Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines
Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice varie...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.797141/full |
| _version_ | 1798014787090644992 |
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| author | Mireia Bundó Héctor Martín-Cardoso Michele Pesenti Jorge Gómez-Ariza Laia Castillo Julien Frouin Julien Frouin Xavier Serrat Salvador Nogués Brigitte Courtois Brigitte Courtois Cécile Grenier Cécile Grenier Gian Attilio Sacchi Blanca San Segundo Blanca San Segundo |
| author_facet | Mireia Bundó Héctor Martín-Cardoso Michele Pesenti Jorge Gómez-Ariza Laia Castillo Julien Frouin Julien Frouin Xavier Serrat Salvador Nogués Brigitte Courtois Brigitte Courtois Cécile Grenier Cécile Grenier Gian Attilio Sacchi Blanca San Segundo Blanca San Segundo |
| author_sort | Mireia Bundó |
| collection | DOAJ |
| description | Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice. |
| first_indexed | 2024-04-11T15:24:04Z |
| format | Article |
| id | doaj.art-d26e6001c2d742d3b45531f643a23adb |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T15:24:04Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d26e6001c2d742d3b45531f643a23adb2022-12-22T04:16:18ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-01-011210.3389/fpls.2021.797141797141Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice LinesMireia Bundó0Héctor Martín-Cardoso1Michele Pesenti2Jorge Gómez-Ariza3Laia Castillo4Julien Frouin5Julien Frouin6Xavier Serrat7Salvador Nogués8Brigitte Courtois9Brigitte Courtois10Cécile Grenier11Cécile Grenier12Gian Attilio Sacchi13Blanca San Segundo14Blanca San Segundo15Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, SpainCentre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, SpainDepartment of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy – DiSAA, University of Milan, Milan, ItalyCentre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, SpainCentre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, SpainCIRAD, UMR AGAP, Montpellier, FranceAGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, FranceDepartament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, SpainDepartament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Secció de Fisiologia Vegetal, Universitat de Barcelona, Barcelona, SpainCIRAD, UMR AGAP, Montpellier, FranceAGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, FranceCIRAD, UMR AGAP, Montpellier, FranceAGAP, CIRAD, INRAE, Institut Agro, University of Montpellier, Montpellier, FranceDepartment of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy – DiSAA, University of Milan, Milan, ItalyCentre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Bellaterra, SpainConsejo Superior de Investigaciones Científicas, Barcelona, SpainRice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.https://www.frontiersin.org/articles/10.3389/fpls.2021.797141/fullgenotyping by sequencing (GBS)Oryza sativa (L.)Saltoltranscriptomicsindica and japonicaintrogression lines (ILs) |
| spellingShingle | Mireia Bundó Héctor Martín-Cardoso Michele Pesenti Jorge Gómez-Ariza Laia Castillo Julien Frouin Julien Frouin Xavier Serrat Salvador Nogués Brigitte Courtois Brigitte Courtois Cécile Grenier Cécile Grenier Gian Attilio Sacchi Blanca San Segundo Blanca San Segundo Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines Frontiers in Plant Science genotyping by sequencing (GBS) Oryza sativa (L.) Saltol transcriptomics indica and japonica introgression lines (ILs) |
| title | Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines |
| title_full | Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines |
| title_fullStr | Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines |
| title_full_unstemmed | Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines |
| title_short | Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines |
| title_sort | integrative approach for precise genotyping and transcriptomics of salt tolerant introgression rice lines |
| topic | genotyping by sequencing (GBS) Oryza sativa (L.) Saltol transcriptomics indica and japonica introgression lines (ILs) |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.797141/full |
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