Genome-wide identification and extensive analysis of rice-endosperm preferred genes using reference expression database

Hong, Woo-Jong; Yoo, Yo-Han; Park, Sun‐A; Moon, Sunok; Kim, Sung-Ruyl; An, Gynheung; Jung, Ki‐Hong

doi:10.1007/s12374-016-0552-z

Cited by 13 publications

(8 citation statements)

References 30 publications

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“…Total RNA was obtained using Trizol following the manufacturer’s protocols and synthesized to complementary DNA (cDNA) by reverse transcriptase (Promega Corp., Madison, WI, United States). The expression of genes was estimated using Qiagen’s real-time PCR system with cycling conditions of 95°C for 30 s, 60°C for 30 s, and 72°C for 60 s. We used rice ubiquitin 5 ( OsUbi5, LOC_Os01g22490 ) as the internal control for all quantitative PCR reactions ( Hong et al, 2017 ). The list of primers used in this study is given in Supplementary Table S1 .…”

Section: Methodsmentioning

confidence: 99%

OsABCG9 Is an Important ABC Transporter of Cuticular Wax Deposition in Rice

et al. 2018

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The importance of the cuticular layer in regulating a plant’s water status and providing protection from environmental challenges has been recognized for a long time. The cuticular layer in plants restricts non-stomatal water loss and protects plants against damage from pathogen infection and UV radiation. Much genetic and biochemical research has been done about cutin and wax transportation in Arabidopsis thaliana, but little is known about it in rice. Here, we report that a rice ATP-binding cassette (ABC) transporter, OsABCG9, is essential for normal development during vegetative growth and could play a critical role in the transportation of epicuticular wax in rice. Rice phenotypes with mutated OsABCG9 exhibited growth retardation and sensitivity to low humidity. The total amount of cuticular wax on the leaves of the osabcg9-1 mutant diminished by 53% compared with the wild type, and wax crystals disappeared completely in osabcg9-2 mutant leaves. However, OsABCG9 does not seem to be involved in cutin transportation, even though its ortholog in Arabidopsis, AtABCG11, transports both wax and cutin. Furthermore, the osabcg9-1 mutant had increased leaf chlorophyll leaching and more severe drought susceptibility. This study provides new insights about differences between rice and A. thaliana in wax and cutin transportation associated with the ABCG family during evolution.

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Section: Methodsmentioning

confidence: 99%

OsABCG9 Is an Important ABC Transporter of Cuticular Wax Deposition in Rice

et al. 2018

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“…To examine GUS expression patterns, we germinated seeds from two promoter trap lines in an MS medium for 7 days. These lines were obtained from a mixed pool of PFG T-DNA tagging lines from POSTECH in Korea ( Lee et al, 2004 ; Jung et al, 2005 , 2006 , 2015 ; Hong et al, 2017 ; Wei et al, 2017 ). The resultant plantlets were then exposed to cold stress (4°C) for 0 or 24 h. Afterward, whole seedlings from all treatment groups were soaked for 8 h in a GUS -staining solution before their roots were photographed with a camera (Canon EOS 550D; Cannon, Tokyo, Japan).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

et al. 2017

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Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in ‘Dongjin,’ the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the ‘L-phenylalanine catabolic process,’ within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified ‘Major Metabolic’ processes and ‘Regulatory Gene Modules’ as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.

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“…To obtain a systemic view of the 1,695 leaf-preferred and ubiquitously expressed plastid-related genes within rice, we performed MapMan analysis as previously described [21]. In detail, we conducted the functional characterization of the genes by uploading the locus list with cluster information to MapMan software (v3.6.0 RC1) [22].…”

Section: Methodsmentioning

confidence: 99%

A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses

Yoo

Hong

Jung

2019

BioMed Research International

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Chloroplasts are intracellular semiautonomous organelles central to photosynthesis and are essential for plant growth and yield. The significance of the function of chloroplast-related genes in response to climate change has not been well studied in crops. In the present study, the initial focus was on genes that were predicted to be located in the chloroplast genome in rice, a model crop plant, with genes either preferentially expressed in the leaf or ubiquitously expressed in all organs. The characteristics were analyzed by Gene Ontology (GO) enrichment and MapMan functional classification tools. It was then identified that 110 GO terms (45 for leaf expression and 65 for ubiquitous expression) and 1,695 genes mapped to MapMan overviews were strongly associated with chloroplasts. In particular, the MapMan cellular response overview revealed a close association between heat stress response and chloroplast-related genes in rice. Moreover, features of these genes in response to abiotic stress were analyzed using a large-scale publicly available transcript dataset. Consequently, the expression of 215 genes was found to be upregulated in response to high temperature stress. Conversely, genes that responded to other stresses were extremely limited. In other words, chloroplast-related genes were found to affect abiotic stress response mainly through high temperature response, with little effect on response to drought and salinity stress. These results suggest that genes involved in diurnal rhythm in the leaves participate in the reaction to recognize temperature changes in the environment. Furthermore, the predicted protein–protein interaction network analysis associated with high temperature stress is expected to provide a very important basis for the study of molecular mechanisms by which chloroplasts will respond to future climate changes.

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Genome-wide identification and extensive analysis of rice-endosperm preferred genes using reference expression database

Cited by 13 publications

References 30 publications

OsABCG9 Is an Important ABC Transporter of Cuticular Wax Deposition in Rice

OsABCG9 Is an Important ABC Transporter of Cuticular Wax Deposition in Rice

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses

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