title: Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes.
abstract: Rice productivity is largely affected by low temperature, which can be harmful throughout plant development, from germination to grain filling. Germination of indica rice cultivars under cold is slow and not uniform, resulting in irregular emergence and small plant population. To identify and characterize novel genes involved in cold tolerance during the germination stage, two indica rice genotypes (sister lines previously identified as cold-tolerant and cold-sensitive) were used in parallel transcriptomic analysis (RNAseq) under cold treatment (seeds germinating at 13 °C for 7 days). We detected 1,361 differentially expressed transcripts. Differences in gene expression found by RNAseq were confirmed for 11 selected genes using RT-qPCR. Biological processes enhanced in the cold-tolerant seedlings include: cell division and expansion (confirmed by anatomical sections of germinating seeds), cell wall integrity and extensibility, water uptake and membrane transport capacity, sucrose synthesis, generation of simple sugars, unsaturation of membrane fatty acids, wax biosynthesis, antioxidant capacity (confirmed by histochemical staining of H2O2), and hormone and Ca(2+)-signaling. The cold-sensitive seedlings respond to low temperature stress increasing synthesis of HSPs and dehydrins, along with enhanced ubiquitin/proteasome protein degradation pathway and polyamine biosynthesis. Our findings can be useful in future biotechnological approaches aiming to cold tolerance in indica rice.
authors.affiliation: Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil.
authors.forename: Andressa
authors.initials: A
authors.lastname: Dametto
authors.affiliation: Centro de Ciências Biológicas e da Saúde (CCBS), Centro Universitário UNIVATES, Lajeado, RS, Brazil; Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Centro Universitário UNIVATES, Lajeado, RS, Brazil. Electronic address: rasperotto@univates.br.
authors.forename: Raul A
authors.initials: RA
authors.lastname: Sperotto
authors.affiliation: Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Janete M
authors.initials: JM
authors.lastname: Adamski
authors.affiliation: Centro de Ciências Biológicas e da Saúde (CCBS), Centro Universitário UNIVATES, Lajeado, RS, Brazil.
authors.forename: Édina A R
authors.initials: ÉA
authors.lastname: Blasi
authors.affiliation: Departamento de Agronomia, Universidade Federal da Fronteira Sul (UFFS), Erechim, RS, Brazil.
authors.forename: Denise
authors.initials: D
authors.lastname: Cargnelutti
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Luiz F V
authors.initials: LF
authors.lastname: de Oliveira
authors.affiliation: Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Felipe K
authors.initials: FK
authors.lastname: Ricachenevsky
authors.affiliation: Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Jeferson N
authors.initials: JN
authors.lastname: Fregonezi
authors.affiliation: Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Jorge E A
authors.initials: JE
authors.lastname: Mariath
authors.affiliation: Departamento de Plantas de Lavoura, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Renata P
authors.initials: RP
authors.lastname: da Cruz
authors.affiliation: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
authors.forename: Rogério
authors.initials: R
authors.lastname: Margis
authors.affiliation: Departamento de Botânica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil. Electronic address: jpfett@cbiot.ufrgs.br.
authors.forename: Janette P
authors.initials: JP
authors.lastname: Fett
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D002455:Cell Division; D003080:Cold Temperature; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D005838:Genotype; D018525:Germination / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006861:Hydrogen Peroxide / Q000378:metabolism; D012275:Oryza / Q000166:cytology / Q000235:genetics* / Q000502:physiology*; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D036226:Seedlings / Q000166:cytology / Q000235:genetics; D012639:Seeds / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D006861:Hydrogen Peroxide
keywords: Cell division; Cold tolerance; Germination; Indica rice; Seed imbibition; Stress response