Liyu Huang

Comparative Transcriptome Profiling of Chilling Stress Responsiveness in Two Contrasting Rice Genotypes

Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed a differential constitutive gene expression prior to stress and distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in chilling-tolerant LTH compared with chilling-sensitive IR29, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in the chilling- tolerant genotype and strong repression in chilling-sensitive genotype. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in the chilling-tolerant genotype, while the chilling-sensitive genotype displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. A number of the chilling-regulated genes identified in this study were co-localized onto previously fine-mapped cold-tolerance-related QTLs, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for chilling tolerance in rice.

Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress

BackgroundRice (Oryza sativa. L) is more sensitive to drought stress than other cereals, and large genotypic variation in drought tolerance (DT) exists within the cultivated rice gene pool and its wild relatives. Selective introgression of DT donor segments into a drought-sensitive (DS) elite recurrent parent by backcrossing is an effective way to improve drought stress tolerance in rice. To dissect the molecular mechanisms underlying DT in rice, deep transcriptome sequencing was used to investigate transcriptome differences among a DT introgression line H471, the DT donor P28, and the drought-sensitive, recurrent parent HHZ under drought stress.ResultsThe results revealed constitutively differential gene expression before stress and distinct global transcriptome reprogramming among the three genotypes under a time series of drought stress, consistent with their different genotypes and DT phenotypes. A set of genes with higher basal expression in both H471 and P28 compared with HHZ were functionally enriched in oxidoreductase and lyase activities, implying their positive role in intrinsic DT. Gene Ontology analysis indicated that common up-regulated genes in all three genotypes under mild drought stress were enriched in signaling transduction and transcription regulation. Meanwhile, diverse functional categories were characterized for the commonly drought-induced genes in response to severe drought stress. Further comparative transcriptome analysis between H471 and HHZ under drought stress found that introgression caused wide-range gene expression changes; most of the differentially expressed genes (DEGs) in H471 relative to HHZ under drought were beyond the identified introgressed regions, implying that introgression resulted in novel changes in expression. Co-expression analysis of these DEGs represented a complex regulatory network, including the jasmonic acid and gibberellin pathway, involved in drought stress tolerance in H471.ConclusionsComprehensive gene expression profiles revealed that genotype-specific drought induced genes and genes with higher expression in the DT genotype under normal and drought conditions contribute jointly to DT improvement. The molecular genetic pathways of drought stress tolerance uncovered in this study, as well as the DEGs co-localized with DT-related QTLs and introgressed intervals, will serve as useful resources for further functional dissection of the molecular mechanisms of drought stress response in rice.

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

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.

Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling

Highlight Comprehensive analyses of phenotypic, metabolic, and transcriptome data from two genotypes with contrasting salt tolerance provided a more complete picture of the molecular mechanisms underlying seedling tolerance in rice.

Comparative Metabolite Profiling and Hormone Analysis of Perennial and Annual Rice

Perenniality is one of the important topics in rice breeding which is generally accompanied by complex physiobiochemical processes. To understand the metabolic characteristics of perennial rice, in the present study, gas chromatography–mass spectrometry and enzyme-linked immunosorbent assays were used to profile the distribution patterns of 33 primary metabolites and hormones [indole-3-acetic acid (IAA) and zeatin riboside (ZR)] of annual (RD23) and perennial (Oryza longistaminata and the line AA with RD23 genetic background) rice genotypes. Results showed that both metabolites and hormones have distinct genotype and organ distribution patterns, and considerable variations were observed between the metabolites in stem bases of perennial and annual rice. Most of the metabolites, including sugars, organic acids, and amino acids, significantly accumulated in the stem bases of perennial rice by decreasing the level in roots and leaves. Fifteen metabolites consistently accumulated significantly in the stem bases of both perennial genotypes. Additionally, the organ-level IAA content and IAA/ZR ratio in the two perennials were considerably higher than those in RD23. The present study indicated that the significant accumulation of the metabolites at stem base and the higher IAA/ZR ratio are involved in the regulatory metabolism for rhizome development.

Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing

Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.

Overlap between Signaling Pathways Responsive to Xanthomonas oryzae pv. oryzae Infection and Drought Stress in Rice Introgression Line Revealed by RNA-Seq

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), and drought stress are common reducers of rice yields in some regions of Asia and Africa. The rice introgression line H471 exhibits broad-spectrum dual resistance to Xoo and drought tolerance. To obtain a deeper understanding of crosstalk between signaling pathways in response to Xoo infection and drought stress, whole-genome transcriptome analyses of H471 and its recurrent parent Huang-Hua-Zhan (HHZ) were performed. A set of significant KEGG pathways involved in dual stress resistance were inferred by comparing H471 and HHZ samples under Xoo infection and drought stress using the gene set enrichment analysis method. We detected 178 genes that were differentially expressed in H471 common in response to the dual stresses when compared with HHZ, including genes for signaling perception and transduction, transcription regulation, and stress response. Putative common co-regulatory networks were constructed using 39 of the differentially expressed genes from the three different functional groups. These results will be a valuable source of information for further investigations on crosstalk between signaling pathways responsive to Xoo infection and drought stress in rice.

Identification and validation of root-specific promoters in rice

Abstract Novel promoters that confer root-specific expression would be useful for engineering resistance against problems of nutrient and water absorption by roots. In this study, the reverse transcriptase polymerase chain reaction was used to identify seven genes with root-specific expression in rice. The isolation and characterization of upstream promoter regions of five selected genes rice root-specific promoter (rRSP) 1 to 5 (rRSP1–rRSP5) and A2P (the promoter of OsAct2) revealed that rRSP1, rRSP3, and rRSP5 are particularly important with respect to root-specific activities. Furthermore, rRSP1, rRSP3, and rRSP5 were observed to make different contributions to root activities in various species. These three promoters could be used for root-specific enhancement of target gene(s).

Interacting Transcriptomes Revealing Molecular Mechanisms Underlying Xa39 Mediated Broad Spectrum Resistance of Rice to Bacterial Blight

Interaction between rice (Oryza sativa L.) and its bacterial blight (BB) pathogen Xanthomonas oryzae pv. oryzae (Xoo) is the model system between monocot plants and their bacterial pathogens. To understand the genome‐wide interactions between Xoo and rice resulting from a broad‐spectrum hypersensitive reaction (BSHR) mediated by a new rice resistance (R) gene, Xa39, comparative dynamic transcriptomic profiles in the incompatible and compatible interactions were investigated using three related rice lines and a highly virulent Xoo isolate, PXO99. Large numbers of rice and Xoo differentially expressed genes (DEGs) were identified in comparisons between the incompatible interactions and compatible ones, suggesting the gene network consisted of 27 genes in four groups of distinct functions involving leading to BSHR of rice in the sequential events from the avrXa39 × Xa39 interaction → signal recognition and transduction → protein modification → programmed cell death. Correspondingly, several groups of Xoo genes expressed or upregulated specifically in the incompatible interaction were those for type III secretion system (T3SS) and type III secretion effectors (T3SEs). Combined evidence suggests LOC_Os11g37759, one of a two‐member CC‐NBS‐LRR gene family on rice chromosome 11, as the most likely candidate for Xa39 in rice and two genes, XopN and XopX involved in T3SS of Xoo, as the most likely candidate genes for the corresponding avrXa39 in Xoo. Our transcriptome data and identified rice and Xoo DEGs provided a valuable source of information for future investigations on the Xoo–rice interactions.

Tissue-specific transcriptomic profiling of Sorghum propinquum using a rice genome array.

Sorghum (Sorghum bicolor) is one of the worlds most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development.