In-Depth Sequence Analysis of Bread Wheat VRN1 Genes

The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large...

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Autores principales:	Beáta Strejčková, Zbyněk Milec, Kateřina Holušová, Petr Cápal, Tereza Vojtková, Radim Čegan, Jan Šafář
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>VRN1</i> allelic variation wheat CNV next generation sequencing alternative splice variants Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/5321fe6c126a4f629627da933dc23a87
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spelling	oai:doaj.org-article:5321fe6c126a4f629627da933dc23a872021-11-25T17:55:01ZIn-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes10.3390/ijms2222122841422-00671661-6596https://doaj.org/article/5321fe6c126a4f629627da933dc23a872021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/22/12284https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The <i>VERNALIZATION1</i> (<i>VRN1</i>) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of <i>VRN1</i> homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of <i>VRN1</i> homoeologs (<i>VRN</i>-<i>A1</i>, <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i>). We performed an in-depth sequence analysis of <i>VRN1</i> homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele <i>Vrn</i>-<i>B1f</i> with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the <i>Vrn</i>-<i>A1b</i> allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of <i>VRN1</i> homoeologs showed that <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i> are present in only one copy. The copy number of recessive <i>vrn</i>-<i>A1</i> ranged from one to four, while that of dominant <i>Vrn</i>-<i>A1</i> was one or two. Different numbers of <i>Vrn</i>-<i>A1a</i> copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more <i>vrn</i>-<i>A1</i> copies.Beáta StrejčkováZbyněk MilecKateřina HolušováPetr CápalTereza VojtkováRadim ČeganJan ŠafářMDPI AGarticle<i>VRN1</i>allelic variationwheatCNVnext generation sequencingalternative splice variantsBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 12284, p 12284 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>VRN1</i> allelic variation wheat CNV next generation sequencing alternative splice variants Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	<i>VRN1</i> allelic variation wheat CNV next generation sequencing alternative splice variants Biology (General) QH301-705.5 Chemistry QD1-999 Beáta Strejčková Zbyněk Milec Kateřina Holušová Petr Cápal Tereza Vojtková Radim Čegan Jan Šafář In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes
description	The <i>VERNALIZATION1</i> (<i>VRN1</i>) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of <i>VRN1</i> homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of <i>VRN1</i> homoeologs (<i>VRN</i>-<i>A1</i>, <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i>). We performed an in-depth sequence analysis of <i>VRN1</i> homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele <i>Vrn</i>-<i>B1f</i> with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the <i>Vrn</i>-<i>A1b</i> allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of <i>VRN1</i> homoeologs showed that <i>VRN</i>-<i>B1</i> and <i>VRN</i>-<i>D1</i> are present in only one copy. The copy number of recessive <i>vrn</i>-<i>A1</i> ranged from one to four, while that of dominant <i>Vrn</i>-<i>A1</i> was one or two. Different numbers of <i>Vrn</i>-<i>A1a</i> copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more <i>vrn</i>-<i>A1</i> copies.
format	article
author	Beáta Strejčková Zbyněk Milec Kateřina Holušová Petr Cápal Tereza Vojtková Radim Čegan Jan Šafář
author_facet	Beáta Strejčková Zbyněk Milec Kateřina Holušová Petr Cápal Tereza Vojtková Radim Čegan Jan Šafář
author_sort	Beáta Strejčková
title	In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes
title_short	In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes
title_full	In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes
title_fullStr	In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes
title_full_unstemmed	In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes
title_sort	in-depth sequence analysis of bread wheat <i>vrn1</i> genes
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/5321fe6c126a4f629627da933dc23a87
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In-Depth Sequence Analysis of Bread Wheat <i>VRN1</i> Genes

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