Evidence map›Paper›PMID 39769145›Full record

ArticleInternational journal of molecular sciences2024

Comparative Transcriptomic Analysis and Candidate Gene Identification for Wild Rice (GZW) and Cultivated Rice (R998) Under Low-Temperature Stress.

Yongmei Yu, Dilin Liu, Feng Wang, Le Kong, Yanhui Lin, Leiqing Chen, Wenjing Jiang, Xueru Hou, Yanxia Xiao, Gongzhen Fu and 2 more

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Yongmei YuCollege of Agriculture, South China Agricultural University, Guangzhou 510642, China.
Dilin LiuRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.
Feng WangRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.
Le KongRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.
Yanhui LinInstitute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou 571100, China.
Leiqing ChenRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.ORCID 0009-0001-9394-6609
Wenjing JiangCollege of Agriculture, South China Agricultural University, Guangzhou 510642, China.
Xueru HouRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.
Yanxia XiaoCollege of Agriculture, South China Agricultural University, Guangzhou 510642, China.
Gongzhen FuCollege of Agriculture, South China Agricultural University, Guangzhou 510642, China.
Wuge LiuRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.
Xing HuoRice Research Institute, Guangdong Academy of Agricultural Sciences/South China High-Quality Rice Breeding Laboratory (Jointly Established by Ministry of Agriculture and Rural Affairs and Provincial Government)/Guangdong Key Laboratory of Rice Science and Technology/Guangdong Rice Engineering Laboratory, Guangzhou 510640, China.

Funding

Guangdong Key Laboratory of Rice Science and Technology 2023B1212060042National Key R&D Program of China 2022YFF1002600Supported by Research Fund of Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture 2022ZD007
6 · The paper itself

Abstract

Rice is a short-day thermophilic crop that originated from the low latitudes of the tropics and subtropics; it requires high temperatures for growth but is sensitive to low temperatures. Therefore, it is highly important to explore and analyze the molecular mechanism of cold tolerance in rice to expand rice planting areas. Here, we report a phenotypic evaluation based on low-temperature stress in indica rice (R998) and wild rice (GZW) and a comparative transcriptomic study conducted at six time points. After 7 days of low-temperature treatment at 10 °C, R998 exhibited obvious yellowing and greening of the leaves, while GZW exhibited high low-temperature resistance, and the leaves maintained their normal morphology and exhibited no yellowing; GZW has a higher survival rate. Principal component analysis (PCA) and cluster analysis of the RNA-seq data revealed that the difference in low-temperature resistance between the two cultivars was caused mainly by the difference in low-temperature treatment after 6 h. Differential expression analysis revealed 2615 unique differentially expressed genes (DEGs) in the R998 material, 1578 unique DEGs in the GZW material, 1874 unique DEGs between R998 and GZW, and 2699 DEGs that were differentially expressed not only between cultivars but also at different time points in the same material under low-temperature treatment. A total of 15,712 DEGs were detected and were significantly enriched in the phenylalanine metabolism, photosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. These 15,712 DEGs included 1937 genes encoding transcription factors (TFs), of which 10 have been identified with functional validation in previous studies. In addition, a gene regulatory network was constructed via weighted gene correlation network analysis (WGCNA), and 12 key genes related to low-temperature tolerance in rice were identified, including five genes encoding TFs, one of which was identified and verified in previous studies. These results provide a theoretical basis for an in-depth understanding of the molecular mechanism of low-temperature tolerance in rice and provide new genetic resources for the study of low-temperature tolerance in rice.

Indexed as

Gene Expression ProfilingGene Expression Regulation, PlantOryzaCold-Shock ResponseCold TemperaturePlant ProteinsTranscriptomePlant Proteinscoexpressionphotosynthesisricestarch and sucrose metabolismTFs

Identifiers

PMID39769145
PMCPMC11676510

What Socratic holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.