Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats
Structural variations (SVs) such as copy number and presence–absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat...
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| Language: | English |
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Frontiers Media S.A.
2020-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00891/full |
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| author | Romain De Oliveira Hélène Rimbert François Balfourier Jonathan Kitt Emeric Dynomant Jan Vrána Jaroslav Doležel Federica Cattonaro Etienne Paux Frédéric Choulet |
| author_facet | Romain De Oliveira Hélène Rimbert François Balfourier Jonathan Kitt Emeric Dynomant Jan Vrána Jaroslav Doležel Federica Cattonaro Etienne Paux Frédéric Choulet |
| author_sort | Romain De Oliveira |
| collection | DOAJ |
| description | Structural variations (SVs) such as copy number and presence–absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species. |
| first_indexed | 2024-12-14T20:00:21Z |
| format | Article |
| id | doaj.art-364cea39f362401c82d9ee8a298a2092 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T20:00:21Z |
| publishDate | 2020-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-364cea39f362401c82d9ee8a298a20922022-12-21T22:49:10ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-08-011110.3389/fgene.2020.00891560998Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in WheatsRomain De Oliveira0Hélène Rimbert1François Balfourier2Jonathan Kitt3Emeric Dynomant4Jan Vrána5Jaroslav Doležel6Federica Cattonaro7Etienne Paux8Frédéric Choulet9Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceUniversité Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceUniversité Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceUniversité Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceUniversité Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceInstitute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CzechiaInstitute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CzechiaIGA, Udine, ItalyUniversité Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceUniversité Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, FranceStructural variations (SVs) such as copy number and presence–absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species.https://www.frontiersin.org/article/10.3389/fgene.2020.00891/fullbread wheatgenome evolutionstructural variationscopy number variationstransposable elementsTriticum |
| spellingShingle | Romain De Oliveira Hélène Rimbert François Balfourier Jonathan Kitt Emeric Dynomant Jan Vrána Jaroslav Doležel Federica Cattonaro Etienne Paux Frédéric Choulet Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats Frontiers in Genetics bread wheat genome evolution structural variations copy number variations transposable elements Triticum |
| title | Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats |
| title_full | Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats |
| title_fullStr | Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats |
| title_full_unstemmed | Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats |
| title_short | Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats |
| title_sort | structural variations affecting genes and transposable elements of chromosome 3b in wheats |
| topic | bread wheat genome evolution structural variations copy number variations transposable elements Triticum |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00891/full |
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