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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| Veröffentlicht in: | Nature biotechnology 2016-05, Vol.34 (5), p.562-570 |
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| creator | Bredeson, Jessen V Lyons, Jessica B Prochnik, Simon E Wu, G Albert Ha, Cindy M Edsinger-Gonzales, Eric Grimwood, Jane Schmutz, Jeremy Rabbi, Ismail Y Egesi, Chiedozie Nauluvula, Poasa Lebot, Vincent Ndunguru, Joseph Mkamilo, Geoffrey Bart, Rebecca S Setter, Tim L Gleadow, Roslyn M Kulakow, Peter Ferguson, Morag E Rounsley, Steve Rokhsar, Daniel S |
| description | 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. |
| doi_str_mv | 10.1038/nbt.3535 |
| format | Article |
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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.</description><identifier>ISSN: 1087-0156</identifier><identifier>EISSN: 1546-1696</identifier><identifier>DOI: 10.1038/nbt.3535</identifier><identifier>PMID: 27088722</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>45 ; 45/23 ; 631/208/457/649 ; 631/449/2491 ; 631/449/2492 ; 631/449/711 ; Agriculture ; BASIC BIOLOGICAL SCIENCES ; Bioinformatics ; Biological diversity ; Biomedical Engineering/Biotechnology ; Biomedicine ; Biotechnology ; Cassava ; Chromosome Mapping - methods ; Chromosomes ; Comparative studies ; Conserved Sequence - genetics ; Crops ; Cultivation ; DNA sequencing ; DNA, Plant - genetics ; Genetic aspects ; Genetic diversity ; Genetic research ; Genetic Variation ; Genome, Plant - genetics ; Genomics ; Hevea ; Hybridization ; Hybridization, Genetic - genetics ; Life Sciences ; Manihot ; Manihot - classification ; Manihot - genetics ; Manihot esculenta ; Methods ; Nucleotide sequencing ; Nutrition ; Pathogens ; Plant breeding ; Plant Breeding - methods ; Plant genetics ; resource ; Rubber ; Rubber trees ; Sequence Analysis, DNA - methods ; Species Specificity ; Tropical environments</subject><ispartof>Nature biotechnology, 2016-05, Vol.34 (5), p.562-570</ispartof><rights>The Author(s) 2016</rights><rights>COPYRIGHT 2016 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group May 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c611t-bdee0220b03976c918c52260d6202a350649776a6ac32b3440f3449a0d5a1a343</citedby><cites>FETCH-LOGICAL-c611t-bdee0220b03976c918c52260d6202a350649776a6ac32b3440f3449a0d5a1a343</cites><orcidid>0000-0002-3016-6795 ; 0000-0003-4756-0411 ; 0000-0002-3886-2146 ; 0000000238862146 ; 0000000347560411 ; 0000000230166795</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nbt.3535$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nbt.3535$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,777,781,882,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27088722$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/1616047$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Bredeson, Jessen V</creatorcontrib><creatorcontrib>Lyons, Jessica B</creatorcontrib><creatorcontrib>Prochnik, Simon E</creatorcontrib><creatorcontrib>Wu, G Albert</creatorcontrib><creatorcontrib>Ha, Cindy M</creatorcontrib><creatorcontrib>Edsinger-Gonzales, Eric</creatorcontrib><creatorcontrib>Grimwood, Jane</creatorcontrib><creatorcontrib>Schmutz, Jeremy</creatorcontrib><creatorcontrib>Rabbi, Ismail Y</creatorcontrib><creatorcontrib>Egesi, Chiedozie</creatorcontrib><creatorcontrib>Nauluvula, Poasa</creatorcontrib><creatorcontrib>Lebot, Vincent</creatorcontrib><creatorcontrib>Ndunguru, Joseph</creatorcontrib><creatorcontrib>Mkamilo, Geoffrey</creatorcontrib><creatorcontrib>Bart, Rebecca S</creatorcontrib><creatorcontrib>Setter, Tim L</creatorcontrib><creatorcontrib>Gleadow, Roslyn M</creatorcontrib><creatorcontrib>Kulakow, Peter</creatorcontrib><creatorcontrib>Ferguson, Morag E</creatorcontrib><creatorcontrib>Rounsley, Steve</creatorcontrib><creatorcontrib>Rokhsar, Daniel S</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><title>Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity</title><title>Nature biotechnology</title><addtitle>Nat Biotechnol</addtitle><addtitle>Nat Biotechnol</addtitle><description>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.</description><subject>45</subject><subject>45/23</subject><subject>631/208/457/649</subject><subject>631/449/2491</subject><subject>631/449/2492</subject><subject>631/449/711</subject><subject>Agriculture</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Bioinformatics</subject><subject>Biological diversity</subject><subject>Biomedical Engineering/Biotechnology</subject><subject>Biomedicine</subject><subject>Biotechnology</subject><subject>Cassava</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes</subject><subject>Comparative studies</subject><subject>Conserved Sequence - genetics</subject><subject>Crops</subject><subject>Cultivation</subject><subject>DNA sequencing</subject><subject>DNA, Plant - genetics</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic research</subject><subject>Genetic 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S</au><aucorp>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity</atitle><jtitle>Nature biotechnology</jtitle><stitle>Nat Biotechnol</stitle><addtitle>Nat Biotechnol</addtitle><date>2016-05-01</date><risdate>2016</risdate><volume>34</volume><issue>5</issue><spage>562</spage><epage>570</epage><pages>562-570</pages><issn>1087-0156</issn><eissn>1546-1696</eissn><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.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>27088722</pmid><doi>10.1038/nbt.3535</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-3016-6795</orcidid><orcidid>https://orcid.org/0000-0003-4756-0411</orcidid><orcidid>https://orcid.org/0000-0002-3886-2146</orcidid><orcidid>https://orcid.org/0000000238862146</orcidid><orcidid>https://orcid.org/0000000347560411</orcidid><orcidid>https://orcid.org/0000000230166795</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1087-0156 |
| ispartof | Nature biotechnology, 2016-05, Vol.34 (5), p.562-570 |
| issn | 1087-0156 1546-1696 |
| language | eng |
| recordid | cdi_osti_scitechconnect_1616047 |
| source | MEDLINE; SpringerLink Journals; Nature Journals Online |
| subjects | 45 45/23 631/208/457/649 631/449/2491 631/449/2492 631/449/711 Agriculture BASIC BIOLOGICAL SCIENCES Bioinformatics Biological diversity Biomedical Engineering/Biotechnology Biomedicine Biotechnology Cassava Chromosome Mapping - methods Chromosomes Comparative studies Conserved Sequence - genetics Crops Cultivation DNA sequencing DNA, Plant - genetics Genetic aspects Genetic diversity Genetic research Genetic Variation Genome, Plant - genetics Genomics Hevea Hybridization Hybridization, Genetic - genetics Life Sciences Manihot Manihot - classification Manihot - genetics Manihot esculenta Methods Nucleotide sequencing Nutrition Pathogens Plant breeding Plant Breeding - methods Plant genetics resource Rubber Rubber trees Sequence Analysis, DNA - methods Species Specificity Tropical environments |
| title | Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-19T10%3A08%3A58IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_osti_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Sequencing%20wild%20and%20cultivated%20cassava%20and%20related%20species%20reveals%20extensive%20interspecific%20hybridization%20and%20genetic%20diversity&rft.jtitle=Nature%20biotechnology&rft.au=Bredeson,%20Jessen%20V&rft.aucorp=Lawrence%20Berkeley%20National%20Laboratory%20(LBNL),%20Berkeley,%20CA%20(United%20States)&rft.date=2016-05-01&rft.volume=34&rft.issue=5&rft.spage=562&rft.epage=570&rft.pages=562-570&rft.issn=1087-0156&rft.eissn=1546-1696&rft_id=info:doi/10.1038/nbt.3535&rft_dat=%3Cgale_osti_%3EA454619627%3C/gale_osti_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1787267787&rft_id=info:pmid/27088722&rft_galeid=A454619627&rfr_iscdi=true |