Transcriptome profiling of rice seedlings under cold stress
Luciano C. da Maia A D , Pablo R. B. Cadore A , Leticia C. Benitez B , Rodrigo Danielowski A , Eugenia J. B. Braga B , Paulo R. R. Fagundes C , Ariano M. Magalhães
+ Author Affiliations
- Author Affiliations
A Universidade Federal de Pelotas, Department of Plant Sciences, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil.
B Universidade Federal de Pelotas, Department of Botany, Campus Universitário, S/N - CEP 96160-000 - Capão do Leão, RS - Brazil.
C EMBRAPA – Brazilian Agricultural Research Corporation, BR-392 Road, Km 78, 9° Distrito, Monte Bonito, Pelotas/RS - Brazil.
D Corresponding author. Email: lucianoc.maia@gmail.com
Functional Plant Biology 44(4) 419-429 https://doi.org/10.1071/FP16239
Submitted: 10 July 2016 Accepted: 11 November 2016 Published: 14 December 2016
Abstract
Rice (Oryza sativa L.) is one of the most important species for food production worldwide, besides being an excellent genetic model among the grasses. Cold is one of the major abiotic factors reducing rice yield, primarily affecting germination and reproduction phases. Currently, the RNAseq technique allows the identification of differential expressed genes in response to a given treatment, such as cold stress. In the present work, a transcriptome (RNAseq) analysis was performed in the V3 phase for contrasting genotypes Oro (tolerant) and Tio Taka (sensitive), in response to cold (13°C). A total of 241 and 244 M readings were obtained, resulting in the alignment of 25.703 and 26.963 genes in genotypes Oro and Tio Taka respectively. The analyses revealed 259 and 5579 differential expressed genes in response to cold in the genotypes Oro and Tio Taka respectively. Ontology classes with larger changes were metabolic process ~27%, cellular process ~21%, binding ~30% and catalytic activity ~22%. In the genotype Oro, 141 unique genes were identified, 118 were common between Oro and Tio Taka and 5461 were unique to Tio Taka. Genes involved in metabolic routes of signal transduction, phytohormones, antioxidant system and biotic stress were identified. These results provide an understanding that breeding for a quantitative trait, such as cold tolerance at germination, several gene loci must be simultaneously selected. In general, few genes were identified, but it was not possible to associate only one gene function as responsible for the cultivar tolerance; since different genes from different metabolic routes were identified. The genes described in the present work will be useful for future investigations and for the detailed validation in marker assisted selection projects for cold tolerance in the germination of rice.
Additional keywords: abiotic stress, chilling, expression, functional genomics, transcripts.
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