1
|
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.
Collapse
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
| |
Collapse
|
2
|
Xue Z, Yan H, Zhen L. For a Better Quality of Beef: The Challenge from Growing Livestock on Limited Grasslands with a Production-Consumption Balance Perspective. Foods 2023; 12:3231. [PMID: 37685164 PMCID: PMC10487039 DOI: 10.3390/foods12173231] [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: 07/16/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The growing population, the transition dietary towards animal-based products, and the preference for the brand of grass-feeding livestock are bringing increasing pressure on natural grasslands, especially for dry-land areas. The Xilingol League of China is famous for its free-range livestock product, however, overgrazing and herders' benefits damage are always serious issues for this semi-arid grassland region. This study focuses on the relationship between the supply of natural grassland and the consumption of free-range livestock in the Xilingol League, and this study employed the grassland carrying capacity as the index to judge the sustainability states and its trends of the local grass-feeding system. Satellite data production of net primary production was used for grassland production, statistical livestock data and the consumption model were used for actual forage consumption, and empirical key informant interview data were used to obtain a more comprehensive understanding. The results show that: (1) the natural grassland carrying capacity of the Xilingol League fluctuated, showing improvement from 2000 to 2021; (2) the grassland management needs to be more diversified in different regions with different natural conditions; and (3) while the demand for free-range, high-quality beef is increasing, attention should be paid to the carrying capacity of natural pastures and more consideration should be taken of the benefits of balancing the livelihood of herders, policy strategies, and the customers' preferences. Potential ways of doing this include employing technologies to improve livestock production, and further exploring and promoting the economic value of the free-range livestock and the geographical indication to get the economic-ecological win-win situation. The research framework and results would be beneficial to reveal the potential threats in pastoral areas and provide support for the optimization of the regional grass-feeding breeding system, especially in middle-income countries.
Collapse
Affiliation(s)
- Zhichao Xue
- School of International Economics and Management, Beijing Technology and Business University, Beijing 100048, China;
| | - Huimin Yan
- Institute of Geographic Resources and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Zhen
- Institute of Geographic Resources and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
3
|
Riggio V, Madder M, Labuschagne M, Callaby R, Zhao R, Djikeng A, Fourie J, Prendergast JGD, Morrison LJ. Meta-analysis of heritability estimates and genome-wide association for tick-borne haemoparasites in African cattle. Front Genet 2023; 14:1197160. [PMID: 37576560 PMCID: PMC10417722 DOI: 10.3389/fgene.2023.1197160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
The control of tick-borne haemoparasites in cattle largely relies on the use of acaricide drugs against the tick vectors, with some vaccination also being used against selected pathogens. These interventions can be difficult in Africa, where accessibility and cost of vaccines can be issues, and the increasing resistance of tick vectors to the widely used acaricides is a complication to disease control. A potential complementary control strategy could be the exploitation of any natural host genetic resistance to the pathogens. However, there are currently very few estimates of the extent of host resistance to tick-borne haemoparasites, and a significant contributing factor to this knowledge gap is likely to be the difficulty of collecting appropriate samples and data in the smallholder systems that predominate livestock production in low- and middle-income countries, particularly at scale. In this study, we have estimated the heritability for the presence/absence of several important haemoparasite species (including Anaplasma marginale, Babesia bigemina, Babesia bovis, and Ehrlichia ruminantium), as well as for relevant traits such as body weight and body condition score (BCS), in 1,694 cattle from four African countries (Burkina Faso, Ghana, Nigeria, and Tanzania). Heritability estimates within countries were mostly not significant, ranging from 0.05 to 0.84 across traits and countries, with standard errors between 0.07 and 0.91. However, the weighted mean of heritability estimates was moderate and significant for body weight and BCS (0.40 and 0.49, respectively), with significant heritabilities also observed for the presence of A. marginale (0.16) and E. ruminantium (0.19). In a meta-analysis of genome-wide association studies (GWAS) for these traits, two peaks were identified as reaching the suggestive significance threshold (p < 1.91 × 10-7 and p < 1.89 × 10-7, respectively): one on chromosome 24 for BCS and one on chromosome 8 for the E. ruminantium infection status. These findings indicate that there is likely to be a genetic basis that contributes to pathogen presence/absence for tick-borne haemoparasite species, which could potentially be exploited to improve cattle resistance in Africa to the economically important diseases caused by these pathogens.
Collapse
Affiliation(s)
- Valentina Riggio
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Rebecca Callaby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Rongrong Zhao
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Appolinaire Djikeng
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - James G. D. Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Liam J. Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
4
|
Houaga I, Mrode R, Opoola O, Chagunda MGG, Mwai OA, Rege JEO, Olori VE, Nash O, Banga CB, Okeno TO, Djikeng A. Livestock phenomics and genetic evaluation approaches in Africa: current state and future perspectives. Front Genet 2023; 14:1115973. [PMID: 37359382 PMCID: PMC10285055 DOI: 10.3389/fgene.2023.1115973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
The African livestock sector plays a key role in improving the livelihoods of people through the supply of food, improved nutrition and consequently health. However, its impact on the economy of the people and contribution to national GDP is highly variable and generally below its potential. This study was conducted to assess the current state of livestock phenomics and genetic evaluation methods being used across the continent, the main challenges, and to demonstrate the effects of various genetic models on the accuracy and rate of genetic gain that could be achieved. An online survey of livestock experts, academics, scientists, national focal points for animal genetic resources, policymakers, extension agents and animal breeding industry was conducted in 38 African countries. The results revealed 1) limited national livestock identification and data recording systems, 2) limited data on livestock production and health traits and genomic information, 3) mass selection was the common method used for genetic improvement with very limited application of genetic and genomic-based selection and evaluation, 4) limited human capacity, infrastructure, and funding for livestock genetic improvement programmes, as well as enabling animal breeding policies. A joint genetic evaluation of Holstein-Friesian using pooled data from Kenya and South Africa was piloted. The pilot analysis yielded higher accuracy of prediction of breeding values, pointing to possibility of higher genetic gains that could be achieved and demonstrating the potential power of multi-country evaluations: Kenya benefited on the 305-days milk yield and the age at first calving and South Africa on the age at first calving and the first calving interval. The findings from this study will help in developing harmonized protocols for animal identification, livestock data recording, and genetic evaluations (both national and across-countries) as well as in designing subsequent capacity building and training programmes for animal breeders and livestock farmers in Africa. National governments need to put in place enabling policies, the necessary infrastructure and funding for national and across country collaborations for a joint genetic evaluation which will revolutionize the livestock genetic improvement in Africa.
Collapse
Affiliation(s)
- Isidore Houaga
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, United Kingdom
| | - Raphael Mrode
- Scotland Rural College (SRUC), Edinburgh, United Kingdom
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Oluyinka Opoola
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, United Kingdom
| | - Mizeck G. G. Chagunda
- Department of Animal Breeding and Husbandry in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - John E. O. Rege
- Emerge Centre for Innovations-Africa (ECI-Africa), Nairobi, Kenya
| | | | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
| | - Cuthbert B. Banga
- Agricultural Research Council (ARC), Pretoria, South Africa
- Department of Animal Sciences, Faculty of Animal and Veterinary Sciences, Botswana University of Agriculture and Natural Resources (BUAN), Gaborone, Botswana
| | - Tobias O. Okeno
- Department of Animal Sciences, Egerton University, Egerton, Kenya
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, United Kingdom
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| |
Collapse
|
5
|
Riggio V, Tijjani A, Callaby R, Talenti A, Wragg D, Obishakin ET, Ezeasor C, Jongejan F, Ogo NI, Aboagye-Antwi F, Toure A, Nzalawahej J, Diallo B, Missohou A, Belem AMG, Djikeng A, Juleff N, Fourie J, Labuschagne M, Madder M, Marshall K, Prendergast JGD, Morrison LJ. Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle. Genet Sel Evol 2022; 54:58. [PMID: 36057548 PMCID: PMC9441065 DOI: 10.1186/s12711-022-00751-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. RESULTS We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. CONCLUSIONS Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.
Collapse
Affiliation(s)
- Valentina Riggio
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK. .,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, P.O Box 5689, Addis Ababa, Ethiopia
| | - Rebecca Callaby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Emmanuel T Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria.,Biomedical Research Centre, Ghent University Global Campus, Songdo, Incheon, South Korea
| | - Chukwunonso Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Frans Jongejan
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ndudim I Ogo
- National Veterinary Research Institute, Vom, Nigeria
| | - Fred Aboagye-Antwi
- Department of Animal Biology and Conservation Sciences, University of Ghana, Accra, Ghana
| | - Alassane Toure
- Laboratoire National d'Appui Au Dévéloppement Agricole(LANADA)/Laboratoire Central Vétérinaire de Bingerville, Bp: 206, Bingerville, Côte d'Ivoire
| | - Jahashi Nzalawahej
- Department of Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Ayao Missohou
- Ecole Inter-Etats des Sciences et Médecine Vétérinaires (EISMV) de Dakar, Dakar, Senegal
| | - Adrien M G Belem
- Université Polytechnique de Bobo-Dioulasso (UPB), Bobo -Dioulasso, Burkina Faso
| | - Appolinaire Djikeng
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Nick Juleff
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Michel Labuschagne
- Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa.,Clinvet, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa
| | - Maxime Madder
- Clinglobal, B03/04, The Tamarin Commercial Hub, Jacaranda Avenue, Tamarin, 90903, Mauritius
| | - Karen Marshall
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya.,International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| |
Collapse
|
6
|
King F, Visser C, Banga C. Genetic characterization of Mozambican Nguni cattle and their relationship with indigenous populations of South Africa. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
7
|
Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus). iScience 2022; 25:104672. [PMID: 35832892 PMCID: PMC9272374 DOI: 10.1016/j.isci.2022.104672] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
Collapse
|
8
|
Omer EA, Hinrichs D, Addo S, Roessler R. Development of a breeding program for improving the milk yield performance of Butana cattle under smallholder production conditions using a stochastic simulation approach. J Dairy Sci 2022; 105:5261-5270. [DOI: 10.3168/jds.2021-21307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/20/2022] [Indexed: 11/19/2022]
|
9
|
Nguyen TH, Nguyen CX, Luu MQ, Nguyen AT, Bui DH, Pham DK, Do DN. Mathematical models to describe the growth curves of Vietnamese Ri chicken. BRAZ J BIOL 2021; 83:e249756. [PMID: 34755795 DOI: 10.1590/1519-6984.249756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
Ri chicken is the most popular backyard chicken breed in Vietnam, but little is known about the growth curve of this breed. This study compared the performances of models with three parameters (Gompertz, Brody, and Logistic) and models containing four parameters (Richards, Bridges, and Janoschek) for describing the growth of Ri chicken. The bodyweight of Ri chicken was recorded weekly from week 1 to week 19. Growth models were fitted using minpack.lm package in R software and Akaike's information criterion (AIC), Bayesian information criterion (BIC), and root mean square error (RMSE) were used for model comparison. Based on these criteria, the models having four parameters showed better performance than the ones with three parameters, and the Richards model was the best one for males and females. The lowest and highest value of asymmetric weights (α) were obtained by Bridges and Brody models for each of sexes, respectively. Age and weight estimated by the Richard model were 8.46 and 7.51 weeks and 696.88 and 487.58 g for males and for females, respectively. Differences in the growth curves were observed between males and female chicken. Overall, the results suggested using the Richards model for describing the growth curve of Ri chickens. Further studies on the genetics and genomics of the obtained growth parameters are required before using them for the genetic improvement of Ri chickens.
Collapse
Affiliation(s)
- T H Nguyen
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - C X Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - M Q Luu
- Ministry of Science and Technology, Hanoi, Vietnam
| | - A T Nguyen
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - D H Bui
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - D K Pham
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - D N Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Canada
| |
Collapse
|
10
|
Nguyen Hoang T, Do HTT, Bui DH, Pham DK, Hoang TA, Do DN. Evaluation of non-linear growth curve models in the Vietnamese indigenous Mia chicken. Anim Sci J 2021; 92:e13483. [PMID: 33462943 DOI: 10.1111/asj.13483] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/31/2022]
Abstract
Understanding of animal growth is important for the improvement of management and feeding practices; however, little is known about the growth curve in Vietnamese indigenous chicken. This study was performed to determine the most appropriate models for describing the growth curve of Vietnamese Mia chicken. The study evaluated the performances of the Logistic, Gompertz, Richards, and Bridges models of body weights in 224 Mia chickens. Models were fitted using minpack.lm package in R software and Akaike's information criterion and Bayesian information criterion were used for model comparison. Based on these criteria, the Gompertz and Bridges were the best models for males and females, respectively. Estimated asymmetric weights (α) were ranged from 2,241.91 ± 14.74 (g) (Logistic) to 2,623.86 ± 30.23 (g) (Gompertz) for males and from 1,537.36 ± 10.97 (g) (Logistic) and 1,958.36 ± 72.92 (g) (Bridges) for females, respectively. The age at the inflection point was estimated from 9.32 to 10.5 weeks and from 8.51 to 9.86 weeks for males and females, respectively. In conclusion, the Gompertz model is the most suitable model for describing the growth curve of Mia chicken. The parameters obtained from growth models could help define feeding programs to meet nutritional needs from hatching to the age of maximum growth, reproduction programs, and marketing strategies.
Collapse
Affiliation(s)
- Thinh Nguyen Hoang
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Huong T T Do
- Bac Giang Agriculture and Forestry University, Bac Giang, Vietnam
| | - Doan H Bui
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Dang K Pham
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Tuan A Hoang
- Faculty of Animal Science, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Duy N Do
- Institute of Research and Development, Duy Tan University, Danang, Vietnam.,Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| |
Collapse
|
11
|
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.
Collapse
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
| | - O Hanotte
- 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
| |
Collapse
|
12
|
Eldawy MH, Lashen MES, Badr HM, Farouk MH. Milk production potential and reproductive performance of Egyptian buffalo cows. Trop Anim Health Prod 2021; 53:282. [PMID: 33890173 DOI: 10.1007/s11250-021-02722-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/12/2021] [Indexed: 11/29/2022]
Abstract
Limited data are available on the phenotypic factors related to the productive and reproductive performance of Egyptian buffalo cows, based on a large sample size. This study aims to estimate the effect of phenotypic factors on productive and reproductive traits of Egyptian buffaloes. Data were collected from five dairy buffalo stations and include 3787 lactation records. For the analysis of variance, four seasons were considered in each year, and the parity included seven classes. Dry periods were divided into three intervals (< 90, 90-170, and > 170 d). Birth weight was divided into four categories (<25, 25-30, 31-35, and >35 kg). The results indicated that winter-calving buffaloes had the highest total milk yield (TMY) of the whole lactation, with the shortest (p<0.001) lactation length (LL), days open (DO), and calving interval (CI). Both, total milk TMY/kg and LL/days were increased (p<0.001), but the CI was linearly decreased (p<0.001). Overall, buffaloes with age at first mating (AFM<25month), age at first calving (AFC<35 month), and a dry period (DP<90days), produced the highest TMY (p<0.001) and maintained the longest LL (p<0.001). By increasing the body weight at birth (BWB), milk production level significantly increased. Buffaloes of BWB<25kg had the shortest DO (p<0.004; 168.10±3.598 days) and CI (p<0.006; 17.01±.135 months). In conclusion, body weight at birth, season, parity, DO, CI, AFM, AFC, and DP could be used as predictors to improve reproductive and productive traits in buffalo breeding programs. The wide range in milk yield and reproductive traits indicated significant potential in increasing the productive and reproductive performances of Egyptian buffalo cows.
Collapse
Affiliation(s)
- Mohammed Hamed Eldawy
- Animal Production Department, Faculty of Agriculture, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Mohamed El-Saeed Lashen
- Animal Production Department, Faculty of Agriculture, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Hussein Mohamed Badr
- Animal Production Department, Faculty of Agriculture, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
| | - Mohammed Hamdy Farouk
- Animal Production Department, Faculty of Agriculture, Al-Azhar University, Nasr City, Cairo, 11884, Egypt.
| |
Collapse
|
13
|
Pham LD, Do DN, Nam LQ, Van Ba N, Ninh PH, Thuy DP, Son PV, Thieu PC. Evaluation of genetic diversity and population structure in four indigenous duck breeds in Vietnam. Anim Biotechnol 2021; 33:1065-1072. [PMID: 33451256 DOI: 10.1080/10495398.2020.1868485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
This study characterized genetic diversity and population structure of four indigenous Vietnamese duck breeds and an exotic breed for setting the conservation priority. A total of 200 samples from four duck breeds (Sincheng, Minhhuong, Muongchieng and Bauben) and an exotic breed (Supermeat) were genotyped for fifteen microsatellite markers. The average number of alleles per locus was 14.07. A moderate genetic diversity was observed for indigenous breeds as mean of observed and expected heterozygosity as Ho = 0.50 and He = 0.57, respectively. The Bauben had the lowest values of Ho (0.41) and He (0.48) while Sincheng had the highest values of Ho (0.6) and He (0.69), respectively. The inbreeding coefficients (FIS) ranged from 0.12 to 0.16, and all breeds were significantly under heterozygote deficit. Nei's genetic distance was the shortest between Minhhuong and Muongkhieng. The discriminant analysis of principal components of studied breeds resulted in four genetic clusters. The Minhhuong and Muongkhieng breeds joined the same genetic cluster while other breeds had their own clusters. These results indicated that the possibility to combine Minhhuong and Muongkhieng for reducing the cost of conservation and suggested that conservation of the Bauben should be prioritized to avoid inbreeding depression and genetic drift.
Collapse
Affiliation(s)
- Lan Doan Pham
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang, Vietnam.,Faculty of Environmental and Chemical Engineering, Duy Tan University, Danang, Vietnam
| | - Le Quang Nam
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Nguyen Van Ba
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Pham Hai Ninh
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Doan Phuong Thuy
- Faculty of Veterinary and Animal Husbandry, BacGiang Agriculture & Forestry University, Bacgiang, Vietnam
| | - Pham Van Son
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| | - Pham Cong Thieu
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Hanoi, Vietnam
| |
Collapse
|
14
|
Omer EAM, Addo S, Roessler R, Schäler J, Hinrichs D. Exploration of production conditions: a step towards the development of a community-based breeding program for Butana cattle. Trop Anim Health Prod 2020; 53:9. [PMID: 33205228 PMCID: PMC7671977 DOI: 10.1007/s11250-020-02459-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/25/2020] [Indexed: 10/28/2022]
Abstract
In Sudan, many Butana cattle farmers practice indiscriminate crossbreeding to improve the milk yield performance of cows, as organized breeding programs are lacking. Objectives of this study were to identify the current production conditions of Butana cattle and to determine farmers' production objectives and trait preferences using a field survey. The overall aim was to explore the possibility of establishing a community-based breeding program for the genetic improvement of the breed. A semi-structured questionnaire and field visits were used to collect data from 202 Butana cattle owners. Data were analyzed using chi-squared test, multiple response analysis, and binary logistic regression. Our results showed that Butana cattle farmers mainly raised their animals for milk production. On a five-point scale (5 = most important), milk yield (4.6 ± 0.05), growth performance (4.0 ± 0.07), and lactation length (3.9 ± 0.08) were highly preferred for future development of the breed. One-third of the farmers kept crossbred cattle with on average 4 crossbred animals per herd. About two-thirds of respondents were willing to adopt crossbreeding using exotic breeds to increase milk performance and about the same proportion were willing to exchange breeding bulls and establish farmers' associations. None of the respondents kept written performance records. However, educated farmers were more likely to adopt record keeping. Farmers' willingness to engage in associations could be useful for the establishment of a community-based breeding program. Based on the current farmers' production objectives, the future breeding program should emphasize increasing milk production of the Butana cattle by using improved Butana bulls in village herds.
Collapse
Affiliation(s)
- Elhady A M Omer
- Department of Organic Agricultural Sciences, University of Kassel, 37213, Witzenhausen, Germany. .,Department of Animal breeding and Genetics, University of Khartoum, Khartoum, Sudan.
| | - Sowah Addo
- Department of Organic Agricultural Sciences, University of Kassel, 37213, Witzenhausen, Germany
| | - Regina Roessler
- Department of Organic Agricultural Sciences, University of Kassel, 37213, Witzenhausen, Germany
| | - Jonas Schäler
- Department of Organic Agricultural Sciences, University of Kassel, 37213, Witzenhausen, Germany
| | - Dirk Hinrichs
- Department of Organic Agricultural Sciences, University of Kassel, 37213, Witzenhausen, Germany
| |
Collapse
|
15
|
Hu G, Do DN, Gray J, Miar Y. Selection for Favorable Health Traits: A Potential Approach to Cope with Diseases in Farm Animals. Animals (Basel) 2020; 10:E1717. [PMID: 32971980 PMCID: PMC7552752 DOI: 10.3390/ani10091717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 12/17/2022] Open
Abstract
Disease is a global problem for animal farming industries causing tremendous economic losses (>USD 220 billion over the last decade) and serious animal welfare issues. The limitations and deficiencies of current non-selection disease control methods (e.g., vaccination, treatment, eradication strategy, genome editing, and probiotics) make it difficult to effectively, economically, and permanently eliminate the adverse influences of disease in the farm animals. These limitations and deficiencies drive animal breeders to be more concerned and committed to dealing with health problems in farm animals by selecting animals with favorable health traits. Both genetic selection and genomic selection contribute to improving the health of farm animals by selecting certain health traits (e.g., disease tolerance, disease resistance, and immune response), although both of them face some challenges. The objective of this review was to comprehensively review the potential of selecting health traits in coping with issues caused by diseases in farm animals. Within this review, we highlighted that selecting health traits can be applied as a method of disease control to help animal agriculture industries to cope with the adverse influences caused by diseases in farm animals. Certainly, the genetic/genomic selection solution cannot solve all the disease problems in farm animals. Therefore, management, vaccination, culling, medical treatment, and other measures must accompany selection solution to reduce the adverse impact of farm animal diseases on profitability and animal welfare.
Collapse
Affiliation(s)
| | | | | | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada; (G.H.); (D.N.D.); (J.G.)
| |
Collapse
|
16
|
Bouraima MB, Qiu Y, Yusupov B, Ndjegwes CM. A study on the development strategy of the railway transportation system in the West African Economic and Monetary Union (WAEMU) based on the SWOT/AHP technique. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
17
|
Josiane M, Gilbert H, Johann D. Genetic Parameters for Growth and Kid Survival of Indigenous Goat under Smallholding System of Burundi. Animals (Basel) 2020; 10:E135. [PMID: 31952116 PMCID: PMC7023424 DOI: 10.3390/ani10010135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 11/29/2022] Open
Abstract
The goal of this study was to estimate genetic parameters for the growth, conformation, and survival of goat kids raised in smallholder farming systems in Burundi. To do this, measurements were taken on live weight, thoracic perimeter, length, and height at birth (n = 1538 animals), at 3 months (n = 1270 animals), at 6 months (n = 992 animals), at 9 months (n = 787 animals), and at 12 months (n = 705 animals). Kids were born between 2016 and 2019, from 645 dams and 106 bucks. Three bivariate animal models were used to estimate genetic parameters of body weight and conformation measurements as potential indicators of this weight. According to the measure, heritability was estimated between 15 and 17% and genetic correlations between 65 and 79%. An accelerated failure time animal model was used to estimate the heritability of survival for kids under one year, adjusted for birth weight. Goat survival was significantly prolonged by 0.64 days per kilogram of birth weight. The estimated heritability for this trait was 2%. Overall, these results suggest that a selection program could be implemented to improve animal growth, either directly on weight or indirectly on conformational traits. At the same time, efforts need to be made to improve rearing conditions to increase the survival of kids.
Collapse
Affiliation(s)
- Manirakiza Josiane
- Department of Animal Health and Productions, Faculty of Agronomy and Bioengineering, University of Burundi, Bujumbura B.P. 2940, Burundi;
- Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liège, 6 Avenue de Cureghem, 4000 Liège, Belgium;
| | - Hatungumukama Gilbert
- Department of Animal Health and Productions, Faculty of Agronomy and Bioengineering, University of Burundi, Bujumbura B.P. 2940, Burundi;
| | - Detilleux Johann
- Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liège, 6 Avenue de Cureghem, 4000 Liège, Belgium;
| |
Collapse
|
18
|
Strategies for Sustainable Use of Indigenous Cattle Genetic Resources in Southern Africa. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11110214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Indigenous cattle breeds are the most important livestock species in the Southern African Development Community (SADC) region owing to their role in human food, nutrition, income, and social security. Despite the role of these breeds in the household and national economies, they are currently underutilised, their productivity remains low, and populations are faced with extinction. In addition, there are insufficient measures taken to secure their present and future value. The current review highlights strategies for sustainable use of indigenous cattle genetic resources in the region, including the use of novel production and marketing practices, women and youth empowerment, and development of the appropriate capacity building, legislative, and policy structures. At present, the lack of coordination among the different stakeholders still poses a challenge to the implementation of these strategies. To this end, partnerships, collaboration, and stakeholders’ participation are recommended to effectively implement strategies for sustainable use of indigenous cattle breeds.
Collapse
|
19
|
Van Ba N, Nam LQ, Do DN, Van Hau N, Pham LD. An assessment of genetic diversity and population structures of fifteen Vietnamese indigenous pig breeds for supporting the decision making on conservation strategies. Trop Anim Health Prod 2019; 52:1033-1041. [DOI: 10.1007/s11250-019-02090-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 09/20/2019] [Indexed: 01/20/2023]
|