Natural variations of SLG1 confer high-temperature tolerance in indica rice

Abstract

With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification of SLG1 (Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice. SLG1 plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction of SLG1 results in plants with thermosensitive phenotype, while overexpression of SLG1 enhances the tolerance of plants to high temperature. SLG1 is differentiated between the two Asian cultivated rice subspecies, indica and japonica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice varieties. Our results demonstrate that the allelic differentiation of SLG1 confers indica rice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe.

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

“…Together, these results indicated indica-japonica differentiation in response to various environments with cell type-specific patterns in root tips, which helps reveal the roles of different cell types in the process of adaptation. In practical applications, DEGs in both indicajaponica rice varieties and under different stress treatments may provide some clues for breeding applications, as with the findings in previous study, which indicated that the selection of COLD1, HAN1, bZIP73, LTG1, LTT7, qCTS-9, and qPSR10 can enhance the cold tolerance of japonica rice (Liu et al, 2013(Liu et al, , 2019Ma et al, 2015;Zhao et al, 2017;Xiao et al, 2018;Mao et al, 2019;Xu et al, 2020). The stress-induced DEGs in our study have potential as target genes for the improvement of stress tolerance in rice breeding applications.…”

“…Although the key roles of natural genetic variations in differentiation between the subspecies of indica and japonica rice varieties address disruption from environment changes and human preferences (Ma et al, 2015;Liu et al, 2019;Xu et al, 2020), differential gene expression also plays an important role in driving the adaptation of plants to divergent habitats (Liu et al, 2020;Wang et al, 2020). In this study, we identified eight cell types in rice root tips (Figures 1A,B) and compared the expression of genes between indica and japonica rice varieties in each cell type (Figures 1C,D) using a single-cell RNA sequencing dataset.…”

“…Both natural genetic variations and changed gene expression play an important role in abiotic stress tolerance in multiple species (Bian et al, 2020). For example, previous studies showed that SNPs or indels in the promoter or the coding sequence of genes (such as COLD1, HAN1, bZIP73, LTG1, LTT7, qCTS-9, qPSR10) can enhance the cold tolerance of japonica rice (Liu et al, 2013(Liu et al, , 2019Ma et al, 2015;Zhao et al, 2017;Xiao et al, 2018;Mao et al, 2019;Xu et al, 2020). A change in the promoter activity led to the modification of HSFB2b expression, which led to salt stress tolerance in soybeans (Glycine max) (Yolcu et al, 2020).…”

“…The differentiation of indica and japonica rice reflects the adaptative evolution of plant species in divergent natural and human-influenced environments, in addition to that through direct artificial selection (Gross and Olsen, 2010). The key to rice subspecific differentiation is natural genetic variations that involve environmental adaptation and human preferences (Ma et al, 2015;Liu et al, 2019;Xu et al, 2020). For example, COLD1 jap and bZIP73 jap were selected as natural variants during the process of japonica domestication, which can partially explain the cold tolerance of japonica rice varieties (Ma et al, 2015;Liu et al, 2019).…”

“…For example, COLD1 jap and bZIP73 jap were selected as natural variants during the process of japonica domestication, which can partially explain the cold tolerance of japonica rice varieties (Ma et al, 2015;Liu et al, 2019). SLG1 indica contributed to adaptation to high-temperature environments through artificial selection in indica domestication (Xu et al, 2020). In addition to the genetic variation between indica and japonica, the level of gene expression is also very important in adaptation to divergent environments (Campbell et al, 2020).…”