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Abbasi Holasou H, Panahi B, Shahi A, Nami Y. Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization. Biochem Biophys Rep 2024; 38:101678. [PMID: 38495412 PMCID: PMC10940787 DOI: 10.1016/j.bbrep.2024.101678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.
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Affiliation(s)
- Hossein Abbasi Holasou
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Bahman Panahi
- Department of Genomics, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Ali Shahi
- Faculty of Agriculture (Meshgin Shahr Campus), Mohaghegh Ardabili University, Ardabil, Iran
| | - Yousef Nami
- Department of Food Biotechnology, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
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Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers. Animals (Basel) 2020; 10:ani10101842. [PMID: 33050450 PMCID: PMC7600759 DOI: 10.3390/ani10101842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023] Open
Abstract
Simple Summary This study aimed to evaluate the genetic diversity of six groups of native Brazilian goats using a panel of single sequence repeats (SSRs). Results indicated a definite genetic differentiation among the Brazilian goat herd, which indicates the existence of at least four breeds according to the international concepts (Moxotó and Repartida; the Grauna and Serrana Azul; Canindé and Marota breeds). Abstract The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds.
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Shahabzadeh Z, Mohammadi R, Darvishzadeh R, Jaffari M. Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers. Mol Biol Rep 2019; 47:655-669. [PMID: 31707600 DOI: 10.1007/s11033-019-05173-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022]
Abstract
Tall fescue is a perennial cool-season grass with economic importance especially in temperate regions of the northern hemisphere. This study was done to assess the genetic diversity and population structure of 90 tall fescue populations and cultivars using ISSR and EST-SSR markers in order to categorize valuable populations for breeding programs and to construct the core collection of tall fescue collection in Iran. The 10 EST-SSR primer pairs amplified 92 alleles. The allele numbers varied from 4 to 13 alleles per locus with an average of 9.2 alleles, of which 84 (90.6%) were polymorphic with an average of 8.4 polymorphic bands per primer. The 39 ISSR primers totally produced 387 scorable bands, of which 335 (86.6%) were polymorphic with an average of 8.6 polymorphic bands per primer. The amplified markers by ISSR primers varied from 6 to 14 markers per primer with an average of 9.92 markers per primer. The 90 tall fescue populations using both EST-SSR and ISSR data were classified into two clusters by UPGMA method that was coincide with PCA and structure analysis results. The turf-type and forage-type populations were clearly separated. Based on the results, the Iranian populations provide a valuable and novel germplasm to employ in tall fescue varietal improvement programs for both forage and turf-type applications. This progression is an important step to introduce this collection for development of a core collection of tall fescue germplasm in Iran.
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Affiliation(s)
- Z Shahabzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - R Mohammadi
- Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
| | - R Darvishzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - M Jaffari
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
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Ginja C, Gama LT, Martínez A, Sevane N, Martin-Burriel I, Lanari MR, Revidatti MA, Aranguren-Méndez JA, Bedotti DO, Ribeiro MN, Sponenberg P, Aguirre EL, Alvarez-Franco LA, Menezes MPC, Chacón E, Galarza A, Gómez-Urviola N, Martínez-López OR, Pimenta-Filho EC, da Rocha LL, Stemmer A, Landi V, Delgado-Bermejo JV. Genetic diversity and patterns of population structure in Creole goats from the Americas. Anim Genet 2017; 48:315-329. [PMID: 28094449 DOI: 10.1111/age.12529] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2016] [Indexed: 01/03/2023]
Abstract
Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora-type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well-differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.
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Affiliation(s)
- C Ginja
- CIBIO-InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas n. 7, 4485-661, Vairão, Portugal
| | - L T Gama
- CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario ceiA3, Córdoba, Spain
| | - N Sevane
- Departamento de Producción Animal, Universidad Complutense de Madrid, Madrid, Spain
| | - I Martin-Burriel
- Martin-Burriel, Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - M R Lanari
- Area de Producción Animal, Instituto Nacional de Tecnología Agropecuaria EEA, Bariloche, Argentina
| | - M A Revidatti
- Facultad de Ciencias Veterinarias, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - J A Aranguren-Méndez
- Facultad de Ciencias Veterinarias, Universidad de Zulia, Maracaibo-Zulia, Venezuela
| | - D O Bedotti
- Instituto Nacional de Tecnología Agropecuaria EEA Anguil "Ing. Agr. Guillermo Covas", Bariloche, Argentina
| | - M N Ribeiro
- Departamento de Zootecnia, Universidade Federal Rural de Pernambuco, Recife, PE, Brazil
| | - P Sponenberg
- Virginia-Maryland Regional College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - E L Aguirre
- Universidad Nacional de Loja, Loja, Ecuador.,Grupo de Melhoramento Animal e Biotecnologias GMAB-FZEA-USP, Brazil
| | | | | | - E Chacón
- Universidad Técnica de Cotopaxi, La Maná, Ecuador
| | - A Galarza
- Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - N Gómez-Urviola
- Universidad Nacional Micaela Bastidas de Apurímac, Abancay, Perú
| | - O R Martínez-López
- Centro Multidisciplinario de Investigaciones Tecnológicas, Dirección General de Investigación Científica y Tecnológica, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | | | - L L da Rocha
- Departamento de Zootecnia, Universidade Federal Rural de Pernambuco, Recife, PE, Brazil
| | - A Stemmer
- Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario ceiA3, Córdoba, Spain
| | - J V Delgado-Bermejo
- Departamento de Genética, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario ceiA3, Córdoba, Spain
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Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2830394. [PMID: 27092309 PMCID: PMC4820616 DOI: 10.1155/2016/2830394] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 11/29/2022]
Abstract
The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P < 0.001) pairwise FST values of each pair of breeds. Exceptionally, FST values calculated for Honamli and Hair breeds were statistically nonsignificant (P > 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers.
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Kim JH, Byun MJ, Choi SB, Suh S, Kim YS, Kim MJ, Ko YG, Cho CY. Detection of a distinct variation site for geographical classification of mitochondrial DNA haplogroup A in the domestic goat (Capra hircus). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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