Research Article: Cold tolerance response mechanisms revealed through comparative analysis of gene and protein expression in multiple rice genotypes

Date Published: June 10, 2019

Publisher: Public Library of Science

Author(s): Gabriela Moraes de Freitas, Julie Thomas, Rohana Liyanage, Jackson O. Lay, Supratim Basu, Venkategowda Ramegowda, Marcelo Nogueira do Amaral, Letícia Carvalho Benitez, Eugenia Jacira Bolacel Braga, Andy Pereira, Niranjan Baisakh.


Due to its tropical origin and adaptation, rice is significantly impacted by cold stress, and consequently sustains large losses in growth and productivity. Currently, rice is the second most consumed cereal in the world and production losses caused by extreme temperature events in the context of “major climatic changes” can have major impacts on the world economy. We report here an analysis of rice genotypes in response to low-temperature stress, studied through physiological gas-exchange parameters, biochemical changes in photosynthetic pigments and antioxidants, and at the level of gene and protein expression, towards an understanding and identification of multiple low-temperature tolerance mechanisms. The first effects of cold stress were observed on photosynthesis among all genotypes. However, the tropical japonica genotypes Secano do Brazil and Cypress had a greater reduction in gas exchange parameters like photosynthesis and water use efficiency in comparison to the temperate japonica Nipponbare and M202 genotypes. The analysis of biochemical profiles showed that despite the impacts of low temperature on tolerant plants, they quickly adjusted to maintain their cellular homeostasis by an accumulation of antioxidants and osmolytes like phenolic compounds and proline. The cold tolerant and sensitive genotypes showed a clear difference in gene expression at the transcript level for OsGH3-2, OsSRO1a, OsZFP245, and OsTPP1, as well as for expression at the protein level for LRR-RLKs, bHLH, GLYI, and LTP1 proteins. This study exemplifies the cold tolerant features of the temperate japonica Nipponbare and M202 genotypes, as observed through the analysis of physiological and biochemical responses and the associated changes in gene and protein expression patterns. The genes and proteins showing differential expression response are notable candidates towards understanding the biological pathways affected in rice and for engineering cold tolerance, to generate cultivars capable of maintaining growth, development, and reproduction under cold stress. We also propose that the mechanisms of action of the genes analyzed are associated with the tolerance response.

Partial Text

Climate change can strongly influence agriculture with temperature extremes, cold temperatures being a significant cause of damage in limiting crop yield. Although rice (Oryza sativa L.), is one of the world’s most important crops consumed as a major part of the diet [1], it is sensitive to cold compared to the temperate crops such as wheat and barley, due to its origin and adaptation for cultivation in tropical and subtropical regions of the world.

Rice is a major global food crop and a model crop for cereals. To understand the basis of acclimation stability under cold, we used a set of rice genotypes contrasting in their tolerance towards cold and evaluated the photosynthetic, biochemical, gene and protein expression response parameters. The results we describe here suggest the presence of complex mechanisms that involve the interaction of many biochemical and physiological pathways along with hormonal cross-talk contributing to cold tolerance.

This study supports that the genotypes Nipponbare and M202 have tolerance to low temperatures with the evidence of physiological responses, such as photosynthesis showing lower reduction, better efficient use of water without suffering photoinhibition, or reduction in the Quantum Efficiency of PSII. The biochemical profile showed that for the same genotypes, chlorophyll biosynthesis was not affected. Among the anthocyanins, a significant decrease in their content was observed, which identified pigments associated with the leaf mesophyll that act directly in the elimination of oxygen radicals produced by the chloroplasts. Accumulation of proline, glucose, and sucrose was also observed, these being osmoprotectants against freezing and dehydration damage. Antioxidants in the same tolerant genotypes, despite showing high production of H2O2 under stress, did not cause a high impact on the plasma membrane or the high activity of the antioxidant enzymes. SOD, CAT, POD and DPPH enzymes play an important role in stress tolerance. Differential expression of genes and proteins: the genes OsGH3-2, OsSRO1a, OsZFP245 and OsTPP1; and the LRR-RLKs, BHLH, GLYI, and LTP1 proteins, showed a clear difference in expression between tolerant and sensitive, thus suggesting that these genes are good candidates for identification of low-temperature tolerant genotypes in rice that are capable of maintaining growth, development, and production at the desired agronomic levels. Finally, based on our studies, a schematic representative model of cold tolerance in rice (Fig 6) is proposed outlining mechanisms of action of the genes analyzed with differential responses in resistant genotypes, with the objective of improving our understanding of the operation of tolerance to low temperatures. To summarize the results, our analysis shows for the first time the role of different antioxidants and osmolytes in modulating the physiological responses contributing to tolerance. In addition, this report also identifies markers for screening of cold tolerance in multiple rice genotypes, along with few putative protein markers identified from LCMS/MS analysis.