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Gene expression profile of rice leaf from selected cultivars

ABSTRACT: The genome structrure of domesticated species is influenced by complexity of breeding practices exercised by humans. Hokkaido is the northern-most regio of Japan, and one of northern limit of rice cultivation of world. The climatic conditions of Hokkaido are considered to be unsuitable for rice cultivation. Rice breeding programs of Hokkaido have focused on adaptability to specific local environmental condiitons (such as short growth period, low temperature conditions). These specific selection pressures have generated the unique genetic structures of Hokkaido rice cultivars. The genotype of sixty-three Hokkaido rice varieties were already analyzed by SSR marker, and the results showed that Hokkaido rice varieties were classified into six groups (Shinada et al, 2014). The unique genomic structures of six groups may have related to specific gene expression. This study analyze the gene expression profiles of Hokkaido rice variety.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE57645 | GEO | 2014/10/31

SECONDARY ACCESSION(S): PRJNA247402

REPOSITORIES: GEO

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Project description:Background: Rice grain production is susceptible to a changing environment that imposes both biotic and abiotic stress conditions. Cold episodes are becoming more frequent in the last years and directly affect rice yield in areas with a temperate climate. Rice is particularly susceptible to cold stress during the reproductive phase, especially in anthers during post-meiotic stages which, in turn, affect pollen production. However, a number of rice cultivars with a certain degree of tolerance to cold have been described, which may represent a good breeding resource for improvement of susceptible commercial varieties. Plants experiencing cold stress activate a molecular response in order to reprogram many metabolic pathways to face these hostile conditions. Results: Here we performed RNA-seq analysis using cold-stressed post-meiotic anther samples from a cold-tolerant, Erythroceros Hokkaido (ERY), and a cold-susceptible commercial cultivar Sant´Andrea (S.AND). Both cultivars displayed an early common molecular response to cold, although the changes in expression levels are much more drastic in the tolerant one. Comparing our datasets, obtained after one-night cold stress, with other similar genome-wide studies showed very few common deregulated genes, leading to the conclusion that molecular responses in cold-stressed anthers strongly depend on conditions and the duration of the cold treatments. Cold-tolerant ERY exhibits specific molecular responses related to ethylene metabolism, which appears to be activated after cold stress. On the other hand, S.AND cold-treated plants showed a general downregulation of photosystem I and II genes, supporting a role of photosynthesis and chloroplasts in cold responses in anthers, which has remained elusive. Conclusions: Our study revealed that a number of ethylene-related transcription factors, as putative master regulators of cold responses, were upregulated in ERY providing promising candidates to confer tolerance to susceptible cultivars. Our results also suggest that the photosynthesis machinery might be a good target to improve cold tolerance in anthers. In summary, our study provides valuable candidates for further analysis and molecular breeding for cold-tolerant rice cultivars.

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Gene expression profile of rice leaf from selected cultivars

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