Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> 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 (<i>Rf</i>) of the male parent. The objective of this study was to identify <i>Rf<...
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2021-08-01
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| author | Mirosław Tyrka Beata Bakera Magdalena Szeliga Magdalena Święcicka Paweł Krajewski Monika Mokrzycka Monika Rakoczy-Trojanowska |
| author_facet | Mirosław Tyrka Beata Bakera Magdalena Szeliga Magdalena Święcicka Paweł Krajewski Monika Mokrzycka Monika Rakoczy-Trojanowska |
| author_sort | Mirosław Tyrka |
| collection | DOAJ |
| 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 (<i>Rf</i>) of the male parent. The objective of this study was to identify <i>Rf</i> 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 <i>Rf</i> 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 <i>cis</i>-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as <i>Rf</i> candidate genes, six of which were identified for the first time in this study. |
| first_indexed | 2024-03-10T08:12:17Z |
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| id | doaj.art-fd95a658a0764982b74729e46f47ec46 |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T08:12:17Z |
| publishDate | 2021-08-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-fd95a658a0764982b74729e46f47ec462023-11-22T10:38:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-08-012217914610.3390/ijms22179146Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog AnalysesMirosław Tyrka0Beata Bakera1Magdalena Szeliga2Magdalena Święcicka3Paweł Krajewski4Monika Mokrzycka5Monika Rakoczy-Trojanowska6Department of Biotechnology and Bioinformatics, Rzeszów University of Technology, Powstańców Warszawy 12, 35-959 Rzeszów, PolandDepartment of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, PolandDepartment of Biotechnology and Bioinformatics, Rzeszów University of Technology, Powstańców Warszawy 12, 35-959 Rzeszów, PolandDepartment of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, PolandInstitute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, PolandInstitute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, PolandDepartment of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warszawa, PolandAmong 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 (<i>Rf</i>) of the male parent. The objective of this study was to identify <i>Rf</i> 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 <i>Rf</i> 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 <i>cis</i>-regulatory elements common among PPR-encoding genes. On the basis of the obtained results, we designated seven genes as <i>Rf</i> candidate genes, six of which were identified for the first time in this study.https://www.mdpi.com/1422-0067/22/17/9146fertility restorationgene expressionmappingmicrosporepentatricopeptide repeat genespollen |
| spellingShingle | Mirosław Tyrka Beata Bakera Magdalena Szeliga Magdalena Święcicka Paweł Krajewski Monika Mokrzycka Monika Rakoczy-Trojanowska Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog Analyses International Journal of Molecular Sciences fertility restoration gene expression mapping microspore pentatricopeptide repeat genes pollen |
| title | Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog Analyses |
| title_full | Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog Analyses |
| title_fullStr | Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog Analyses |
| title_full_unstemmed | Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog Analyses |
| title_short | Identification of <i>Rf</i> Genes in Hexaploid Wheat (<i>Triticum</i><i>aestivum</i> L.) by RNA-Seq and Paralog Analyses |
| title_sort | identification of i rf i genes in hexaploid wheat i triticum i i aestivum i l by rna seq and paralog analyses |
| topic | fertility restoration gene expression mapping microspore pentatricopeptide repeat genes pollen |
| url | https://www.mdpi.com/1422-0067/22/17/9146 |
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