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 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 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.

Ex-situ conservation of medicinal plant genetic resources managed by national agrobiodiversity center of Korea

Planta Medica ◽  
2012 ◽  
Vol 78 (11) ◽  
Author(s):  
JS Sung ◽  
CW Jeong ◽  
YY Lee ◽  
HS Lee ◽  
YA Jeon ◽  
...  
Keyword(s):  
Medicinal Plant ◽  
Genetic Resources ◽  
Ex Situ Conservation ◽  
Plant Genetic Resources ◽  
Ex Situ

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

scholarly journals UJI DAYA HASIL UBIKAYU (Manihot esculenta Crantz) VARIETAS UJ5 PADA BERBAGAI UMUR PANEN

2016 ◽  
Vol 10 (1) ◽  
pp. 63-70
Author(s):  
Palupi Puspitorini ◽  
Dyah Pitaloka ◽  
Tri Kurniastuti
Keyword(s):  
Manihot Esculenta ◽  
Starch Content ◽  
Block Design ◽  
Research Direction ◽  
Index Number ◽  
Fresh Weight ◽  
Manihot Esculenta Crantz ◽  
Randomized Block Design ◽  
Tuber Crop ◽  
Cassava Varieties

This study aims to find out the results of cassava tuber crop UJ5 variety at different harvest ages. Research direction is that cassava varieties have been planted throughout Indonesia as the best producer of cassava varieties. High levels of starch and high HCN content makes this variety was selected by the factory - tapioca factory in Indonesia. Research design used randomized block design with 7 treatments of harvesting (UP) were repeated 3 times. UP6 (harvesting 6 MAP), UP7 (harvesting 7 MAP), UP8 (harvesting 8 MAP), UP9 (harvesting 9 MAP), UP10 (harvesting 10 MAP), UP11 (harvesting 11 MAP), UP12 ( harvesting 12 MAP). The research variables are the fresh weight of tuber, tuber starch content (%), the weight of biomass, harvest index, number of tubers per plant. The results showed that the best harvesting time is UP9 the results did not differ with UP10, UP11 and UP12

scholarly journals THE PORTUGUESE NATIONAL INVENTORY ON PLANT GENETIC RESOURCES 2018 - DEVELOPMENT AND STATUS

2018 ◽  
Vol 6 (11) ◽  
pp. 109-120
Author(s):  
Filomena Rocha
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
National Level ◽  
Fruit Trees ◽  
Grain Legumes ◽  
Ex Situ ◽  
Seed Collection ◽  
National Inventory ◽  
Cultivated Species ◽  
Global Platform

Since the 1970s, Portugal has been endeavouring systematic and coordinated efforts for ex situ conservation of plant genetic resources. Portugal maintains in ex situ a large seed collection of cultivated species (cereals, fibres, grain legumes, vegetables), wild species (forages, MAP species), also national clone collections of olive, fruit trees and grapes. In 2011 the Portuguese National Genebank (BPGV) and ISOPLEXIS implemented the GRIN-Global platform, as provides the opportunity to increase data quality, to have long term sustainability for data curation, integrates all collections in one management system optimizing the costs and staff resources. Now, the main objective in Portugal is to implement the Grin Global Platform at the national level to consolidate its National Programme of Plant Genetic Resources (NPPGR) with all national partners directly involved in the conservation of PGR. The main objectives of this communication are: to demonstrate the valuable contribution of the Grin-Global platform to the NPPGR; discuss the development and status of the Portugal’s National Inventory 2018 in EURISCO, analyse the evolution of the amount of passport information in EURISCO from 2015 to 2018; to address the steps that are being taken in Portugal for the Implementation of the Grin-Global Platform at the national level.

scholarly journals Starch and flour extraction and nutrient composition of tuber in seven cassava accessions

2013 ◽  
Vol 10 (2) ◽  
pp. 217-222 ◽  
Author(s):  
MSA Fakir ◽  
M Jannat ◽  
MG Mostafa ◽  
H Seal
Keyword(s):  
Hydrogen Cyanide ◽  
Manihot Esculenta ◽  
Crude Protein ◽  
Dry Matter ◽  
Raw Materials ◽  
Starch Content ◽  
Staple Food ◽  
Manihot Esculenta Crantz ◽  
Crude Fiber Content ◽  
Cassava Plant

Cassava (Manihot esculenta Crantz) roots (tubers) are used as staple food. Starch extracted from tubers is widely utilized as raw materials in industries. Dry matter (DM) content, starch and flour extraction and proximate composition were investigated in seven cassava accessions (Coc-A1, Kh-A2, Cow-A3, Sa-A4, Me-A5, Va-A6 and Sy-A8.) in 2010- 2011. Leaf DM varied from 20.51% in Me-A5 to 29.01% in Sy-A8; that of stem from 27.24% in Va-A6 to 32.10% (average of Sy-A8, Me-A5 and Sa-A4); and that of tuber from 37.30% in Kh-A2 to 45.26% in Sy-A8. Starch was extracted by blending chopped tuber followed by decantation. Tubers were sliced, sun dried and milled into flour. Tuber starch content (fresh wt. basis) varied between 15.04% in Sy-A8 and 24.97% (average of Coc-A1 and Me-A5); that of peel from 4.54% in Va-A6 to 5.85% in Coc-A1. Crude protein varied from 1.80% (average of Kh-A2, Cow-A3 and Sy-A8) to 4.53% in Va-A6. Crude fiber content varied from 1.95% (average of Sa-A4 and Coc-A1) to 4.27% in Cow-A3. Cyanogens present in cassava plant escape as hydrogen cyanide (HCN) during harvesting and processing. Variation for HCN existed and it was 140.95 mg/kg fresh tuber (average of Sy-A8 and Coc-A1) to 546.0 mg/kg fresh tuber in Va-A6. There was no detectable HCN in the extracted flour and starch. It may be concluded that genetic variation for DM, starch, protein and HCN existed in seven cassava accessions, and Coc-A1 may be a better one due to its lower HCN, higher DM and starch content. DOI: http://dx.doi.org/10.3329/jbau.v10i2.14698 J. Bangladesh Agril. Univ. 10(2): 217-222, 2012

Key issues facing genebanks in preserving crop genetic diversity ex situ: overview of the range of challenges

2021 ◽  
pp. 139-154
Author(s):  
Paula Bramel ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Cost Effective ◽  
Ex Situ ◽  
Crop Genetic Diversity ◽  
Ex Situ Collections ◽  
Key Issues ◽  
Market Preference ◽  
The Impact

This chapter reviews the key issues and challenges facing genebanks in preserving crop genetic diversity ex situ. Local crop genetic diversity is challenged with changes in land use, urbanization, land degradation, changes in agricultural practises, availability of improved varieties, changes in market preference, and the impact of climate change. Efforts have been made to secure plant genetic resources ex situ for future use but there are significant issues related to cost effective, efficient, secure, rational, and sustainable long-term ex situ conservation. It begins by addressing issues for the composition of ex situ collections and moves on to discuss issues for routine operations for conservation. The chapter also highlights issues for the use of conserved genetic resources, before concluding with a summary of why the development of sustainable genebank systems is so important.

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