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Soro M, Zida SMFWP, Somé K, Tiendrébéogo F, Otron DH, Pita JS, Néya JB, Koné D. Estimation of Genetic Diversity and Number of Unique Genotypes of Cassava Germplasm from Burkina Faso Using Microsatellite Markers. Genes (Basel) 2024; 15:73. [PMID: 38254963 PMCID: PMC10815475 DOI: 10.3390/genes15010073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Genetic diversity is very important in crop improvement. This study was carried out to assess the genetic diversity and the number of unique multilocus genotypes (MLGs) in a cassava collection in Burkina Faso. To achieve this objective, 130 cassava accessions were genotyped using 32 simple sequence repeat (SSR) markers. The results revealed that among these markers, twelve (12) were highly informative, with polymorphic information content (PIC) values greater than 0.50; twelve (12) were moderately informative, with PIC values ranging between 0.25 and 0.50; and eight (8) were not very informative, with PIC values lower than 0.25. A moderate level of genetic diversity was found for the population, indicated by the average expected heterozygosity (0.45) and the observed heterozygosity (0.48). About 83.8% of unique multilocus genotypes were found in the cassava collection, indicating that SSR markers seem to be most appropriate for MLG identification. Population structure analysis based on hierarchical clustering identified two subpopulations and the Bayesian approach suggested five clusters. Additionally, discriminant analysis of principal components (DAPC) separated the cassava accessions into 13 subpopulations. A comparison of these results and those of a previous study using single nucleotide polymorphisms (SNP) suggests that each type of marker can be used to assess the genetic structure of cassava grown in Burkina Faso.
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Affiliation(s)
- Monique Soro
- Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d’Innovation de Bingerville, Université Félix Houphouët-Boigny (UFHB), Bingerville 08 BP 2035, Côte d’Ivoire; (D.H.O.); (J.S.P.)
- Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso; (K.S.); (J.B.N.)
- Laboratoire Mixte International Patho-Bios, Institut de l’Environnement et de Recherches Agricoles, Ouagadougou 01 BP 476, Burkina Faso
| | - Serge Marie Felicien Wend-Pagnagdé Zida
- Laboratoire de Génétique et de Biotechnologies Végétales, Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso;
| | - Koussao Somé
- Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso; (K.S.); (J.B.N.)
- Laboratoire de Génétique et de Biotechnologies Végétales, Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso;
| | - Fidèle Tiendrébéogo
- Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso; (K.S.); (J.B.N.)
| | - Daniel H. Otron
- Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d’Innovation de Bingerville, Université Félix Houphouët-Boigny (UFHB), Bingerville 08 BP 2035, Côte d’Ivoire; (D.H.O.); (J.S.P.)
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan 22 BP 582, Côte d’Ivoire;
| | - Justin S. Pita
- Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d’Innovation de Bingerville, Université Félix Houphouët-Boigny (UFHB), Bingerville 08 BP 2035, Côte d’Ivoire; (D.H.O.); (J.S.P.)
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan 22 BP 582, Côte d’Ivoire;
| | - James B. Néya
- Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso; (K.S.); (J.B.N.)
- Laboratoire Mixte International Patho-Bios, Institut de l’Environnement et de Recherches Agricoles, Ouagadougou 01 BP 476, Burkina Faso
| | - Daouda Koné
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan 22 BP 582, Côte d’Ivoire;
- Centre d’Excellence Africain sur le Changement Climatique, la Biodiversité et l’Agriculture Durable, Université Félix Houphouët-Boigny, Abidjan 22 BP 463, Côte d’Ivoire
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Soro M, Tiendrébéogo F, Pita JS, Traoré ET, Somé K, Tibiri EB, Néya JB, Mutuku JM, Simporé J, Koné D. Epidemiological assessment of cassava mosaic disease in Burkina Faso. Plant Pathol 2021; 70:2207-2216. [PMID: 35873883 PMCID: PMC9291739 DOI: 10.1111/ppa.13459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/05/2021] [Indexed: 05/11/2023]
Abstract
Surveys were conducted in 2016 and 2017 across the main cassava-growing regions of Burkina Faso to assess the status of cassava mosaic disease (CMD) and to determine the virus strains causing the disease, using field observation and phylogenetic analysis. CMD incidence varied between regions and across years but was lowest in Hauts-Bassins (6.0%, 2016 and 5.4%, 2017) and highest in Centre-Sud (18.5%, 2016) and in Boucle du Mouhoun (51.7%, 2017). The lowest CMD severity was found in Est region (2.0) for both years and the highest in Sud-Ouest region (3.3, 2016) and Centre-Sud region (2.8, 2017). The CMD infection was primarily associated with contaminated cuttings in all regions except in Hauts-Bassins, where whitefly-borne infection was higher than cuttings-borne infection in 2016. PCR screening of 687 samples coupled with sequence analysis revealed the presence of African cassava mosaic-like (ACMV-like) viruses and East African cassava mosaic-like (EACMV-like) viruses as single infections at 79.5% and 1.1%, respectively. Co-infections of ACMV-like and EACMV-like viruses were detected in 19.4% of the tested samples. In addition, 86.7% of the samples positive for EACMV-like virus were found to be positive for East African cassava mosaic Cameroon virus (EACMCMV). Phylogenetic analysis revealed the segregation of cassava mosaic geminiviruses (CMGs) from Burkina Faso into three clades specific to ACMV, African cassava mosaic Burkina Faso virus (ACMBFV), and EACMCMV, confirming the presence of these viruses. The results of this study show that EACMCMV occurrence may be more prevalent in Burkina Faso than previously thought.
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Affiliation(s)
- Monique Soro
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanIvory Coast
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Fidèle Tiendrébéogo
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Justin S. Pita
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanIvory Coast
| | - Edwig T. Traoré
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE)Université Joseph Ki‐ZerboOuagadougouBurkina Faso
| | - Koussao Somé
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Laboratoire de Génétique et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
| | - Ezechiel B. Tibiri
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - James B. Néya
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - J. Musembi Mutuku
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
| | - Jacques Simporé
- Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE)Université Joseph Ki‐ZerboOuagadougouBurkina Faso
| | - Daouda Koné
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanIvory Coast
- Centre d’Excellence Africain sur le Changement Climatique, la Biodiversité et l’Agriculture Durable (WASCAL/CEA‐CCBAD, Université Félix Houphouët‐Boigny)PSI‐Université Félix Houphouët‐BoignyAbidjanIvory Coast
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Tibiri EB, Pita JS, Tiendrébéogo F, Bangratz M, Néya JB, Brugidou C, Somé K, Barro N. Characterization of virus species associated with sweetpotato virus diseases in Burkina Faso. Plant Pathol 2020; 69:1003-1017. [PMID: 32742024 PMCID: PMC7386933 DOI: 10.1111/ppa.13190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Sweetpotato (Ipomoea batatas) production in sub-Saharan Africa is severely affected by viral diseases caused by several interacting viruses, including sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), and sweet potato leaf curl virus (SPLCV). However, the aetiology of viral symptoms on sweetpotato is rarely established in most countries in Africa. Here, we aimed to investigate and characterize the incidence of sweetpotato viruses in Burkina Faso. We performed a countrywide survey in 18 districts of Burkina Faso and collected 600 plants, with and without symptoms, from 80 fields. Viral strains were identified using nitrocellulose membrane-ELISA, PCR, and reverse transcription-PCR. Three scions from each of 50 selected plants with symptoms were grafted to healthy Ipomoea setosa and then serological and molecular tests were performed on the 150 recorded samples. Three viruses were detected: 24% of samples were positive for SPFMV, 18% for SPLCV, and 2% for SPCSV. Across all diagnostic tests, 40% of all plant samples were virus-negative. Coinfections were found in 16% of samples. Partial sequences were obtained, including 13 that matched SPFMV, one that matched SPLCV, and one that matched SPCSV. All identified SPFMV isolates belonged to either phylogroup B or A-II. The SPCSV-positive isolates had 98% gene sequence homology with SPCSV-West Africa for the coat protein. Begomovirus-positive isolates clustered with SPLCV-United States. This first study of sweetpotato viral diseases in Burkina Faso indicates widespread occurrence and suggests a need for further epidemiological investigations, breeding programmes focused on virus-resistant varieties, and improved farming practices to control disease spread.
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Affiliation(s)
- Ezechiel B. Tibiri
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire de Génétique et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Laboratoire d’Epidémiologie et de Surveillance des bactéries et virus Transmissibles par les Aliments et l’eauLabESTA/UFR/SVTUniversité Joseph Ki‐ZerboOuagadougouBurkina Faso
| | - Justin S. Pita
- Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleCôte d’Ivoire
| | - Fidèle Tiendrébéogo
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Martine Bangratz
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Interactions Plants Microorganismes et Environnement (IPME)IRD, CiradUniversité MontpellierMontpellierCedexFrance
| | - James B. Néya
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Christophe Brugidou
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Interactions Plants Microorganismes et Environnement (IPME)IRD, CiradUniversité MontpellierMontpellierCedexFrance
| | - Koussao Somé
- Laboratoire de Génétique et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Nicolas Barro
- Laboratoire d’Epidémiologie et de Surveillance des bactéries et virus Transmissibles par les Aliments et l’eauLabESTA/UFR/SVTUniversité Joseph Ki‐ZerboOuagadougouBurkina Faso
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