Contents lists available at ScienceDirect Environmental and Experimental Botany journal homepage: www.elsevier.com/locate/envexpbot Transcriptional memory contributes to drought tolerance in coffee (Coffea canephora) plants Fernanda Alves de Freitas Guedes a , Priscilla Nobres a , Daniela Cristina Rodrigues Ferreira b , Paulo Eduardo Menezes-Silva c , Marcelo Ribeiro-Alves d , Régis Lopes Correa b , Fábio Murilo DaMatta e , Márcio Alves-Ferreira a, ⁎ a Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia, s/n Prédio do CCS 2° andar - sala 93, Rio de Janeiro, RJ, 219410- 970, Brazil b Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia, s/n Prédio do CCS, 2° andar - sala 66, Rio de Janeiro, RJ, 219410- 970, Brazil c Instituto Federal de Educação, Ciência e Tecnologia Goiano - Campus Rio Verde Rua do Ipê Amarelo, Loteamento Gameleira, Rio Verde, GO 75901-970, Brazil d Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz - (FIOCRUZ) ABrasil, 4365v. Brasil, 4365 - Manguinhos, Rio de Janeiro, RJ 21040-900, Brazil e Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV) Av. Peter Henry Rolfs Campus Universitário, Viçosa, MG 36570-900, Brazil ARTICLE INFO Keywords: Abscisic acid Coffea canephora Drought Oxidative stress Receptor-like kinases Transcriptional memory ABSTRACT Water deprivation is an important limiting factor in the productivity of crops like coffee. In addition to tran- scription factors (TFs) and small non-coding RNAs, transcriptional memory seems to act in gene expression modulation during plant drought response. Here, a RNA-Seq approach was used to investigate the drought responses of Coffea canephora clones 109 and 120, which are respectively sensitive and tolerant to drought. Illumina sequencing allowed us to identify differentially expressed genes (DEG) in the tolerant (826) and sen- sitive (135) clones and their enriched categories. Our results indicate that the sensitive clone may trigger an oxidative stress response, possibly leading to programmed cell death, when exposed to multiple drought epi- sodes. The acclimation of tolerant plants, on the other hand, seems to involve antioxidant secondary metabolism and the ABA response. Most importantly, 49 memory genes were identified in the tolerant clone. They were mainly linked to the ABA pathway, protein folding and biotic stress. Small RNA profiling also identified reg- ulatory microRNAs in coffee leaves, including hundreds of putative novel ones. Our findings strongly suggest that transcriptional memory modulates the expression of drought-responsive genes and contributes to drought tolerance in C. canephora. 1. Introduction Harsh environmental conditions trigger a wide range of responses in plants, from altered gene expression and cellular metabolism to changes in growth rates and crop yields (Bray et al., 2000; Cavatte et al., 2012; Krasensky and Jonak, 2012). Since drought is the most important en- vironmental stress in agriculture and drought events are expected to be exacerbated by climate change, understanding plant responses to this stress type and the cross-talk between different stresses (Fujita et al., 2006; Atkinson and Urwin, 2012; Rejeb et al., 2014) is important to increasing crop productivity while using less water. Drought responses depend on plant species/genotypes, water deficit severity and duration (Cavatte et al., 2012) and on the imprint that previous stress episodes have left on the plant (Walter et al., 2011; Ding et al., 2014; Wang et al., 2014; Virlouvet and Fromm, 2015; Fleta- Soriano and Munné-Bosch, 2016). The imprint, or stress memory, can be defined as the structural, genetic and biochemical modifications resulting from a stress exposure that allows plants to “remember” past environmental events (Fleta-Soriano and Munné-Bosch, 2016). These “memories” can improve plant adaptation and resistance to future stress episodes (Kinoshita and Seki, 2014; Fleta-Soriano and Munné- Bosch, 2016). Even though the mechanisms underpinning plant stress https://doi.org/10.1016/j.envexpbot.2017.12.004 Received 6 November 2017; Received in revised form 2 December 2017; Accepted 2 December 2017 ⁎ Corresponding author. E-mail addresses: fernandaafguedes@gmail.com (F.A.d.F. Guedes), priscillanobres@gmail.com (P. Nobres), ferreiradcr@gmail.com (D.C. Rodrigues Ferreira), paulo.menezes@ifgoiano.edu.br (P.E. Menezes-Silva), marcelo.ribeiro@ini.fiocruz.br (M. Ribeiro-Alves), regis@biologia.ufrj.br (R.L. Correa), fdamatta@ufv.br (F.M. DaMatta), alvesfer@uol.com.br, marcioaf@ufrj.br (M. Alves-Ferreira). Abbreviations: Cq, Quantification Cycles; DEG, Differentially Expressed Genes; FC, Fold Change; TF, Transcription Factor Environmental and Experimental Botany 147 (2018) 220–233 Available online 10 December 2017 0098-8472/ © 2017 Elsevier B.V. All rights reserved. T