Vol.:(0123456789) 1 3 Plant Cell Reports https://doi.org/10.1007/s00299-017-2234-9 ORIGINAL ARTICLE Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage Raul Antonio Sperotto 1  · Artur Teixeira de Araújo Junior 2  · Janete Mariza Adamski 3  · Denise Cargnelutti 4  · Felipe Klein Ricachenevsky 5  · Ben‑Hur Neves de Oliveira 2  · Renata Pereira da Cruz 6  · Rinaldo Pires dos Santos 3  · Leila Picolli da Silva 7  · Janette Palma Fett 2,3 Received: 21 July 2017 / Accepted: 8 November 2017 © Springer-Verlag GmbH Germany, part of Springer Nature 2017 Abstract Key message Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and diferential expression of several newly identifed genes. Abstract Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed. Diferentially expressed genes were identifed: 831 and 357 sequences more expressed in the tolerant and in the sensitive genotype, respectively. The genes with higher expres- sion in the CT genotype were used in systems biology analyses to identify protein–protein interaction (PPI) networks and nodes (proteins) that are hubs and bottlenecks in the PPI. From the genes more expressed in the tolerant plants, 60% were reported as afected by cold in previous transcriptome experiments and 27% are located within QTLs related to cold tolerance during the vegetative stage. Novel cold-responsive genes were identifed. Quantitative RT-PCR confrmed the high-quality of RNAseq libraries. Several genes related to cell wall assembly or reinforcement are cold-induced or constitutively highly expressed in the tolerant genotype. Cold-tolerant plants have increased cellulose deposition under cold. Genes related to lipid metabolism are more expressed in the tolerant genotype, which has higher membrane fatty acids unsaturation, with increasing levels of linoleic acid under cold. The CT genotype seems to have higher photosynthetic efciency and antioxidant capacity, as well as more efective ethylene, Ca 2+ and hormone signaling than the CS. These genes could be useful in future biotechnological approaches aiming to increase cold tolerance in rice. Keywords Cellulose · Cold tolerance · Cell wall · Transcriptome · Fatty acid · Indica rice Introduction Rice is one of the world’s most important staple foods; how- ever, several abiotic stresses afect the physiological status of rice plants, leading to decreased grain yield. Low tem- perature is one of the major environmental factors limiting rice production, mostly in temperate and high altitude areas, due to the tropical origin of the rice species (Cruz et al. 2013). Cold temperature has the potential to afect growth and development of rice plants during any developmental stage, from germination to grain flling (Ye et al. 2009). During early growth stages, it can severely afect seedling establishment, leading to leaf chlorosis, growth retardation and decreased tillering (Cruz et al. 2013). Improved cold Communicated by Marcelo Menossi. Raul Antonio Sperotto, Artur Teixeira de Araújo Junior and Janete Mariza Adamski contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00299-017-2234-9) contains supplementary material, which is available to authorized users. * Raul Antonio Sperotto rasperotto@univates.br * Janette Palma Fett jpfett@cbiot.ufrgs.br Extended author information available on the last page of the article