Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding

Autores
Federico, María Laura; Diniz, Augusto L.; Souza, Glaucia M.; Snowdon, Rod; Erazzu, Luis Ernesto
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Large-scale evaluation of genetic diversity in crops with large and complex genomes benefits from the selective enrichment of relevant genomic regions prior to sequencing. Given the complexity of the sugarcane (Saccharum spp.) genome and the limited exploration of quantitative trait loci (QTL) for important energy traits, we used comparative genomics with the related diploid crop sorghum (Sorghum bicolor) to mine for regions associated with bioenergy production. Twenty-one meta-QTL (mQTL) were identified after surveying 286 QTL from 24 different studies using the Sorghum QTL Atlas. Comparative genomics revealed that at least 35% of genes located within QTL can be found in highly conserved sorghum/sugarcane collinear chromosome blocks. Additionally, a targeted candidate search identified 200 genes known for their involvement in sugar and cell wall metabolism. For a subset of these sorghum genes, we evaluated sugarcane gene copy number, sequence identity, and homoeolog expression in target tissues. This work is an initial step towards targeting and resequencing sugarcane orthologous genomic regions to discover single nucleotide polymorphisms (SNPs) as a resource for genomics-assisted breeding.
EEA Famaillá
Fil: Federico, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Federico, María Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.
Fil: Federico, María Laura. Universidad de San Pablo-Tucumán. IDITEC; Argentina
Fil: Diniz, Augusto L. Universidade de São Paulo. Departamento de Bioquímica. Instituto de Química; Brasil
Fil: Souza, Glaucia M. Universidade de São Paulo. Departamento de Bioquímica. Instituto de Química; Brasil
Fil: Snowdon, Rod. Justus Liebig University. Department of Plant Breeding; Alemania
Fil: Erazzú, Luis E. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.
Fuente
Plant Breeding (First published: 01 April 2022)
Materia
Sorghum bicolor
Sorgos
Caña de Azúcar
Genética
Bioenergía
Genómica
Saccharum
Sorghum Grain
Sugar Cane
Genetics
Bioenergy
Genomics
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/11570
Acceder
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oai_identifier_str oai:localhost:20.500.12123/11570
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network_name_str INTA Digital (INTA)
spelling Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breedingFederico, María LauraDiniz, Augusto L.Souza, Glaucia M.Snowdon, RodErazzu, Luis ErnestoSorghum bicolorSorgosCaña de AzúcarGenéticaBioenergíaGenómicaSaccharumSorghum GrainSugar CaneGeneticsBioenergyGenomicsLarge-scale evaluation of genetic diversity in crops with large and complex genomes benefits from the selective enrichment of relevant genomic regions prior to sequencing. Given the complexity of the sugarcane (Saccharum spp.) genome and the limited exploration of quantitative trait loci (QTL) for important energy traits, we used comparative genomics with the related diploid crop sorghum (Sorghum bicolor) to mine for regions associated with bioenergy production. Twenty-one meta-QTL (mQTL) were identified after surveying 286 QTL from 24 different studies using the Sorghum QTL Atlas. Comparative genomics revealed that at least 35% of genes located within QTL can be found in highly conserved sorghum/sugarcane collinear chromosome blocks. Additionally, a targeted candidate search identified 200 genes known for their involvement in sugar and cell wall metabolism. For a subset of these sorghum genes, we evaluated sugarcane gene copy number, sequence identity, and homoeolog expression in target tissues. This work is an initial step towards targeting and resequencing sugarcane orthologous genomic regions to discover single nucleotide polymorphisms (SNPs) as a resource for genomics-assisted breeding.EEA FamailláFil: Federico, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Federico, María Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.Fil: Federico, María Laura. Universidad de San Pablo-Tucumán. IDITEC; ArgentinaFil: Diniz, Augusto L. Universidade de São Paulo. Departamento de Bioquímica. Instituto de Química; BrasilFil: Souza, Glaucia M. Universidade de São Paulo. Departamento de Bioquímica. Instituto de Química; BrasilFil: Snowdon, Rod. Justus Liebig University. Department of Plant Breeding; AlemaniaFil: Erazzú, Luis E. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.Wiley2022-04-06T12:41:59Z2022-04-06T12:41:59Z2022-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/11570https://onlinelibrary.wiley.com/doi/abs/10.1111/pbr.130130179-95411439-0523https://doi.org/10.1111/pbr.13013Plant Breeding (First published: 01 April 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-04T09:49:19Zoai:localhost:20.500.12123/11570instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:49:19.514INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
title Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
spellingShingle Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
Federico, María Laura
Sorghum bicolor
Sorgos
Caña de Azúcar
Genética
Bioenergía
Genómica
Saccharum
Sorghum Grain
Sugar Cane
Genetics
Bioenergy
Genomics
title_short Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
title_full Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
title_fullStr Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
title_full_unstemmed Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
title_sort Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding
dc.creator.none.fl_str_mv Federico, María Laura
Diniz, Augusto L.
Souza, Glaucia M.
Snowdon, Rod
Erazzu, Luis Ernesto
author Federico, María Laura
author_facet Federico, María Laura
Diniz, Augusto L.
Souza, Glaucia M.
Snowdon, Rod
Erazzu, Luis Ernesto
author_role author
author2 Diniz, Augusto L.
Souza, Glaucia M.
Snowdon, Rod
Erazzu, Luis Ernesto
author2_role author
author
author
author
dc.subject.none.fl_str_mv Sorghum bicolor
Sorgos
Caña de Azúcar
Genética
Bioenergía
Genómica
Saccharum
Sorghum Grain
Sugar Cane
Genetics
Bioenergy
Genomics
topic Sorghum bicolor
Sorgos
Caña de Azúcar
Genética
Bioenergía
Genómica
Saccharum
Sorghum Grain
Sugar Cane
Genetics
Bioenergy
Genomics
dc.description.none.fl_txt_mv Large-scale evaluation of genetic diversity in crops with large and complex genomes benefits from the selective enrichment of relevant genomic regions prior to sequencing. Given the complexity of the sugarcane (Saccharum spp.) genome and the limited exploration of quantitative trait loci (QTL) for important energy traits, we used comparative genomics with the related diploid crop sorghum (Sorghum bicolor) to mine for regions associated with bioenergy production. Twenty-one meta-QTL (mQTL) were identified after surveying 286 QTL from 24 different studies using the Sorghum QTL Atlas. Comparative genomics revealed that at least 35% of genes located within QTL can be found in highly conserved sorghum/sugarcane collinear chromosome blocks. Additionally, a targeted candidate search identified 200 genes known for their involvement in sugar and cell wall metabolism. For a subset of these sorghum genes, we evaluated sugarcane gene copy number, sequence identity, and homoeolog expression in target tissues. This work is an initial step towards targeting and resequencing sugarcane orthologous genomic regions to discover single nucleotide polymorphisms (SNPs) as a resource for genomics-assisted breeding.
EEA Famaillá
Fil: Federico, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Federico, María Laura. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.
Fil: Federico, María Laura. Universidad de San Pablo-Tucumán. IDITEC; Argentina
Fil: Diniz, Augusto L. Universidade de São Paulo. Departamento de Bioquímica. Instituto de Química; Brasil
Fil: Souza, Glaucia M. Universidade de São Paulo. Departamento de Bioquímica. Instituto de Química; Brasil
Fil: Snowdon, Rod. Justus Liebig University. Department of Plant Breeding; Alemania
Fil: Erazzú, Luis E. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina.
description Large-scale evaluation of genetic diversity in crops with large and complex genomes benefits from the selective enrichment of relevant genomic regions prior to sequencing. Given the complexity of the sugarcane (Saccharum spp.) genome and the limited exploration of quantitative trait loci (QTL) for important energy traits, we used comparative genomics with the related diploid crop sorghum (Sorghum bicolor) to mine for regions associated with bioenergy production. Twenty-one meta-QTL (mQTL) were identified after surveying 286 QTL from 24 different studies using the Sorghum QTL Atlas. Comparative genomics revealed that at least 35% of genes located within QTL can be found in highly conserved sorghum/sugarcane collinear chromosome blocks. Additionally, a targeted candidate search identified 200 genes known for their involvement in sugar and cell wall metabolism. For a subset of these sorghum genes, we evaluated sugarcane gene copy number, sequence identity, and homoeolog expression in target tissues. This work is an initial step towards targeting and resequencing sugarcane orthologous genomic regions to discover single nucleotide polymorphisms (SNPs) as a resource for genomics-assisted breeding.
publishDate 2022
dc.date.none.fl_str_mv 2022-04-06T12:41:59Z
2022-04-06T12:41:59Z
2022-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/11570
https://onlinelibrary.wiley.com/doi/abs/10.1111/pbr.13013
0179-9541
1439-0523
https://doi.org/10.1111/pbr.13013
url http://hdl.handle.net/20.500.12123/11570
https://onlinelibrary.wiley.com/doi/abs/10.1111/pbr.13013
https://doi.org/10.1111/pbr.13013
identifier_str_mv 0179-9541
1439-0523
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv Plant Breeding (First published: 01 April 2022)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.623145

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