10.1186/s40850-024-00192-1] [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: 05/18/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Budorcas taxicolor bedfordi is a rare animal uniquely distributed in the Qinling Mountains (China). Human disturbance and habitat fragmentation have directly affected the survival of B. t. bedfordi. It is urgent to clarify the genetic diversity and genetic structure of the B. t. bedfordi population and implement effective conservation measures. In this study, 20 new polymorphic microsatellite loci were isolated by Illumina sequencing. The genetic diversity and population structure of 124 B. t. bedfordi individuals from three populations (Niubeliang population, Zhouzhi population, and Foping population) were analysed according to these 20 microsatellite loci. Our results indicated that B. t. bedfordi had a low level of genetic variability and that there was inbreeding in the three populations. The population genetic structure analyses showed that the Niubeliang population had a trend of differentiation from other populations. National roads can affect population dispersal, while ecological corridors can promote population gene exchange. None of the three B. t. bedfordi populations experienced bottleneck effects. For conservation management plans, the Zhouzhi population and Foping population should be considered one management unit, and the Niubeliang population should be considered another management unit. We suggest building an ecological corridor to keep the habitat connected and formulating tourism management measures to reduce the influence of human disturbance on B. t. bedfordi.
Collapse
Affiliation(s)
- Hui Feng
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China.
| | - Fangjun Cao
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China
| | - Tiezhi Jin
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China
| | - Lu Wang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China
| |
Collapse
|