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

Abstract

BackgroundRice 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.ResultsA 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.ConclusionsGenome-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.

Global transcriptional profiling of a cold‐tolerant rice variety under moderate cold stress reveals different cold stress response mechanisms

“…Using the same rice genotype (LTH) but severe cold condition (4°C), Zhang et al () observed that cold stress induced a continuous increase in DEGs and the number of upregulated genes clearly exceeded that of downregulated genes. Similar result was observed by Zhang et al () using two contrasting rice genotypes and 4°C for cold treatment. However, using the cold‐tolerant rice genotype Nipponbare and a milder cold stress (10°C), Yun et al () observed that the number of DEGs increased with time, but the number of downregulated genes was much more than that of upregulated genes during cold stress.…”

“…However, many of these studies were conducted under severe cold stress, i.e. 4°C (Rabbani et al , Zhang et al , ). Previous studies had shown that exposure to different low temperatures resulted in dissimilar injury symptoms, and tolerance to these different temperatures was conferred by separate QTLs (Andaya and Mackill , Zhan et al , Zhang et al ).…”

Identification and physiological characterization of two sister lines ofindicarice (Oryza sativaL.) with contrasting levels of cold tolerance

“…Although cold stress has an important impact on indica rice production in sub-tropical areas, reports about cold responses in different indica genotypes are rare (Zhang et al 2012a). Therefore, comparative studies between indica genotypes sensitive and tolerant to low temperature may help to understand possible tolerance mechanisms and to provide useful information to breeding programs aiming at indica genotypes adapted to temperature oscillations.…”

Fine Mapping of qRC10-2, a Quantitative Trait Locus for Cold Tolerance of Rice Roots at Seedling and Mature Stages

“…The collinearity of cold-tolerant genes between different species and the conservation in the cold-responsive pathway has been reported [30], [43], [44]. Therefore, Nipponbare ( japonica ) was selected as the reference genome to screen candidate genes.…”

“…Yang et al also identified Os10g0489500 as a gene up-regulated by low temperatures in a cold-tolerant variety [52]. After analyzing differentially-expressed transcripts in indica (K354) and japonica (C418) under controlled conditions (25°C) and cold stress (4°C) for 48 h, Zhang et al identified two terpene synthase genes ( Os02g36140 and Os08g07100 ) that were associated with signal transduction cascades from K354 during cold-stress responses in seedlings [44]. Another gene differentially-expressed between cold-tolerant and -sensitive plants was Os10g0490100 , which encoded virulence factors that degraded the pectin components of the plant cell wall [54], [55].…”