Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication
Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava ( Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian...
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| Veröffentlicht in: | Theoretical and applied genetics 2021-05, Vol.134 (5), p.1343-1362 |
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| creator | Ogbonna, Alex C. Braatz de Andrade, Luciano Rogerio Mueller, Lukas A. de Oliveira, Eder Jorge Bauchet, Guillaume J. |
| description | Key message
Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.
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
)
, effective population size estimate
(
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. |
| doi_str_mv | 10.1007/s00122-021-03775-5 |
| format | Article |
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Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.
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
)
, effective population size estimate
(
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.</description><identifier>ISSN: 0040-5752</identifier><identifier>ISSN: 1432-2242</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-021-03775-5</identifier><identifier>PMID: 33575821</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agriculture ; Banks (Finance) ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Breeding ; Cassava ; Chromosome Mapping - methods ; Chromosomes, Plant - genetics ; Domestication ; Ethylenediaminetetraacetic acid ; Gene frequency ; Gene mapping ; Genetic aspects ; Genetic resources ; Genetics, Population ; Genome, Plant ; Genotyping ; Germplasm ; Heterozygosity ; Life Sciences ; Linkage Disequilibrium ; Manihot - genetics ; Manihot - growth & development ; Manihot - metabolism ; Manihot esculenta ; Original ; Original Article ; Plant Biochemistry ; Plant Breeding ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Polymorphism, Single Nucleotide ; Population genetics ; Population structure ; Quantitative genetics ; Quantitative Trait Loci ; Seed Bank - statistics & numerical data ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism</subject><ispartof>Theoretical and applied genetics, 2021-05, Vol.134 (5), p.1343-1362</ispartof><rights>The Author(s) 2021</rights><rights>COPYRIGHT 2021 Springer</rights><rights>The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c541t-572a1b175984972fc3f50ce70640453cc2be53ca70b86e7a3a76be12630f700e3</citedby><cites>FETCH-LOGICAL-c541t-572a1b175984972fc3f50ce70640453cc2be53ca70b86e7a3a76be12630f700e3</cites><orcidid>0000-0003-3311-7726</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-021-03775-5$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-021-03775-5$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,27922,27923,41486,42555,51317</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33575821$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ogbonna, Alex C.</creatorcontrib><creatorcontrib>Braatz de Andrade, Luciano Rogerio</creatorcontrib><creatorcontrib>Mueller, Lukas A.</creatorcontrib><creatorcontrib>de Oliveira, Eder Jorge</creatorcontrib><creatorcontrib>Bauchet, Guillaume J.</creatorcontrib><title>Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>Key message
Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.
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
)
, effective population size estimate
(
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.</description><subject>Agriculture</subject><subject>Banks (Finance)</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Breeding</subject><subject>Cassava</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes, Plant - genetics</subject><subject>Domestication</subject><subject>Ethylenediaminetetraacetic acid</subject><subject>Gene frequency</subject><subject>Gene mapping</subject><subject>Genetic aspects</subject><subject>Genetic resources</subject><subject>Genetics, Population</subject><subject>Genome, Plant</subject><subject>Genotyping</subject><subject>Germplasm</subject><subject>Heterozygosity</subject><subject>Life Sciences</subject><subject>Linkage Disequilibrium</subject><subject>Manihot - genetics</subject><subject>Manihot - growth & development</subject><subject>Manihot - metabolism</subject><subject>Manihot esculenta</subject><subject>Original</subject><subject>Original Article</subject><subject>Plant Biochemistry</subject><subject>Plant Breeding</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Quantitative genetics</subject><subject>Quantitative Trait Loci</subject><subject>Seed Bank - statistics & numerical data</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><issn>0040-5752</issn><issn>1432-2242</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9Uk2P0zAQjRCILYU_wAFZ4rIcsow_EqcckJaKL2kRFzhbE8dpvSR2sdNKuz-BX82Ull0WIeTDWDPvPeuNX1E85XDGAfTLDMCFKEHwEqTWVVndK2ZcSVEKocT9YgagoKx0JU6KRzlfAoCoQD4sTqSkbiP4rPixjOMmubUL2e8cW7kQp6uNDysWe4bsTcJrP3gMzGLOuEN2-gmDX8eJuWy3gwsTsmXCMF2_IHIaNwPmkbUYvr1injRX6ynTZYqsI_2Ufe8tTj4GhqFjXRxdno6dx8WDHofsnhzrvPj67u2X5Yfy4vP7j8vzi9JWik_kRyBvua4WjVpo0VvZV2CdhlqBqqS1onVUUEPb1E6jRF23jotaQq8BnJwXrw-6m207us6Sh4SD2SQ_YroyEb25OyG_ZhV3poGG140mgdOjQIrft2TAjD5bNwwYXNxmI1SzEJVStOt58fwv6GXcpkD2jKj4gitF4FvUCgdnfOgjvWv3oua8rgEaSXYJdfYPFJ3Ojd7G4HpP_TsEcSDYFHNOrr_xyMHsE2QOCTKUIPMrQWZPevbndm4ovyNDAHkAZBoF-vNbS_-R_Qm2OdJJ</recordid><startdate>20210501</startdate><enddate>20210501</enddate><creator>Ogbonna, Alex C.</creator><creator>Braatz de Andrade, Luciano Rogerio</creator><creator>Mueller, Lukas A.</creator><creator>de Oliveira, Eder Jorge</creator><creator>Bauchet, Guillaume J.</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-3311-7726</orcidid></search><sort><creationdate>20210501</creationdate><title>Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication</title><author>Ogbonna, Alex C. ; Braatz de Andrade, Luciano Rogerio ; Mueller, Lukas A. ; de Oliveira, Eder Jorge ; Bauchet, Guillaume J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c541t-572a1b175984972fc3f50ce70640453cc2be53ca70b86e7a3a76be12630f700e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Agriculture</topic><topic>Banks (Finance)</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Breeding</topic><topic>Cassava</topic><topic>Chromosome Mapping - methods</topic><topic>Chromosomes, Plant - genetics</topic><topic>Domestication</topic><topic>Ethylenediaminetetraacetic acid</topic><topic>Gene frequency</topic><topic>Gene mapping</topic><topic>Genetic aspects</topic><topic>Genetic resources</topic><topic>Genetics, Population</topic><topic>Genome, Plant</topic><topic>Genotyping</topic><topic>Germplasm</topic><topic>Heterozygosity</topic><topic>Life Sciences</topic><topic>Linkage Disequilibrium</topic><topic>Manihot - genetics</topic><topic>Manihot - growth & development</topic><topic>Manihot - metabolism</topic><topic>Manihot esculenta</topic><topic>Original</topic><topic>Original Article</topic><topic>Plant Biochemistry</topic><topic>Plant Breeding</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Genetics and Genomics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population genetics</topic><topic>Population structure</topic><topic>Quantitative genetics</topic><topic>Quantitative Trait Loci</topic><topic>Seed Bank - statistics & numerical data</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ogbonna, Alex C.</creatorcontrib><creatorcontrib>Braatz de Andrade, Luciano Rogerio</creatorcontrib><creatorcontrib>Mueller, Lukas A.</creatorcontrib><creatorcontrib>de Oliveira, Eder Jorge</creatorcontrib><creatorcontrib>Bauchet, Guillaume J.</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ogbonna, Alex C.</au><au>Braatz de Andrade, Luciano Rogerio</au><au>Mueller, Lukas A.</au><au>de Oliveira, Eder Jorge</au><au>Bauchet, Guillaume J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2021-05-01</date><risdate>2021</risdate><volume>134</volume><issue>5</issue><spage>1343</spage><epage>1362</epage><pages>1343-1362</pages><issn>0040-5752</issn><issn>1432-2242</issn><eissn>1432-2242</eissn><abstract>Key message
Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation.
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
)
, effective population size estimate
(
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.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>33575821</pmid><doi>10.1007/s00122-021-03775-5</doi><tpages>20</tpages><orcidid>https://orcid.org/0000-0003-3311-7726</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Theoretical and applied genetics, 2021-05, Vol.134 (5), p.1343-1362 |
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| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8081687 |
| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Agriculture Banks (Finance) Biochemistry Biomedical and Life Sciences Biotechnology Breeding Cassava Chromosome Mapping - methods Chromosomes, Plant - genetics Domestication Ethylenediaminetetraacetic acid Gene frequency Gene mapping Genetic aspects Genetic resources Genetics, Population Genome, Plant Genotyping Germplasm Heterozygosity Life Sciences Linkage Disequilibrium Manihot - genetics Manihot - growth & development Manihot - metabolism Manihot esculenta Original Original Article Plant Biochemistry Plant Breeding Plant Breeding/Biotechnology Plant Genetics and Genomics Polymorphism, Single Nucleotide Population genetics Population structure Quantitative genetics Quantitative Trait Loci Seed Bank - statistics & numerical data Single nucleotide polymorphisms Single-nucleotide polymorphism |
| title | Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication |
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