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Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses

Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat ge...

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Autores principales: Tyrka, Mirosław, Bakera, Beata, Szeliga, Magdalena, Święcicka, Magdalena, Krajewski, Paweł, Mokrzycka, Monika, Rakoczy-Trojanowska, Monika
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8431562/
https://www.ncbi.nlm.nih.gov/pubmed/34502055
http://dx.doi.org/10.3390/ijms22179146
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author Tyrka, Mirosław
Bakera, Beata
Szeliga, Magdalena
Święcicka, Magdalena
Krajewski, Paweł
Mokrzycka, Monika
Rakoczy-Trojanowska, Monika
author_facet Tyrka, Mirosław
Bakera, Beata
Szeliga, Magdalena
Święcicka, Magdalena
Krajewski, Paweł
Mokrzycka, Monika
Rakoczy-Trojanowska, Monika
author_sort Tyrka, Mirosław
collection PubMed
description Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study.
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spelling pubmed-84315622021-09-11 Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses Tyrka, Mirosław Bakera, Beata Szeliga, Magdalena Święcicka, Magdalena Krajewski, Paweł Mokrzycka, Monika Rakoczy-Trojanowska, Monika Int J Mol Sci Article Among the natural mechanisms used for wheat hybrid breeding, the most desirable is the system combining the cytoplasmic male sterility (cms) of the female parent with the fertility-restoring genes (Rf) of the male parent. The objective of this study was to identify Rf candidate genes in the wheat genome on the basis of transcriptome sequencing (RNA-seq) and paralog analysis data. Total RNA was isolated from the anthers of two fertility-restorer (Primépi and Patras) and two non-restorer (Astoria and Grana) varieties at the tetrad and late uninucleate microspore stages. Of 36,912 differentially expressed genes (DEGs), 21 encoding domains in known fertility-restoring proteins were selected. To enrich the pool of Rf candidates, 52 paralogs (PAGs) of the 21 selected DEGs were included in the analyses. The expression profiles of most of the DEGs and PAGs determined bioinformatically were as expected (i.e., they were overexpressed in at least one fertility-restorer variety). However, these results were only partially consistent with the quantitative real-time PCR data. The DEG and PAG promoters included cis-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as Rf candidate genes, six of which were identified for the first time in this study. MDPI 2021-08-24 /pmc/articles/PMC8431562/ /pubmed/34502055 http://dx.doi.org/10.3390/ijms22179146 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tyrka, Mirosław
Bakera, Beata
Szeliga, Magdalena
Święcicka, Magdalena
Krajewski, Paweł
Mokrzycka, Monika
Rakoczy-Trojanowska, Monika
Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses
title Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses
title_full Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses
title_fullStr Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses
title_full_unstemmed Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses
title_short Identification of Rf Genes in Hexaploid Wheat (Triticum aestivum L.) by RNA-Seq and Paralog Analyses
title_sort identification of rf genes in hexaploid wheat (triticum aestivum l.) by rna-seq and paralog analyses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8431562/
https://www.ncbi.nlm.nih.gov/pubmed/34502055
http://dx.doi.org/10.3390/ijms22179146
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