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Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley

KEY MESSAGE: Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. ABSTRACT: Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important gene...

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Autores principales: Guerra, Davide, Morcia, Caterina, Badeck, Franz, Rizza, Fulvia, Delbono, Stefano, Francia, Enrico, Milc, Justyna Anna, Monostori, Istvan, Galiba, Gabor, Cattivelli, Luigi, Tondelli, Alessandro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8866391/
https://www.ncbi.nlm.nih.gov/pubmed/34757472
http://dx.doi.org/10.1007/s00122-021-03985-x
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author Guerra, Davide
Morcia, Caterina
Badeck, Franz
Rizza, Fulvia
Delbono, Stefano
Francia, Enrico
Milc, Justyna Anna
Monostori, Istvan
Galiba, Gabor
Cattivelli, Luigi
Tondelli, Alessandro
author_facet Guerra, Davide
Morcia, Caterina
Badeck, Franz
Rizza, Fulvia
Delbono, Stefano
Francia, Enrico
Milc, Justyna Anna
Monostori, Istvan
Galiba, Gabor
Cattivelli, Luigi
Tondelli, Alessandro
author_sort Guerra, Davide
collection PubMed
description KEY MESSAGE: Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. ABSTRACT: Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-021-03985-x.
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spelling pubmed-88663912022-03-02 Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley Guerra, Davide Morcia, Caterina Badeck, Franz Rizza, Fulvia Delbono, Stefano Francia, Enrico Milc, Justyna Anna Monostori, Istvan Galiba, Gabor Cattivelli, Luigi Tondelli, Alessandro Theor Appl Genet Original Article KEY MESSAGE: Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley. ABSTRACT: Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-021-03985-x. Springer Berlin Heidelberg 2021-11-10 2022 /pmc/articles/PMC8866391/ /pubmed/34757472 http://dx.doi.org/10.1007/s00122-021-03985-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Original Article
Guerra, Davide
Morcia, Caterina
Badeck, Franz
Rizza, Fulvia
Delbono, Stefano
Francia, Enrico
Milc, Justyna Anna
Monostori, Istvan
Galiba, Gabor
Cattivelli, Luigi
Tondelli, Alessandro
Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
title Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
title_full Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
title_fullStr Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
title_full_unstemmed Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
title_short Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
title_sort extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8866391/
https://www.ncbi.nlm.nih.gov/pubmed/34757472
http://dx.doi.org/10.1007/s00122-021-03985-x
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