scholarly journals DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers’ field and genebank collections

2021 ◽  
Author(s):  
John Ocampo ◽  
Tatiana Ovalle ◽  
Ricardo Labarta ◽  
Dung Phuong Le ◽  
Stefan de Haan ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Snp Markers ◽  
Ex Situ ◽  
Conservation Programs ◽  
Manihot Esculenta Crantz ◽  
Ecological Zones ◽  
Genetic Groups ◽  
Central Highlands ◽  
Genebank Collections ◽  
Agro Ecological Zones

Abstract Key message A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers’ field and genebank collections Abstract 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.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals On-farm management and participatory evaluation of pigeonpea (Cajanus cajan [L.] Millspaugh) diversity across the agro-ecological zones of Benin Republic

2019 ◽  
Author(s):  
Géofroy KINHOEGBE ◽  
Gustave Djèdatin ◽  
Laura Estelle Yêyinou Loko ◽  
Abraham Gnimassou Favi ◽  
Aristide Adomou ◽  
...  
Keyword(s):  
Participatory Evaluation ◽  
High Rate ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Ecological Zones ◽  
Pests And Diseases ◽  
Seed System ◽  
Four Square ◽  
Sudanian Zone ◽  
Agro Ecological Zones

Abstract Background: Pigeonpea is a multipurpose food legume that contributes to food security in Benin. However, its production declined and some landraces are being threatened of disappearance. Previous investigations on pigeonpea in Benin have been restricted to South and Central Benin. Therefore, pigeonpea diversity in northern is still unknown. This study aimed to have a better knowledge of pigeonpea genetic diversity, for its promotion and valorization.Methods: 500 producers of pigeonpea belonging to thirteen sociolinguistic groups were selected through 50 villages. Data were collected using methods and tools of participatory research appraisal. Folk nomenclatures, taxonomy of pigeonpea and seed system were investigated. The distribution and extent of pigeonpea landraces were evaluated using Four Square Analysis method. A comparative analysis of pigeonpea uses categories, production systems, pigeonpea production constraints, famers’ preference criteria and participative evaluation for existing landraces across agro-ecological zones was done.Result: Folk nomenclature and taxonomy were mainly based on seed coat colour and size colour. Seven pigeonpea uses category were recorded including sacrifice, grain processing and fertilization. The results showed that pigeonpea seed system is informal. Based on seed characteristics, fifteen landraces were recorded with seven new landraces. A high rate of landraces threatened of disappearance was observed across the ecological zones. Ten constraints are known affecting pigeonpea production in Benin with pests and diseases as the most important in all agro-ecological zones. This study revealed that pigeonpea cultivation is increasing in the Sudanian zone. Landraces to be produced must be selected on the basis of 11 criteria among them precocity and resistance to pests and diseases, in the three ecological zones and adaptability to any type of soil in the Sudanian zone were the most important. The participatory evaluation revealed the existence of a few performing landraces.Conclusions: The development of performing varieties is important to enhance pigeonpea production in Benin. Morphological and molecular characterizations of identified landrace are highly recommended to help select suitable varieties for breeding programs. In situ and ex situ conservation strategies are important to preserve landraces threatened of disappearance.

scholarly journals On-farm management and participatory evaluation of pigeonpea (Cajanus cajan [L.] Millspaugh) diversity across the agro-ecological zones of Benin Republic

2020 ◽  
Author(s):  
Géofroy KINHOEGBE ◽  
Gustave Djèdatin ◽  
Laura Estelle Yêyinou Loko ◽  
Abraham Gnimansou Favi ◽  
Aristide Adomou ◽  
...  
Keyword(s):  
Participatory Evaluation ◽  
Ex Situ ◽  
Breeding Programs ◽  
Ecological Zones ◽  
Pests And Diseases ◽  
Production Constraints ◽  
Seed System ◽  
Sudanian Zone ◽  
Benin Republic ◽  
Agro Ecological Zones

Abstract Background: Pigeonpea is a multipurpose food legume that contributes to food security in Benin. However, its production declined and some landraces are being threatened with disappearance. For establishment of conservation and breeding programs previous ethnobotanical surveys on pigeonpea were done in Benin but restricted to south and central regions. Knowing that pigeonpea is also grown in northern Benin, and that the varieties cultivated in this region can show agronomic performances, it is therefore important to evaluate the diversity of this legume in this region. However, an exhaustive documentation of pigeonpea diversity grown in Benin Republic are necessary for effective breeding and conservation programs. Therefore, this study aimed to document genetic diversity of pigeonpea, across the agro-ecological zones of Benin Republic for its promotion and valorization. Methods: 500 producers of pigeonpea belonging to thirteen sociolinguistic groups were selected through 50 villages. Data were collected using methods and tools of participatory research appraisal. Folk nomenclatures, taxonomy of pigeonpea and seed system were investigated. The distribution and extent of pigeonpea landraces were evaluated using Four Square Analysis method. A comparative analysis of pigeonpea uses categories, production systems, pigeonpea production constraints, famers’ preference criteria and participative evaluation for existing landraces across agro-ecological zones was done. Result: Folk nomenclature and taxonomy were mainly based on seed coat colour and size. Seven pigeonpea use category were recorded including sacrifice, grain processing and fertilization. The results showed that pigeonpea seed system is informal. Based on seed characteristics, fifteen landraces were recorded with seven new landraces. The Sudano-Guinean zone contained the highest number (11) of landraces. The average number of landraces per village was 2.7. A high rate of landraces threatened with disappearance was observed across the ecological zones. Ten constraints are known affecting pigeonpea production in Benin with pests and diseases as the most important in all agro-ecological zones. This study revealed that pigeonpea cultivation is increasing in the Sudanian zone. Varieties to be produced must be selected on the basis of 11 criteria among them precocity and resistance to pests and diseases, in the three ecological zones and adaptability to any type of soil in the Sudanian zone were the most important. The participatory evaluation revealed the existence of a few performing cultivars. Conclusions: Our results show that to implement a pigeonpea genetic conservation program in Benin, it would be necessary to take into account the diversity, production constraints and criteria of varietal preference, which varied according to agro-ecological zones. In situ and ex situ conservation strategies are important to preserve pigeonpea landraces. Morphological and molecular characterizations of identified cultivars are highly recommended to help select suitable varieties for breeding programs.

scholarly journals High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz)

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255290
Author(s):  
Bright Gyamfi Adu ◽  
Richard Akromah ◽  
Stephen Amoah ◽  
Daniel Nyadanu ◽  
Alex Yeboah ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Resources ◽  
Manihot Esculenta ◽  
Polymorphic Information Content ◽  
Starch Content ◽  
Plant Genetic Resources ◽  
Snp Markers ◽  
Ex Situ ◽  
Manihot Esculenta Crantz ◽  
Expected Heterozygosity

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower’s genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

scholarly journals Comprehensive genotyping of Brazilian Cassava (Manihot esculenta Crantz) Germplasm Bank: insights into diversification and domestication

2020 ◽  
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Eder Jorge de Oliveira ◽  
Lukas A. Mueller ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

AbstractCassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonas region. In this study, 3,354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 Single Nucleotide Polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1,536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, 1,300 to 4,700 SNP markers were selected for large quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity (Ho), effective population size estimate and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggest earliest population split from Amazonas to Atlantic forest and Caatinga eco-regions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These Findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.Key messageBrazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups, and spatial genetic differentiation.

scholarly journals Is the Genetic Integrity of Wild Coffea Canephora From Ivory Coast Threatened by Hybridization With Introduced Coffee Trees From Central Africa?

2021 ◽  
Author(s):  
GNAPI Diane Estelle ◽  
Desire POKOU ◽  
LEGNATE Hyacinthe ◽  
DAPENG Zhang ◽  
Christophe MONTAGNON ◽  
...  
Keyword(s):  
Gene Pool ◽  
Ex Situ Conservation ◽  
Central Africa ◽  
Genetic Erosion ◽  
Coffea Canephora ◽  
Snp Markers ◽  
Ex Situ ◽  
Genetic Integrity ◽  
Genetic Groups

Abstract Canephora coffee is an important source of income and employment, contributing significantly to the economies of many developing countries. This species is split into two genetic groups: Guinean and Congolese. Côte-d’Ivoire is the primary diversification center of the Guinean pool, which offers great potential for genetic improvement. However, genetic erosion of this group is currently a threat in this country because of the massive introduction of Congolese accessions in the previous decades. In this work, we analyzed the progenies of isolated population of C. canephora composed of a mix of Guinean and Congolese using SNP markers. The analysis is focus on the male parents’ contribution on open pollination progenies. The result shows that the introduction of cultivars from the Congolese gene pool threat the genetic integrity of wild populations of the Guinean gene pool. We recommend that a conservation program be put in place to ensure the entegrity of wild population of C. canephora through in situ or ex situ conservation.

Sign in / Sign up

Export Citation Format

Share Document