Abstract
Rice (Oryza sativa L.) is one of the most important species for food production worldwide. Low temperature is a major abiotic factor that affects rice germination and reproduction. Here, the underlying regulatory mechanism in seedlings of a TGMS variety (33S) and a cold-sensitive variety (Nipponbare) was investigated by comparative transcriptome. There were 795 differentially expressed genes (DEGs) identified only in cold-treated 33S, suggesting that 33S had a unique cold-resistance system. Functional and enrichment analysis of these DEGs revealed that, in 33S, several metabolic pathways, such as photosynthesis, amino acid metabolism, secondary metabolite biosynthesis, were significantly repressed. Moreover, pathways related to growth and development, including starch and sucrose metabolism, and DNA biosynthesis and damage response/repair, were significantly enhanced. The expression of genes related to nutrient reserve activity were significantly up-regulated in 33S. Finally, three NAC and several ERF transcription factors were predicted to be important in this transcriptional reprogramming. This present work provides valuable information for future investigations of low-temperature response mechanisms and genetic improvement of cold-tolerant rice seedlings.
Highlights
Rice (Oryza sativa L.) is one of the most important staple crop species, feeding more than half of the global population
The samples were subjected to total RNA extraction and RNA sequencing (RNA-seq) analysis using the Illumina HiSeq 2500 platform
938 and 762 differentially expressed genes (DEGs) were identified under low-temperature stress in 33S and Nipponbare, respectively
Summary
Rice (Oryza sativa L.) is one of the most important staple crop species, feeding more than half of the global population. Increasing rice yield is a priority to ensure global food security. Low temperature is one of the major environmental stresses that negatively impacts plant growth and yield potential. Due to its tropical and subtropical origin, rice is sensitive to low temperature [1]. The optimal temperature is 25–35 ̊C for rice at the germination stage. Temperatures below 15 ̊C would lead to a number of developmental damage in rice, including reduced germination rate, delayed seedling emergence and initial seedling growth, and high seedling mortality [2]. The current high-yield production of superhybrid rice cultivars are frequently affected by cold stress in tropical or subtropical areas. Improving rice cold stress tolerance could help maintain
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