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Adomako K, Sovi S, Kyei B, Hamidu JA, Olympio OS, Aggrey SE. Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology. PLoS One 2024; 19:e0297643. [PMID: 38696379 PMCID: PMC11065228 DOI: 10.1371/journal.pone.0297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/05/2024] [Indexed: 05/04/2024] Open
Abstract
Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.
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Affiliation(s)
- Kwaku Adomako
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Selorm Sovi
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
| | - Bismark Kyei
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jacob Alhassan Hamidu
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio
- Department of Animal Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel E. Aggrey
- Nutrigenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, Georgia, United States of America
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Azalou M, Assani AS, Kpomasse CC, Tona K, Alkoiret IT, Pitala W. Phenotypic and morphometric characterization of domestic geese raised in northern Benin. Poult Sci 2024; 103:103563. [PMID: 38417339 PMCID: PMC10909896 DOI: 10.1016/j.psj.2024.103563] [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: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
Documentation on the domestic geese (Anser anser) in Benin is scarce, making it objectively difficult to exploit. Its production depends on small flocks raised by livestock farmers in different areas. The aim of the study was to describe the phenotypic and morphometric characteristics of geese encountered in northern Benin. To this end, a total of 576 adult geese (353 males and 223 females) from 102 farms in 4 agro-ecological zones of northern Benin were evaluated for 11 quantitative and 5 qualitative body traits. There are 6 plumage colors with white (42.01%), white-brown magpie (24.65%) and white-grey magpie (17.19%) as dominant colors. The proportions of white-grey (75%) and multicolored (51.85%) in Far northern zone of Benin (FNZB) were higher (P < 0.05) than those in the cotton zone of northern Benin (CZNB), Food-producing zone of southern Borgou (FZSB) and West-Atacora Zone (WAZ). The red coloring of the tarsi was more dominant in the FZSB (63.09%) and the FZSB (61.79%) (P < 0.05). Orange (57.47%) and yellow (28.82%) colored beaks were dominant but did not vary (P > 0.05) from one agro-ecological zone to another. Quantitative traits such as body length, tarsus length, wing span and thoracic circumference of geese varied (P < 0.05) between 71.34 to73.22 cm, 10.08 to 10.6 cm, 131.95 to 135.42 cm and between 42.07 to 43.86 cm respectively. Males differed significantly from females (P < 0.05) for all morphometric traits. The live weight of geese in the FNZB showed higher values than those of other agro-ecological zones (P ˂ 0.05). In addition, white phenotype geese (3.76 kg) were heavier (P ˂ 0.05) than other phenotypes. All correlations between weight and body measurements of domestic geese were positive, but the correlations between live weight and wing span (r = 0.68) were the strongest. These correlations could be used to assess the live weight of the geese population studied and for selection based on live weight. This study provides a reference for morpho-biometric traits and will be complemented by molecular characterization.
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Affiliation(s)
- M Azalou
- Regional Center of Excellency on Avian Sciences, University of Lomé, 1515 Lomé, Republic of Togo; Laboratory of Ecology, Health and Animal Productions (LESPA), University of Parakou, 123 Parakou, Republic of Benin.
| | - A S Assani
- Laboratory of Ecology, Health and Animal Productions (LESPA), University of Parakou, 123 Parakou, Republic of Benin; Faculty of Agronomy, University of Parakou, 123, Parakou, Republic of Benin
| | - C C Kpomasse
- Regional Center of Excellency on Avian Sciences, University of Lomé, 1515 Lomé, Republic of Togo
| | - K Tona
- Regional Center of Excellency on Avian Sciences, University of Lomé, 1515 Lomé, Republic of Togo
| | - I T Alkoiret
- Laboratory of Ecology, Health and Animal Productions (LESPA), University of Parakou, 123 Parakou, Republic of Benin; Faculty of Agronomy, University of Parakou, 123, Parakou, Republic of Benin
| | - W Pitala
- Regional Center of Excellency on Avian Sciences, University of Lomé, 1515 Lomé, Republic of Togo; Higher School of Agronomy, University of Lomé, 1515 Lomé, Republic of Togo
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Badjibassa A, Ouédraogo D, Burger PA, Rosen BD, Van Tassell CP, Sölkner J, Soudré A. Participatory investigation of goat farmers' breeding practices, trait preference, and selection criteria in Burkina Faso. Trop Anim Health Prod 2024; 56:35. [PMID: 38189997 DOI: 10.1007/s11250-023-03869-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: 09/14/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024]
Abstract
The community-based breeding program (CBBP) is an innovative approach recommended for genetic improvement and sustainable use of animal genetic resources in extensive farming systems. Successful implementation of this approach requires an understanding of the characteristics of production systems, breeding objectives, and farmers' trait preference. This study aimed to identify the selection criteria of goat farmers in rural areas of Burkina Faso and their potential implications in establishing CBBP. Following focus group discussions, a well-structured questionnaire was designed and administered to 372 randomly selected goat farmers in two different agro-ecological zones. A list of traits obtained during focus group discussions was provided to farmers individually, and they were asked to rank the ones they preferentially use to select breeding animals. Statistical tests were conducted to compare data between the two agro-ecological zones. The results showed that the average goat flock per household was higher (P < 0.05) in the Sudanian (15.68 ± 13.76), compared to the Sudano-Sahelian area (12.93 ± 13.3). Adult females were the dominant age-sex group in both areas. Reasons for culling, keeping breeding bucks, and castration practice were significantly different (P < 0.05) among agro-ecological zones. The most important common criterion for selection in the two zones was body size, coat color, and growth rate for the bucks and does, while fertility (0.06) parameters including twining ability (0.18), kidding frequency (0.11), and mothering ability (0.15) were furthermore considered for breeding does selection. These findings provide valuable insights for developing CBBPs tailored to goat production in the study areas.
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Affiliation(s)
- Akounda Badjibassa
- Unité de Formation et de Recherches Sciences et Technologie, Université Norbert ZONGO, BP 376, Koudougou, Burkina Faso
| | - Dominique Ouédraogo
- Centre Universitaire de Ziniaré, Université Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Benjamin D Rosen
- United States Department of Agriculture, Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - Curtis P Van Tassell
- United States Department of Agriculture, Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave, Beltsville, MD, 20705, USA
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor-Mendel Strasse, 1180, Vienna, Austria
| | - Albert Soudré
- Unité de Formation et de Recherches Sciences et Technologie, Université Norbert ZONGO, BP 376, Koudougou, Burkina Faso.
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Bionda A, Lopreiato V, Amato A, Cortellari M, Cavallo C, Chiofalo V, Crepaldi P, Liotta L. Phenotypic and Genomic Characterization of the Comune di Sicilia Goat: Towards the Conservation of an Endangered Local Breed. Animals (Basel) 2023; 13:3207. [PMID: 37893931 PMCID: PMC10603724 DOI: 10.3390/ani13203207] [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: 09/01/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The Comune di Sicilia, a local goat breed from Sicily (Italy), is currently undergoing recognition as a distinct breed. This study aims to characterize the population both phenotypically and genomically to advance its recognition process. A total of 78 subjects from two locations were enrolled, and their phenotypic data, including qualitative traits and morphometric measurements of adult animals, were recorded and statistically analyzed. The goats were genotyped using the Illumina 50 k Goat SNPchip, comparing them with 473 goats from 15 Italian breeds. Population structure, phylogenetic relationships, admixture, and genomic inbreeding were analyzed. Additionally, subjects with different morphological traits were compared using FST and runs of homozygosity, leading to the identification of potential candidate genes associated with anotia and wattle presence in goats. The Comune di Sicilia breed exhibited distinctive genomic and phenotypic features, setting it apart from other breeds in the same region. However, moderate variability, possibly influenced by selection practices, was also observed. To ensure the breed's preservation and prevent excessive inbreeding, a comprehensive approach considering both morphology and genomic background is recommended. This study contributes valuable insights into the genetic peculiarities of the Comune di Sicilia goat, supporting its recognition as a unique and valuable breed.
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Affiliation(s)
- Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milan, Via Celoria 2, 20133 Milan, Italy; (A.B.); (P.C.)
| | - Vincenzo Lopreiato
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (V.L.); (A.A.); (C.C.); (V.C.); (L.L.)
| | - Annalisa Amato
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (V.L.); (A.A.); (C.C.); (V.C.); (L.L.)
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milan, Via Celoria 2, 20133 Milan, Italy; (A.B.); (P.C.)
| | - Carmelo Cavallo
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (V.L.); (A.A.); (C.C.); (V.C.); (L.L.)
| | - Vincenzo Chiofalo
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (V.L.); (A.A.); (C.C.); (V.C.); (L.L.)
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milan, Via Celoria 2, 20133 Milan, Italy; (A.B.); (P.C.)
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy; (V.L.); (A.A.); (C.C.); (V.C.); (L.L.)
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Okoro VMO, Chikereuba U, Iheanacho G, Ogundu A, Chukwuocha C, Chikaodinaka F, Ifediba C, Kadurumba OE, Ogundu U, Iloeje M. West African Dwarf goat populations of tropical rainforest zone: application of multivariate analysis tools on their characterization using morpho-biometric traits. Trop Anim Health Prod 2023; 55:222. [PMID: 37221420 DOI: 10.1007/s11250-023-03641-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/16/2023] [Indexed: 05/25/2023]
Abstract
This research was carried out to characterize the West African Dwarf (WAD) goats using multivariate approach based on their morpho-biometric traits in the tropical rainforest zone of Nigeria. Data on four physical qualitative traits, six morphology indicators, and nine morphological characters were generated from 279 goats. Descriptive statistics, non-parametric analysis and one-way approach of ANOVA with post hoc tests, discriminant analysis (canonical), principal component analysis (categorical), and regression tree analysis were employed to discern the effects of location and sex on the parameters, as well as characterize the goats. The frequencies of the qualitative traits show black coat color predominated (60.2%) over other coat colors, plain color predominated (75.3%) over other color patterns, straight horns (38.1%) predominate over other horn shape, and beard presence (66.7%) predominated over non-beard presence among the goats in terms of locations and sexes. Location and age were significantly affected on the biometric characters (p<0.05 and p<0.001) with goats from Enugu having higher values than other states, while only head length (HL) was affected significantly by sex (p< 0.05). The morphological indicators were not significantly affected by location and sex (p>0.05 and p>0.001), while age was significant. The discriminant analysis revealed a sparse, non-intermingling populations for the physical traits, biometric characters, and body indices implying they are different distinct populations from each other. Generally, the goat populations could be characterized using heart girth (HG), rump height (RH), and body weight (BW) due to the principal components, while the CHAID and Exhaustive CHAID algorithm analysis revealed BW and HL as the genetic classifiers of the WAD goats, both in terms of locations. Basically, the goats from the 3 locations appeared to be more homogeneous in nature, implying that a deployment of specific complimentary genomics work targeted at future selection and breeding programs to improve their productivity in the tropical rainforest of Nigeria is necessary.
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Affiliation(s)
- Victor Mela Obinna Okoro
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria.
| | - Uzoamaka Chikereuba
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Gabrella Iheanacho
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Andrew Ogundu
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Clara Chukwuocha
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Febechi Chikaodinaka
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Chukwuebuka Ifediba
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Ogechi Evangeline Kadurumba
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Uduak Ogundu
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Michael Iloeje
- Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
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Yakubu A, Jegede P, Wheto M, Shoyombo AJ, Adebambo AO, Popoola MA, Osaiyuwu OH, Olafadehan OA, Alabi OO, Ukim CI, Vincent ST, Mundi HL, Olayanju A, Adebambo OA. Multivariate characterisation of morpho-biometric traits of indigenous helmeted Guinea fowl (Numida meleagris) in Nigeria. PLoS One 2022; 17:e0261048. [PMID: 35696370 PMCID: PMC9191719 DOI: 10.1371/journal.pone.0261048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
This study was conducted to characterise phenotypically helmeted Guinea fowls in three agro-ecologies in Nigeria using multivariate approach. Eighteen biometric characters, four morphological indices and eleven qualitative physical traits were investigated in a total of 569 adult birds (158 males and 411 females). Descriptive statistics, non-parametric Kruskal–Wallis H test followed by the Mann–Whitney U and Dunn-Bonferroni tests for post hoc, Multiple Correspondence Analysis (MCA), Univariate Analysis, Canonical Discriminant Analysis, Categorical Principal Component Analysis and Decision Trees were employed to discern the effects of agro-ecological zone and sex on the morphostructural parameters. Agro-ecology had significant effect (P<0.05; P<0.01) on all the colour traits. In general, the most frequently observed colour phenotype of Guinea fowl had pearl plumage colour (54.0%), pale red skin colour (94.2%), black shank colour (68.7%), brown eye colour (49.7%), white earlobe colour (54.8%) and brown helmet colour (72.6%). The frequencies of helmet shape and wattle size were significantly influenced (P<0.01) by agro-ecology and sex. Overall, birds from the Southern Guinea Savanna zone had significantly higher values (P<0.05) for most biometric traits compared to their Sudano-Sahelian and Tropical Rainforest counterparts. They were also more compact (120.00 vs. 110.00 vs. 107.69) but had lesser condition index (7.66 vs. 9.45 vs. 9.30) and lower long-leggedness (19.71 vs. 19.23 vs. 9.51) than their counterparts from the two other zones. Sexual dimorphism (P<0.05) was in favour of male birds especially those in Southern Guinea Savanna and Sudano-Sahelian zones. However, the MCA and discriminant analysis revealed considerable intermingling of the qualitative physical traits, biometric traits and body indices especially between the Sudano-Sahelian and Tropical Rainforest birds. In spite of the high level of genetic admixture, the Guinea fowl populations could to a relative extent be distinguished using wing length, body length and eye colour. Generally, the birds from the three zones appeared to be more homogeneous than heterogeneous in nature. However, further complementary work on genomics will guide future selection and breeding programs geared towards improving the productivity, survival and environmental adaptation of indigenous helmeted Guinea fowls in the tropics.
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Affiliation(s)
- Abdulmojeed Yakubu
- Department of Animal Science/Centre for Sustainable Agriculture and Rural Development, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria
- * E-mail: (AY); (AJS); (AOA)
| | - Praise Jegede
- Department of Animal Science/Centre for Sustainable Agriculture and Rural Development, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria
- National Biotechnology Development Agency, Abuja, Nigeria
| | - Mathew Wheto
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Ayoola J. Shoyombo
- Department of Animal Science, Landmark University, Omu-Aran, Nigeria
- * E-mail: (AY); (AJS); (AOA)
| | - Ayotunde O. Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
- * E-mail: (AY); (AJS); (AOA)
| | | | - Osamede H. Osaiyuwu
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria
| | | | - Olayinka O. Alabi
- Department of Animal Science, Landmark University, Omu-Aran, Nigeria
| | | | - Samuel T. Vincent
- Department of Animal Science/Centre for Sustainable Agriculture and Rural Development, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria
| | - Harirat L. Mundi
- Department of Animal Science/Centre for Sustainable Agriculture and Rural Development, Faculty of Agriculture, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria
- Department of Animal Science, Faculty of Agriculture, Federal University of Lafia, Lafia, Nigeria
| | - Adeniyi Olayanju
- Department of Animal Science, Landmark University, Omu-Aran, Nigeria
| | - Olufunmilayo A. Adebambo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
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