Selection of transcripts related to low-temperature tolerance using RNA sequencing from F2 plants between japonica and indica rice (Oryza sativa L.) cultivars
Akari Fukuda A E , Tatsuro Hirose B , Yoichi Hashida B , Naohiro Aoki C and Atsushi J. Nagano DA Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
B Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan.
C Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
D Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan.
E Corresponding author. Email: akfukuda@affrc.go.jp
Functional Plant Biology 48(10) 984-993 https://doi.org/10.1071/FP21088
Submitted: 23 March 2021 Accepted: 21 May 2021 Published: 11 June 2021
Journal Compilation © CSIRO 2021 Open Access CC BY-NC-ND
Abstract
At low temperatures (18°C), seedlings of an indica rice (Oryza sativa L.) cultivar Kasalath showed symptoms of chlorosis, although the leaves of a japonica cultivar Arroz da Terra remained green. In this study, transcripts related to the chlorophyll content of rice seedlings grown at 18°C were investigated using RNA-sequencing (RNA-Seq) data for F2 crosses between cultivars Arroz da Terra and Kasalath, as well as their parental cultivars. Differential expression analysis revealed that gene ontology terms related to ‘photosynthesis’ were significantly enriched in lowly expressed genes at 18°C than at 25°C in Kasalath. However, the gene ontology terms related to ‘response to stress’ were significantly enriched in highly expressed genes at 18°C than at 25°C in Kasalath. When the F2 plants were grown at 18°C, their chlorophyll contents varied. Transcripts with expression levels related to chlorophyll content were statistically selected using RNA-Seq data from 21 F2 plants. In regression models, frequently selected genes included four photosynthetic and two stress-responsive genes. The expression values of four photosynthetic and two stress-responsive genes in high-frequency selected genes were significantly correlated with chlorophyll content not only in plants analysed using RNA-Seq but also in 95 F2 plants.
Keywords: cold tolerance, low temperature, LASSO, POX22.3, RNA sequencing (RNA-Seq), TIFY11C, transcriptome, rice, Oryza sativa L.
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