Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping

Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping

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Main Authors: Bhattacharjee, R., Luseni, M.M., Ametefe, K., Agre, P.A., Kumar, P.L., Grenville-Briggs, L.J.
Format: Journal Article biblioteca
Language:English
Published: 2023
Subjects:theobroma cacao, genetic diversity, population structure, single nucleotide polymorphism, germplasm, genotypes, west africa,
Online Access:https://hdl.handle.net/10568/132760
https://doi.org/10.21203/rs.3.rs-3345739/v1
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spelling dig-cgspace-10568-1327602023-12-23T10:39:21Z Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping Bhattacharjee, R. Luseni, M.M. Ametefe, K. Agre, P.A. Kumar, P.L. Grenville-Briggs, L.J. theobroma cacao genetic diversity population structure single nucleotide polymorphism germplasm genotypes west africa Open Access Journal Background Cacao (Theobroma cacao L.) is a tropical tree species belonging to Malvaceae family and originated in the lowland rainforests of the Amazon. It is one of the major agricultural commodities contributing towards the GDP (gross domestic product) of West African countries contributing about 70% of world’s production. Methodology A sample of 376 cacao (Theobroma cacao L.) germplasm accessions (235 from Sierra Leone and 141 from Togo) collected from different seed gardens and farmers’ fields across the cacao producing states/regions of these countries were assembled for genetic diversity and population structure studies using single nucleotide polymorphism (SNP) markers. The 376 cacao accessions were genotyped using 20 highly informative and reproducible KASP-SNPs markers. The genetic diversity among different accessions was assessed using three complementary clustering methods including the model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. A network analysis was further carried out to understand the genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) was carried out to estimate the genetic differentiation among and within groups. Results The STRUCTURE and DAPC exhibited some consistency in the allocation of accessions in subpopulations or groups, although some discrepancy was identified in the grouping based on these two methods. Hierarchical clustering analysis grouped all the individuals into two major groups and represented several sub-clusters. AMOVA revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. Conclusion This study demonstrates the use of KASP-SNPs for fingerprinting that can help identify mislabeled accessions and provide strong evidence for improving the accuracy and efficiency in cacao germplasm management as well as distribution of correct materials to farmers. 2023 2023-11-06T12:08:42Z 2023-11-06T12:08:42Z Journal Article Bhattacharjee, R., Luseni, M.M., Ametefe, K., Agre, P.A., Kumar, P.L. & Grenville-Briggs, L.J. (2023). Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP-SNP genotyping. BMC Plant Biology, 1-21. 1471-2229 https://hdl.handle.net/10568/132760 https://doi.org/10.21203/rs.3.rs-3345739/v1 BIOTECH & PLANT BREEDING PLANT PRODUCTION & HEALTH en CC-BY-4.0 Open Access 1-21 application/pdf BMC Plant Biology
institution CGIAR
collection DSpace
country Francia
countrycode FR
component Bibliográfico
access En linea
databasecode dig-cgspace
tag biblioteca
region Europa del Oeste
libraryname Biblioteca del CGIAR
language English
topic theobroma cacao
genetic diversity
population structure
single nucleotide polymorphism
germplasm
genotypes
west africa
theobroma cacao
genetic diversity
population structure
single nucleotide polymorphism
germplasm
genotypes
west africa
spellingShingle theobroma cacao
genetic diversity
population structure
single nucleotide polymorphism
germplasm
genotypes
west africa
theobroma cacao
genetic diversity
population structure
single nucleotide polymorphism
germplasm
genotypes
west africa
Bhattacharjee, R.
Luseni, M.M.
Ametefe, K.
Agre, P.A.
Kumar, P.L.
Grenville-Briggs, L.J.
Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping
description Open Access Journal
format Journal Article
topic_facet theobroma cacao
genetic diversity
population structure
single nucleotide polymorphism
germplasm
genotypes
west africa
author Bhattacharjee, R.
Luseni, M.M.
Ametefe, K.
Agre, P.A.
Kumar, P.L.
Grenville-Briggs, L.J.
author_facet Bhattacharjee, R.
Luseni, M.M.
Ametefe, K.
Agre, P.A.
Kumar, P.L.
Grenville-Briggs, L.J.
author_sort Bhattacharjee, R.
title Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping
title_short Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping
title_full Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping
title_fullStr Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping
title_full_unstemmed Genetic diversity and population structure of cacao (Theobroma cacao L.) germplasm from Sierra Leone and Togo based on KASP- SNP genotyping
title_sort genetic diversity and population structure of cacao (theobroma cacao l.) germplasm from sierra leone and togo based on kasp- snp genotyping
publishDate 2023
url https://hdl.handle.net/10568/132760
https://doi.org/10.21203/rs.3.rs-3345739/v1
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