Comparative analysis of gene expression in response to cold stress in diverse rice genotypes

Abstract

Cold stress is a major factor affecting rice (Oryza sativa) growth and productivity, limiting its distribution worldwide. Rice production is affected primarily due to its vulnerability to cold stress at seedling stage, as well as reproductive stage leading to spikelet sterility. We report here the analysis of 21 diverse rice genotypes from the USDA mini-core collection for cold tolerance and categorized their tolerance levels on the basis of reduction in growth measured by root and shoot length. The screening identified 12 cold tolerant genotypes from which six tolerant genotypes were characterized at the vegetative stage for cold tolerance and gas-exchange parameters. Two tolerant and two sensitive genotypes were used further for gene expression analysis. Lipid Transfer Protein (LTP) genes showed a clear difference in expression between cold tolerant and sensitive genotypes suggesting that they are good candidates for engineering cold tolerance in rice. Nipponbare was identified as a cold tolerant genotype with stress tolerance mechanism potentially operating via both ABA dependent and independent pathways.

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

“…Lipid transfer proteins (LTPs) play an important role in abiotic stress tolerance [89], and can facilitate the inter-membrane exchange and transfer of various amphiphilic molecules including phospholipids, glycolipids, steroids, acyl-CoAs, and fatty acids [90]. Transcript levels of LTPs increased in response to drought [91], salt [92] and cold [93] and the increase of non-specific lipid-transfer protein 1 expression in tolerant genotypes give more support to its role of increasing tolerance to abiotic stress.…”

Physiological and transcriptional responses to low-temperature stress in rice genotypes at the reproductive stage

“…31 Previously, it was shown that LTPs are differentially expressed in response to cold stress in different rice genotypes. 22,27 Therefore, the role of LTPs was further investigated in response to low-temperature stress, for four rice genotypes in different tissues (flag leaf and inflorescence). The OsLTP7, OsLTP8, OsLTP10, OsLTP12, OsLTP14 and OsLTP25 genes are differentially expressed in different tissues in response to cold stress (Figure 3).…”

“…Rice genotypes Nipponbare (tolerant), M202 (tolerant), Cypress (sensitive) and Secano do Brazil (sensitive) were selected based on data collected from a previous screening experiment. 22 Seed were germinated and individual seedlings transplanted into 500 ml plastic pots, containing commercial potting soil substrate (Redi Earth). All genotypes were grown in the greenhouse (26/22°C ± 1°C with a photon flux density of 600 μmol −2 s −1 , light/dark cycle of 14/10 h), and the pots placed in trays full of water simulating flooded conditions.…”

“…Total RNA was extracted from the rice genotypes using Trizol reagent (Invitrogen), and cDNA was synthesized from 2 μg of total DNAseI-treated RNA using the GoScript™ reverse transcription system (Promega). The RT-qPCR reactions were performed using a GoTaq® qPCR Master Mix (Promega) kit with Ubiquitin as the internal reference gene 22 in the CFX-96 thermal cycler (Bio-Rad). A temperature gradient (0.5°C 10 s -1 ) from 55°C to 95°C was used for the analysis of the melting curve, and untranscribed RNA was used as a negative control.…”

“…In this study, four rice genotypes with contrasting response to cold identified from a previous study on cold stress at the vegetative growth stage, 22 were evaluated for the level of tolerance and sensitivity to cold stress caused by low temperatures at the reproductive stage and analyzed using physiological and productivity parameters. In addition, changes in gene expression of the flag leaf and inflorescence were characterized to study the association with the phenotypic response parameters in response to the stress treatments.…”