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Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene usin...

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Autores principales: Abrouk, Michael, Athiyannan, Naveenkumar, Müller, Thomas, Pailles, Yveline, Stritt, Christoph, Roulin, Anne C., Chu, Chenggen, Liu, Shuyu, Morita, Takumi, Handa, Hirokazu, Poland, Jesse, Keller, Beat, Krattinger, Simon G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979816/
https://www.ncbi.nlm.nih.gov/pubmed/33742098
http://dx.doi.org/10.1038/s42003-021-01908-6
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author Abrouk, Michael
Athiyannan, Naveenkumar
Müller, Thomas
Pailles, Yveline
Stritt, Christoph
Roulin, Anne C.
Chu, Chenggen
Liu, Shuyu
Morita, Takumi
Handa, Hirokazu
Poland, Jesse
Keller, Beat
Krattinger, Simon G.
author_facet Abrouk, Michael
Athiyannan, Naveenkumar
Müller, Thomas
Pailles, Yveline
Stritt, Christoph
Roulin, Anne C.
Chu, Chenggen
Liu, Shuyu
Morita, Takumi
Handa, Hirokazu
Poland, Jesse
Keller, Beat
Krattinger, Simon G.
author_sort Abrouk, Michael
collection PubMed
description The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20(th) century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.
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spelling pubmed-79798162021-04-12 Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color Abrouk, Michael Athiyannan, Naveenkumar Müller, Thomas Pailles, Yveline Stritt, Christoph Roulin, Anne C. Chu, Chenggen Liu, Shuyu Morita, Takumi Handa, Hirokazu Poland, Jesse Keller, Beat Krattinger, Simon G. Commun Biol Article The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20(th) century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits. Nature Publishing Group UK 2021-03-19 /pmc/articles/PMC7979816/ /pubmed/33742098 http://dx.doi.org/10.1038/s42003-021-01908-6 Text en © The Author(s) 2021 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Abrouk, Michael
Athiyannan, Naveenkumar
Müller, Thomas
Pailles, Yveline
Stritt, Christoph
Roulin, Anne C.
Chu, Chenggen
Liu, Shuyu
Morita, Takumi
Handa, Hirokazu
Poland, Jesse
Keller, Beat
Krattinger, Simon G.
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
title Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
title_full Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
title_fullStr Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
title_full_unstemmed Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
title_short Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
title_sort population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7979816/
https://www.ncbi.nlm.nih.gov/pubmed/33742098
http://dx.doi.org/10.1038/s42003-021-01908-6
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