Integrative approach for precise genotyping and transcriptomics of salt tolerant introgression rice lines

Bundó Mireia, Martín-Cardoso Héctor, Pesenti Michele, Gomez-Ariza Jorge, Castillo Laia, Frouin Julien, Serrat Xavier, Nogués Salvador, Courtois Brigitte, Grenier Cécile, Sacchi Gian Attilio, San Segundo Blanca. 2022. Integrative approach for precise genotyping and transcriptomics of salt tolerant introgression rice lines. Frontiers in Plant Science, 12:797141, 20 p.

https://doi.org/10.3389/fpls.2021.797141

Article de revue ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total

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Résumé : 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.

Mots-clés Agrovoc : tolérance au sel, génotype, génétique intégrative, Oryza sativa, stress osmotique, génotypage, transcriptome

Mots-clés libres : Genotyping by sequencing, Oryza sativa, Saltol, Transcriptomics, Salinity stress

Classification Agris : F30 - Génétique et amélioration des plantes
F60 - Physiologie et biochimie végétale
H50 - Troubles divers des plantes

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Commission

Programme de financement européen : H2020

Projets sur financement : (EU) New commercial EUropean RICE (Oryza sativa) harbouring salt tolerance alleles to protect the rice sector against climate change and apple snail (Pomacea insularum) invasion

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