Genetic Regulation of Rice Development

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 3182

Special Issue Editors


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Guest Editor
Department of Crop Genetics and Breeding,China Agricultural University, Beijing 100193, China
Interests: rice grain yield; lodging resistance
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Guest Editor
College of Tropical Crops, Hainan University, Haikou 570228, China
Interests: rice; grain development; panicle development; grain size
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
Interests: plants; agriculture; plant breeding; crop science; rice germplasm; rice genetics

Special Issue Information

Dear Colleagues,

Rice originated in the tropics and subtropics and provides a staple food for more than half of the world's population. With the publication of the genome sequencing of rice varieties and the completion of re-sequencing of a large number of germplasm resources in recent decades, rice has become a classic model crop. It is used to explore the genetic formation of important agronomic traits and the molecular environmental adaptability of food crops. Genetic resources are the basis of crops’ genetic improvement. However, only about 10% of rice genes have been found and validated so far.  Therefore, it is of great significance to accelerate the accurate identification of rice genetic resources and their regulation during development, including rice plants’ architecture, grain yield, biological and abiotic stresses responses, and so on. Thus, this journal (Plants) organized a Special Issue on ’Genetic Regulation of Rice Development’, providing an excellent platform to present research on the genetic regulation of rice development.

Dr. Zhanying Zhang
Prof. Dr. Ran Xu
Dr. Yinghua Pan
Guest Editors

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Keywords

  • rice
  • genetics
  • germplasm
  • development

Published Papers (3 papers)

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Research

15 pages, 3567 KiB  
Article
SMS2, a Novel Allele of OsINV3, Regulates Grain Size in Rice
by Jianzhi Huang, Zelong Zhou, Ying Wang, Jing Yang, Xinyue Wang, Yijun Tang, Ran Xu, Yunhai Li and Lian Wu
Plants 2024, 13(9), 1219; https://doi.org/10.3390/plants13091219 - 28 Apr 2024
Viewed by 536
Abstract
Grain size has an important effect on rice yield. Although several key genes that regulate seed size have been reported in rice, their molecular mechanisms remain unclear. In this study, a rice small grain size 2 (sms2) mutant was identified, and [...] Read more.
Grain size has an important effect on rice yield. Although several key genes that regulate seed size have been reported in rice, their molecular mechanisms remain unclear. In this study, a rice small grain size 2 (sms2) mutant was identified, and MutMap resequencing analysis results showed that a 2 bp insertion in the second exon of the LOC_Os02g01590 gene resulted in a grain length and width lower than those of the wild-type Teqing (TQ). We found that SMS2 encoded vacuolar acid invertase, a novel allele of OsINV3, which regulates grain size. GO and KEGG enrichment analyses showed that SMS2 was involved in endoplasmic reticulum protein synthesis, cysteine and methionine metabolism, and propionic acid metabolism, thereby regulating grain size. An analysis of sugar content in young panicles showed that SMS2 reduced sucrose, fructose, and starch contents, thus regulating grain size. A haplotype analysis showed that Hap2 of SMS2 had a longer grain and was widely present in indica rice varieties. Our results provide a new theoretical basis for the molecular and physiological mechanisms by which SMS2 regulates grain size. Full article
(This article belongs to the Special Issue Genetic Regulation of Rice Development)
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30 pages, 6326 KiB  
Article
Physiological, Cytological, and Transcriptomic Analysis of Magnesium Protoporphyrin IX Methyltransferase Mutant Reveal Complex Genetic Regulatory Network Linking Chlorophyll Synthesis and Chloroplast Development in Rice
by Youming Yao, Hongyu Zhang, Rong Guo, Jiangmin Fan, Siyi Liu, Jianglin Liao, Yingjin Huang and Zhaohai Wang
Plants 2023, 12(21), 3785; https://doi.org/10.3390/plants12213785 - 6 Nov 2023
Cited by 1 | Viewed by 1311
Abstract
Functional defects in key genes for chlorophyll synthesis usually cause abnormal chloroplast development, but the genetic regulatory network for these key genes in regulating chloroplast development is still unclear. Magnesium protoporphyrin IX methyltransferase (ChlM) is a key rate-limiting enzyme in the process of [...] Read more.
Functional defects in key genes for chlorophyll synthesis usually cause abnormal chloroplast development, but the genetic regulatory network for these key genes in regulating chloroplast development is still unclear. Magnesium protoporphyrin IX methyltransferase (ChlM) is a key rate-limiting enzyme in the process of chlorophyll synthesis. Physiological analysis showed that the chlorophyll and carotenoid contents were significantly decreased in the chlm mutant. Transmission electron microscopy demonstrated that the chloroplasts of the chlm mutant were not well developed, with poor, loose, and indistinct thylakoid membranes. Hormone content analysis found that jasmonic acid, salicylic acid, and auxin accumulated in the mutant. A comparative transcriptome profiling identified 1534 differentially expressed genes (DEGs) between chlm and the wild type, including 876 up-regulated genes and 658 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these DEGs were highly involved in chlorophyll metabolism, chloroplast development, and photosynthesis. Protein−protein interaction network analysis found that protein translation played an essential role in the ChlM gene-regulated process. Specifically, 62 and 6 DEGs were annotated to regulate chlorophyll and carotenoid metabolism, respectively; 278 DEGs were predicted to be involved in regulating chloroplast development; 59 DEGs were found to regulate hormone regulatory pathways; 192 DEGs were annotated to regulate signal pathways; and 49 DEGs were putatively identified as transcription factors. Dozens of these genes have been well studied and reported to play essential roles in chlorophyll accumulation or chloroplast development, providing direct evidence for the reliability of the role of the identified DEGs. These findings suggest that chlorophyll synthesis and chloroplast development are actively regulated by the ChlM gene. And it is suggested that hormones, signal pathways, and transcription regulation were all involved in these regulation processes. The accuracy of transcriptome data was validated by quantitative real-time PCR (qRT-PCR) analysis. This study reveals a complex genetic regulatory network of the ChlM gene regulating chlorophyll synthesis and chloroplast development. The ChlM gene’s role in retrograde signaling was discussed. Jasmonic acid, salicylic acid, or their derivatives in a certain unknown state were proposed as retrograde signaling molecules in one of the signaling pathways from the chloroplast to nucleus. Full article
(This article belongs to the Special Issue Genetic Regulation of Rice Development)
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13 pages, 1609 KiB  
Article
In Silico Verification of Predicted Potential Promoter Sequences in the Rice (Oryza sativa) Genome
by Anastasiya N. Bubnova, Irina V. Yakovleva, Eugene V. Korotkov and Anastasiya M. Kamionskaya
Plants 2023, 12(20), 3573; https://doi.org/10.3390/plants12203573 - 14 Oct 2023
Viewed by 967
Abstract
The exact identification of promoter sequences remains a serious problem in computational biology, as the promoter prediction algorithms under development continue to produce false-positive results. Therefore, to fully assess the validity of predicted sequences, it is necessary to perform a comprehensive test of [...] Read more.
The exact identification of promoter sequences remains a serious problem in computational biology, as the promoter prediction algorithms under development continue to produce false-positive results. Therefore, to fully assess the validity of predicted sequences, it is necessary to perform a comprehensive test of their properties, such as the presence of downstream transcribed DNA regions behind them, or chromatin accessibility for transcription factor binding. In this paper, we examined the promoter sequences of chromosome 1 of the rice Oryza sativa genome from the Database of Potential Promoter Sequences predicted using a mathematical algorithm based on the derivation and calculation of statistically significant promoter classes. In this paper TATA motifs and cis-regulatory elements were identified in the predicted promoter sequences. We also verified the presence of potential transcription start sites near the predicted promoters by analyzing CAGE-seq data. We searched for unannotated transcripts behind the predicted sequences by de novo assembling transcripts from RNA-seq data. We also examined chromatin accessibility in the region of the predicted promoters by analyzing ATAC-seq data. As a result of this work, we identified the predicted sequences that are most likely to be promoters for further experimental validation in an in vivo or in vitro system. Full article
(This article belongs to the Special Issue Genetic Regulation of Rice Development)
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