Abstract
Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei’ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.
Highlights
Half of the world population depends on rice as a staple food
The products of these genes were classified into two groups: one group consisting of function proteins such as late embryogenesis-abundant (LEA) proteins, cold-acclimation proteins, carbohydrate metabolism-related proteins; the other group consisting of various types of transcription factors such as Myeloblastosis (MYB), NAM-ATAF-CUC (NAC), and basic region/Leu zipper motif family transcription factors [5]
Metabolism, transport, and transcription factor (TF) genes were found among the up-regulated differentially expressed genes (DEGs) that were common to both genotypes
Summary
Half of the world population depends on rice as a staple food. increasing rice yields to help meet and ensure world food security is a significant and pressing technological goal. Previous transcriptome studies of cold responses in rice were performed using only the leaves of rice at the seedling stage, ignoring the relatively more cold-sensitive booting stage and further ignoring gene expression in organs that are known to be highly related to yield, such as anthers. RNA-Seq was used to investigate two different PTGMS lines under both fertility temperatures (22 °C for 10 days) and cold treatment conditions (17.5 °C for 10 days) at the booting stage. This study of differentially expressed genes following cold stress treatment furthers our understanding of the cold response mechanisms of rice and contributes to the technological resources available for the improvement of cold tolerance in rice PTGMS lines
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