DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections
Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/118382 |
| _version_ | 1855528059997782016 |
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| author | Ocampo, John Ovalle, Tatiana Labarta, Ricardo Antonio Phuong Le, Dung Haan, Stefan de Vu, Nguyen Anh Kha, Le Quy Becerra López Lavelle, Luis Augusto |
| author_browse | Becerra López Lavelle, Luis Augusto Haan, Stefan de Kha, Le Quy Labarta, Ricardo Antonio Ocampo, John Ovalle, Tatiana Phuong Le, Dung Vu, Nguyen Anh |
| author_facet | Ocampo, John Ovalle, Tatiana Labarta, Ricardo Antonio Phuong Le, Dung Haan, Stefan de Vu, Nguyen Anh Kha, Le Quy Becerra López Lavelle, Luis Augusto |
| author_sort | Ocampo, John |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers’ needs. |
| format | Journal Article |
| id | CGSpace118382 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1183822025-11-11T18:51:42Z DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections Ocampo, John Ovalle, Tatiana Labarta, Ricardo Antonio Phuong Le, Dung Haan, Stefan de Vu, Nguyen Anh Kha, Le Quy Becerra López Lavelle, Luis Augusto single nucleotide polymorphism genetic markers genetic variation cassava germplasm genotypes polimorfismo de un solo nucleótido marcadores genéticos variación genética manihot esculenta Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers’ needs. 2022-06 2022-03-15T16:26:15Z 2022-03-15T16:26:15Z Journal Article https://hdl.handle.net/10568/118382 en Open Access application/pdf Springer Ocampo, J.; Ovalle, T.; Labarta, R.; Phuong Le, D.; de Haan, S.; Vu, N.A.; Kha, L.Q.; Becerra Lopez-Lavalle, L.A. (2021) DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections. Plant Molecular Biology, Online first paper (25 February 2021). 18 p. ISSN: 1573-5028 |
| spellingShingle | single nucleotide polymorphism genetic markers genetic variation cassava germplasm genotypes polimorfismo de un solo nucleótido marcadores genéticos variación genética manihot esculenta Ocampo, John Ovalle, Tatiana Labarta, Ricardo Antonio Phuong Le, Dung Haan, Stefan de Vu, Nguyen Anh Kha, Le Quy Becerra López Lavelle, Luis Augusto DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections |
| title | DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections |
| title_full | DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections |
| title_fullStr | DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections |
| title_full_unstemmed | DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections |
| title_short | DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections |
| title_sort | dna fingerprinting reveals varietal composition of vietnamese cassava germplasm manihot esculenta crantz from farmers field and genebank collections |
| topic | single nucleotide polymorphism genetic markers genetic variation cassava germplasm genotypes polimorfismo de un solo nucleótido marcadores genéticos variación genética manihot esculenta |
| url | https://hdl.handle.net/10568/118382 |
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