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microRNAs differentially modulated in response to heat and drought stress in durum wheat cultivars with contrasting water use efficiency

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Abstract

Plant stress response is a complex molecular process based on transcriptional and posttranscriptional regulation of many stress-related genes. microRNAs are the best-studied class of small RNAs known to play key regulatory roles in plant response to stress, besides being involved in plant development and organogenesis. We analyzed the leaf miRNAome of two durum wheat cultivars (Cappelli and Ofanto) characterized by a contrasting water use efficiency, exposed to heat stress, and mild and severe drought stress. On the whole, we identified 98 miRNA highly similar to previously known miRNAs and grouped in 47 MIR families, as well as 85 novel candidate miRNA, putatively wheat specific. A total of 80 known and novel miRNA precursors were found differentially expressed between the two cultivars or modulated by stress and many of them showed a cultivar-specific expression profile. Interestingly, most in silico predicted targets of the miRNAs coming from the differentially expressed precursors have been experimentally linked in other species to mechanisms controlling stomatal movement, a finding in agreement with previous results showing that Cappelli has a lower stomatal conductance than Ofanto. Selected miRNAs were validated through a standardized and reliable stem-loop qRT-PCR procedure.

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Acknowledgments

This work was supported by the Italian Ministry of Education, University and Research, project “PON01_01145-ISCOCEM.”

Author contributions

LG conducted the wet lab work and data analysis. EM interpreted the bioinformatics data and wrote the manuscript. EB designed and carried out all the computational analyses for microRNA identification and differential expression analysis. AMDL prepared the plants and RNA samples. PF contributed to bioinformatics analysis. LC designed the study, contributed to the development of the project, and edited the manuscript. CC conducted the wet lab work and wrote the manuscript. All authors have read, edited, and approved the manuscript.

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    1. Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso, 302, Fiorenzuola d’Arda, 29017, Italy

      Lorenzo Giusti, Erica Mica, Primetta Faccioli, Luigi Cattivelli & Cristina Crosatti

    2. Institute of Life Sciences, Scuola Superiore Sant’Anna, Piazza Martiri della Libertà, 33, Pisa, 56127, Italy

      Erica Mica & Edoardo Bertolini

    3. Council for Agricultural Research and Economics, Cereal Research Centre, SS 673 km 25,200, Foggia, 71122, Italy

      Anna Maria De Leonardis

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    1. Lorenzo Giusti
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    Correspondence to Cristina Crosatti.

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    This article forms part of a special issue of Functional & Integrative Genomics entitled “miRNA in model and complex organisms” (Issue Editors: Hikmet Budak and Baohong Zhang)

    Lorenzo Giusti and Erica Mica contributed equally to this work.

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    Giusti, L., Mica, E., Bertolini, E. et al. microRNAs differentially modulated in response to heat and drought stress in durum wheat cultivars with contrasting water use efficiency. Funct Integr Genomics 17, 293–309 (2017). https://doi.org/10.1007/s10142-016-0527-7

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