Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background.

Fan Zhang,Xiuqin Zhao,Zhikang Li,Liyu Huang,Binying Fu,Wensheng Wang,Linghua Zhu

doi:10.1186/1471-2164-13-461

Abstract

Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354. A total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice. Genome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.

Highlights

Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss
A marked difference in survival rate was observed between K354 and C418 (Additional file 1), with K354 showing better cold tolerant (CT) and recovery ability than C418
Under control conditions K354 exhibited significantly lower superoxide dismutase (SOD) activity and soluble protein concentrations than C418, after 48 h of cold stress these parameters increased dramatically and reached higher values, even with different changing trends, in K354 compared with C418 (Additional file 2C and 2E)

Summary

Introduction

Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Low temperature stress retards rice seedling establishment and plant development, directly impacting yield. Cold stress tolerance mechanisms in plants include cold signal perception, activation of transcription factors (TFs) by signal transduction, and expression of coldresponsive genes for mediating stress tolerance [2]. OsFAD8 has a functional role in maintaining levels of trienoic fatty acids and stress tolerance at low temperatures in rice [5]. A plant of tropical and subtropical origin, lacks mechanisms for cold acclimation, it possesses components of this CBF cold-response pathway [8,9]. The rice R2R3-type OsMyb TF controls a hierarchical network comprising several regulatory sub-clusters associated with cellular defense and rescue, metabolism, and development This network is independent of CBF/DREB, and its sub-regulons operate with possible co-regulators, including nuclear factor-Y [11]. Constitutive and noncold responsive regulons, which have a differential effect on the cold responsive DRE regulon, play a key role in CT [13]

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Results

Conclusion