Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement
Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Maize Improvement, DArT-Seq Markers, LAND RACES, GENETIC DIVERSITY, POPULATION STRUCTURE, MAIZE, CROP IMPROVEMENT, GENETIC MARKERS, |
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dig-cimmyt-10883-211742023-01-30T16:39:49Z Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement Nelimor, C. Badu-Apraku, B. Garcia Oliveira, A.L. Tetteh, A.Y. Paterne, A.A. N’guetta, A.S. Gedil, M. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Maize Improvement DArT-Seq Markers LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE MAIZE CROP IMPROVEMENT GENETIC MARKERS Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines. 2021-01-27T01:05:13Z 2021-01-27T01:05:13Z 2020 Article Published Version https://hdl.handle.net/10883/21174 10.3390/genes11091054 English https://www.mdpi.com/2073-4425/11/9/1054#supplementary CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose Open Access Sahel West Africa Basel (Switzerland) MDPI 9 11 2073-4425 Genes 1054 |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Maize Improvement DArT-Seq Markers LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE MAIZE CROP IMPROVEMENT GENETIC MARKERS AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Maize Improvement DArT-Seq Markers LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE MAIZE CROP IMPROVEMENT GENETIC MARKERS |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Maize Improvement DArT-Seq Markers LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE MAIZE CROP IMPROVEMENT GENETIC MARKERS AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Maize Improvement DArT-Seq Markers LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE MAIZE CROP IMPROVEMENT GENETIC MARKERS Nelimor, C. Badu-Apraku, B. Garcia Oliveira, A.L. Tetteh, A.Y. Paterne, A.A. N’guetta, A.S. Gedil, M. Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement |
description |
Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Maize Improvement DArT-Seq Markers LAND RACES GENETIC DIVERSITY POPULATION STRUCTURE MAIZE CROP IMPROVEMENT GENETIC MARKERS |
author |
Nelimor, C. Badu-Apraku, B. Garcia Oliveira, A.L. Tetteh, A.Y. Paterne, A.A. N’guetta, A.S. Gedil, M. |
author_facet |
Nelimor, C. Badu-Apraku, B. Garcia Oliveira, A.L. Tetteh, A.Y. Paterne, A.A. N’guetta, A.S. Gedil, M. |
author_sort |
Nelimor, C. |
title |
Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement |
title_short |
Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement |
title_full |
Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement |
title_fullStr |
Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement |
title_full_unstemmed |
Genomic analysis of selected maize landraces from Sahel and coastal West Africa reveals their variability and potential for genetic enhancement |
title_sort |
genomic analysis of selected maize landraces from sahel and coastal west africa reveals their variability and potential for genetic enhancement |
publisher |
MDPI |
publishDate |
2020 |
url |
https://hdl.handle.net/10883/21174 |
work_keys_str_mv |
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1756515230072963072 |