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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Thong T, Singchat W, Ahmad SF, Chaiyes A, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. Optimizing Microsatellite Marker Panels for Genetic Diversity and Population Genetic Studies: An Ant Colony Algorithm Approach with Polymorphic Information Content. BIOLOGY 2023; 12:1280. [PMID: 37886990 PMCID: PMC10604496 DOI: 10.3390/biology12101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/28/2023]
Abstract
Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC-ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the global solution discovery speed while reducing the likelihood of becoming trapped in local solutions. This process facilitated the acquisition of a cost-efficient and optimized microsatellite marker panel for studying genetic diversity and population genetic datasets. The established microsatellite efficiency metrics such as PIC, allele richness, and heterozygosity were correlated with the actual effectiveness of the microsatellite marker panel. This approach could substantially reduce budgetary barriers to population genetic assessments, breeding, and conservation programs.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Pakkret Nonthaburi 11120, Thailand;
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand; (R.R.); (P.W.); (T.P.); (T.T.); (W.S.); (S.F.A.); (K.H.); (E.K.); (N.M.); (A.K.); (P.D.)
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University, Bangkok 10900, Thailand
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Sambe BS, Diouf MN, Houaga I, Ndiaye B, Badji MN, Diop M, Sembene M. Genetic diversity of bovine populations raised in Senegal. Vet Med Sci 2022; 8:2173-2182. [PMID: 35781798 PMCID: PMC9514503 DOI: 10.1002/vms3.873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background The Gobra zebu and N'dama taurine cattle breeds are important genetic animal resources for Senegal. For several decades, genetic breeding programmes have been devoted to them at the Centre de Recherches Zootechniques de Dahra and Kolda. Since then, these animals have been subjected to mass selection, mainly in closed selection nuclei. Objective This study aims to assess the genetic diversity within these selection nuclei in order to orient future selection strategies. Material and methods The study was carried out on the Gobra zebu and N'dama taurine populations from selection nuclei of Dahra and Kolda respectively, which were compared to 5 other populations of the main cattle breeds in Senegal. One hundred eighty (180) animals were genotyped with 21 microsatellite markers recommended by the Food and Agriculture Organisation. Results All populations were found to be polymorphic with a PIC of over 55%. However, animals from the CRZ‐Dahra (indigenous) and CRZ‐Kolda stations had the lowest mean heterozygosity (0.643 and 0.591 respectively). The other populations had an average heterozygosity between 0.650 and 0.737. Conclusion The cattle populations maintained at the different CRZs show a lower genetic diversity than the other populations described in our study. The main reasons for this are reproductive isolation and selection pressure on these populations.
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Affiliation(s)
| | - Mame Nahé Diouf
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
| | - Isidore Houaga
- Centre International de Recherche‐Développement sur l'Elevage en zone Subhumide (CIRDES) Bobo‐Dioulasso Burkina Faso
| | - Bakary Ndiaye
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
- Département de Biologie Animale Université Cheikh Anta Diop (UCAD) Dakar Sénégal
| | - Marc Noël Badji
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
- Département de Biologie Animale Université Cheikh Anta Diop (UCAD) Dakar Sénégal
| | - Mamadou Diop
- Laboratoire National de l'Elevage et de Recherches Vétérinaires (LNERV) Dakar Sénégal
| | - Mbacké Sembene
- Département de Biologie Animale Université Cheikh Anta Diop (UCAD) Dakar Sénégal
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