Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity
The global genetic diversity of cassava and related Manihot species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268 African cassavas, providing a vital resource for breeding. Cassava ( Manihot esculenta ) provides calories and nutrition for more than half a billi...
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| Published in | Nature Biotechnology Vol. 34; no. 5; pp. 562 - 570 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Springer Science and Business Media LLC
01.05.2016
Nature Publishing Group US Nature Publishing Group Springer Nature |
| Subjects | |
| Online Access | Get full text |
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| Abstract | The global genetic diversity of cassava and related
Manihot
species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268 African cassavas, providing a vital resource for breeding.
Cassava (
Manihot esculenta
) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor
M. esculenta
ssp.
flabellifolia
and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree
Hevea
, providing a resource for comparative studies. We also sequence a global collection of 58
Manihot
accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (
M. glaziovii
), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. |
|---|---|
| AbstractList | Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceara or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Cear or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. The global genetic diversity of cassava and related Manihot species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268 African cassavas, providing a vital resource for breeding. Cassava ( Manihot esculenta ) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea , providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber ( M. glaziovii ), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop. |
| Audience | Academic |
| Author | Cindy M. Ha G Albert Wu Vincent Lebot Jeremy Schmutz Tim L. Setter Geoffrey Mkamilo Morag Ferguson Chiedozie Egesi Roslyn M. Gleadow Jessica B. Lyons Rebecca Bart Jessen V. Bredeson Poasa Nauluvula Jane Grimwood Eric Edsinger-Gonzales Ismail Y. Rabbi Daniel S. Rokhsar Joseph Ndunguru Peter Kulakow Simon E. Prochnik Steve Rounsley |
| Author_xml | – sequence: 1 givenname: Jessen V surname: Bredeson fullname: Bredeson, Jessen V email: jessenbredeson@berkeley.edu organization: Department of Molecular and Cell Biology, University of California – sequence: 2 givenname: Jessica B orcidid: 0000-0002-3886-2146 surname: Lyons fullname: Lyons, Jessica B organization: Department of Molecular and Cell Biology, University of California – sequence: 3 givenname: Simon E surname: Prochnik fullname: Prochnik, Simon E organization: United States Department of Energy Joint Genome Institute (DOE JGI) – sequence: 4 givenname: G Albert surname: Wu fullname: Wu, G Albert organization: United States Department of Energy Joint Genome Institute (DOE JGI) – sequence: 5 givenname: Cindy M surname: Ha fullname: Ha, Cindy M organization: Department of Molecular and Cell Biology, University of California, Present addresses: Anschutz Medical Campus, University of Colorado, Denver, Colorado, USA (C.M.H.); Marine Biological Laboratory, Woods Hole, Massachusetts, USA (E.E.-G.); South Pacific Community, Kolonia, Federated States of Micronesia (P.N.) – sequence: 6 givenname: Eric surname: Edsinger-Gonzales fullname: Edsinger-Gonzales, Eric organization: Department of Molecular and Cell Biology, University of California, Present addresses: Anschutz Medical Campus, University of Colorado, Denver, Colorado, USA (C.M.H.); Marine Biological Laboratory, Woods Hole, Massachusetts, USA (E.E.-G.); South Pacific Community, Kolonia, Federated States of Micronesia (P.N.) – sequence: 7 givenname: Jane surname: Grimwood fullname: Grimwood, Jane organization: United States Department of Energy Joint Genome Institute (DOE JGI), HudsonAlpha Institute for Biotechnology – sequence: 8 givenname: Jeremy surname: Schmutz fullname: Schmutz, Jeremy organization: United States Department of Energy Joint Genome Institute (DOE JGI), HudsonAlpha Institute for Biotechnology – sequence: 9 givenname: Ismail Y surname: Rabbi fullname: Rabbi, Ismail Y organization: International Institute of Tropical Agriculture (IITA) – sequence: 10 givenname: Chiedozie surname: Egesi fullname: Egesi, Chiedozie organization: National Root Crops Research Institute (NRCRI) – sequence: 11 givenname: Poasa surname: Nauluvula fullname: Nauluvula, Poasa organization: Department of Agriculture, Ministry of Primary Industries, Koronivia Research Station, Present addresses: Anschutz Medical Campus, University of Colorado, Denver, Colorado, USA (C.M.H.); Marine Biological Laboratory, Woods Hole, Massachusetts, USA (E.E.-G.); South Pacific Community, Kolonia, Federated States of Micronesia (P.N.) – sequence: 12 givenname: Vincent surname: Lebot fullname: Lebot, Vincent organization: Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) – sequence: 13 givenname: Joseph surname: Ndunguru fullname: Ndunguru, Joseph organization: Mikocheni Agricultural Research Institute (MARI) – sequence: 14 givenname: Geoffrey surname: Mkamilo fullname: Mkamilo, Geoffrey organization: Naliendele Agricultural Research Institute (NARI) – sequence: 15 givenname: Rebecca S surname: Bart fullname: Bart, Rebecca S organization: Donald Danforth Plant Science Center – sequence: 16 givenname: Tim L surname: Setter fullname: Setter, Tim L organization: Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University – sequence: 17 givenname: Roslyn M orcidid: 0000-0003-4756-0411 surname: Gleadow fullname: Gleadow, Roslyn M organization: School of Biological Sciences, Monash University – sequence: 18 givenname: Peter surname: Kulakow fullname: Kulakow, Peter organization: International Institute of Tropical Agriculture (IITA) – sequence: 19 givenname: Morag E surname: Ferguson fullname: Ferguson, Morag E organization: International Institute of Tropical Agriculture (IITA) – sequence: 20 givenname: Steve orcidid: 0000-0002-3016-6795 surname: Rounsley fullname: Rounsley, Steve organization: Dow AgroSciences – sequence: 21 givenname: Daniel S surname: Rokhsar fullname: Rokhsar, Daniel S email: dsrokhsar@gmail.com organization: Department of Molecular and Cell Biology, University of California, United States Department of Energy Joint Genome Institute (DOE JGI), Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University |
| BackLink | https://cir.nii.ac.jp/crid/1871991017737828736$$DView record in CiNii https://www.ncbi.nlm.nih.gov/pubmed/27088722$$D View this record in MEDLINE/PubMed https://www.osti.gov/servlets/purl/1616047$$D View this record in Osti.gov |
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| Snippet | The global genetic diversity of cassava and related
Manihot
species is revealed by sequencing of 53 cultivated and wild accessions and genotyping of 268... Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through... |
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| SubjectTerms | 45 45/23 631/208/457/649 631/449/2491 631/449/2492 631/449/711 Agriculture amélioration des plantes BASIC BIOLOGICAL SCIENCES Bioinformatics Biological diversity Biological Sciences Biomedical Engineering/Biotechnology Biomedicine Biotechnology Cassava Chromosome Mapping Chromosome Mapping - methods Chromosomes Comparative studies Conserved Sequence Conserved Sequence - genetics Crops Cultivation DNA DNA sequencing DNA, Plant DNA, Plant - genetics Ecology F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie Genetic Genetic aspects Genetic diversity Genetic research Genetic Variation Genetics Genome Genome, Plant Genome, Plant - genetics Genomics génome Hevea http://aims.fao.org/aos/agrovoc/c_1070 http://aims.fao.org/aos/agrovoc/c_1556 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1767 http://aims.fao.org/aos/agrovoc/c_1972 http://aims.fao.org/aos/agrovoc/c_24126 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_27812 http://aims.fao.org/aos/agrovoc/c_2895 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_32886 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_4579 http://aims.fao.org/aos/agrovoc/c_4580 http://aims.fao.org/aos/agrovoc/c_5159 http://aims.fao.org/aos/agrovoc/c_5182 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_714 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_7690 http://aims.fao.org/aos/agrovoc/c_7701 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_8355 Human Genome hybridation interspécifique Hybridization Hybridization, Genetic Hybridization, Genetic - genetics Life Sciences Manihot Manihot - classification Manihot - genetics Manihot esculenta Manihot glaziovii Methods Nucleotide sequencing Nutrition Pathogens Plant Plant breeding Plant Breeding - methods plant domestication Plant genetics plante de culture plante sauvage resource Rubber Rubber trees Sequence Analysis Sequence Analysis, DNA Sequence Analysis, DNA - methods Species Specificity séquence d'adn Tropical environments tétraploïdie variation génétique variété variété indigène |
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| Title | Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity |
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