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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 35395

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Prof. Dr. Prasanta K. Subudhi

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School of Plant, Environmental, and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Interests: abiotic stress; rice; maize
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Rice (Oryza sativa L.) is a crop of global importance because it provides sustenance to more than half of the world population. Since the global population is expected to reach 9 billion by 2050, increased rice production will have a significant positive impact on global food security. However, rice farming in many parts of the world is threatened by a number of biotic and abiotic stresses due to climate change. To design novel rice genotypes, it is imperative to devise novel approaches to exploit world germplasm, understand the molecular basis of yield and yield component traits, tolerance to various biotic and abiotic stresses, and development of molecular tools to transfer desirable traits/genes. Due to spectacular advances in molecular biology, genetic engineering, and various omics fields, new molecular tools and technologies have been developed to realize these goals. As a model cereal crop due to its small genome size and genetic closeness to major cereal crops, advances in molecular research in rice will not only accelerate development of high yielding and stress tolerant rice varieties but also will help improve other cereal crops.

Contributions of both original research articles and reviews are welcome for this Special Issue on the following topics: novel approaches of germplasm utilization, application of next generation sequencing for rice improvement, mapping and cloning of genes and QTLs, development of tools for marker-assisted selection, molecular basis of biotic and abiotic stress tolerance, nutrient use efficiency, grain quality, and yield enhancing traits.

Prof. Dr. Prasanta K. Subudhi
Guest Editor

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Keywords

Molecular breeding and marker-assisted selection
QTL/Gene cloning
Next generation sequencing
Genetic engineering
Candidate genes
Germplasm enhancement
Biotic and abiotic stresses
Yield and quality traits

Published Papers (11 papers)

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Editorial

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5 pages, 200 KiB

Open AccessEditorial

Molecular Research in Rice

by Prasanta K. Subudhi

Int. J. Mol. Sci. 2023, 24(12), 10063; https://doi.org/10.3390/ijms241210063 - 13 Jun 2023

Cited by 2 | Viewed by 814

Abstract

Rice is the most important source of nutrition for approximately half of the human population [...] Full article

(This article belongs to the Special Issue Molecular Research in Rice)

Research

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25 pages, 16701 KiB

Open AccessArticle

OsMADS1 Regulates Grain Quality, Gene Expressions, and Regulatory Networks of Starch and Storage Protein Metabolisms in Rice

by Zhijian Liu, Penghui Li, Lan Yu, Yongzhi Hu, Anping Du, Xingyue Fu, Cuili Wu, Dagang Luo, Binhua Hu, Hui Dong, Haibo Jiang, Xinrong Ma, Weizao Huang, Xiaocheng Yang, Shengbin Tu and Hui Li

Int. J. Mol. Sci. 2023, 24(9), 8017; https://doi.org/10.3390/ijms24098017 - 28 Apr 2023

Cited by 4 | Viewed by 8137

Abstract

OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the ‘Oat-like rice’ mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1^Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1^Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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17 pages, 3580 KiB

Open AccessArticle

The Bph45 Gene Confers Resistance against Brown Planthopper in Rice by Reducing the Production of Limonene

by Charng-Pei Li, Dong-Hong Wu, Shou-Horng Huang, Menghsiao Meng, Hsien-Tzung Shih, Ming-Hsin Lai, Liang-Jwu Chen, Kshirod K. Jena, Sherry Lou Hechanova, Ting-Jyun Ke, Tai-Yuan Chiu, Zong-Yuan Tsai, Guo-Kai Chen, Kuan-Chieh Tsai and Wei-Ming Leu

Int. J. Mol. Sci. 2023, 24(2), 1798; https://doi.org/10.3390/ijms24021798 - 16 Jan 2023

Cited by 8 | Viewed by 2696

Abstract

Brown planthopper (BPH), a monophagous phloem feeder, consumes a large amount of photoassimilates in rice and causes wilting. A near-isogenic line ‘TNG71-Bph45’ was developed from the Oryza sativa japonica variety ‘Tainung 71 (TNG71) carrying a dominant BPH-resistance locus derived from Oryza nivara (IRGC 102165) near the centromere of chromosome 4. We compared the NIL (TNG71-Bph45) and the recurrent parent to explore how the Bph45 gene confers BPH resistance. We found that TNG71-Bph45 is less attractive to BPH at least partially because it produces less limonene. Chiral analysis revealed that the major form of limonene in both rice lines was the L-form. However, both L- and D-limonene attracted BPH when applied exogenously to TNG71-Bph45 rice. The transcript amounts of limonene synthase were significantly higher in TNG71 than in TNG71-Bph45 and were induced by BPH infestation only in the former. Introgression of the Bph45 gene into another japonica variety, Tainan 11, also resulted in a low limonene content. Moreover, several dominantly acting BPH resistance genes introduced into the BPH-sensitive IR24 line compromised its limonene-producing ability and concurrently decreased its attractiveness to BPH. These observations suggest that reducing limonene production may be a common resistance strategy against BPH in rice. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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15 pages, 2717 KiB

Open AccessArticle

The Role of Exogenous Gibberellic Acid and Methyl Jasmonate against White-Backed Planthopper (Sogatella furcifera) Stress in Rice (Oryza sativa L.)

by Saleem Asif, Yoon-Hee Jang, Eun-Gyeong Kim, Rahmatullah Jan, Sajjad Asaf, Muhammad Aaqil Khan, Muhammad Farooq, Lubna, Nari Kim, In-Jung Lee and Kyung-Min Kim

Int. J. Mol. Sci. 2022, 23(23), 14737; https://doi.org/10.3390/ijms232314737 - 25 Nov 2022

Cited by 3 | Viewed by 1719

Abstract

Rice (Oryza sativa L.) is one of the essential staple foods for more than half of the world’s population, and its production is affected by different environmental abiotic and biotic stress conditions. The white-backed planthopper (WBPH, Sogatella furcifera) causes significant damage to rice plants, leading to substantial economic losses due to reduced production. In this experiment, we applied exogenous hormones (gibberellic acid and methyl jasmonate) to WBPH-infested rice plants and examined the relative expression of related genes, antioxidant accumulation, the recovery rate of affected plants, endogenous hormones, the accumulation of H₂O₂, and the rate of cell death using DAB and trypan staining, respectively. The expression of the transcriptional regulator (OsGAI) and gibberellic-acid-mediated signaling regulator (OsGID2) was upregulated significantly in GA 50 µM + WBPH after 36 h. OsGAI was upregulated in the control, GA 50 µM + WBPH, GA 100 µM + WBPH, and MeJA 100 µM + WBPH. However, after 48 h, the OsGID2 was significantly highly expressed in all groups of plants. The glutathione (GSH) values were significantly enhanced by GA 100 µM and MeJA 50 µM treatment. Unlike glutathione (GSH), the catalase (CAT) and peroxidase (POD) values were significantly reduced in control + WBPH plants. However, a slight increase in CAT and POD values was observed in GA 50 + WBPH plants and a reduction in the POD value was observed in GA 100 µM + WBPH and MeJA 50 µM + WBPH plants. GA highly recovered the WBPH-affected rice plants, while no recovery was seen in MeJA-treated plants. MeJA was highly accumulated in control + WBPH, MeJA 50 µM + WBPH, and GA 100 µM + WBPH plants. The H₂O₂ accumulation was highly decreased in GA-treated plants, while extensive cell death was observed in MeJA-treated plants compared with GA-treated plants. From this study, we can conclude that the exogenous application of GA can overcome the effects of the WBPH and enhance resistance in rice. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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14 pages, 4270 KiB

Open AccessArticle

Identification of a Major QTL and Validation of Related Genes for Tiller Angle in Rice Based on QTL Analysis

by Dan-Dan Zhao, Yoon-Hee Jang, Muhammad Farooq, Jae-Ryoung Park, Eun-Gyeong Kim, Xiao-Xuan Du, Rahmatullah Jan, Kyung-Hwan Kim, Soo In Lee, Gang-Seob Lee and Kyung-Min Kim

Int. J. Mol. Sci. 2022, 23(9), 5192; https://doi.org/10.3390/ijms23095192 - 6 May 2022

Cited by 4 | Viewed by 2692

Abstract

An ideal plant architecture is an important condition to achieve high crop yields. The tiller angle is an important and complex polygenic trait of rice (Oryza sativa L.) plant architecture. Therefore, the discovery and identification of tiller angle-related genes can aid in the improvement of crop architecture and yield. In the present study, 222 SSR markers were used to establish a high-density genetic map of rice doubled haploid population, and a total of 8 quantitative trait loci (QTLs) were detected based on the phenotypic data of the tiller angle and tiller crown width over 2 years. Among them, four QTLs (qTA9, qCW9, qTA9-1, and qCW9-1) were overlapped at marker interval RM6235–RM24288 on chromosome 9 with a large effect value regarded as a stable major QTL. The selected promising related genes were further identified by relative gene expression analysis, which gives us a basis for the future cloning of these genes. Finally, OsSAURq9, which belongs to the SMALL AUXIN UP RNA (SAUR), an auxin-responsive protein family, was selected as a target gene. Overall, this work will help broaden our knowledge of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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19 pages, 2547 KiB

Open AccessArticle

Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-Wide Association Study of Thai Rice Populations

by Thammaporn Kojonna, Thiti Suttiyut, Nopphakhun Khunpolwattana, Monnat Pongpanich, Duangjai Suriya-arunroj, Luca Comai, Teerapong Buaboocha and Supachitra Chadchawan

Int. J. Mol. Sci. 2022, 23(3), 1842; https://doi.org/10.3390/ijms23031842 - 6 Feb 2022

Cited by 7 | Viewed by 2442

Abstract

Salt stress is a major limiting factor in crop production and yield in many regions of the world. The objective of this study was to identify the genes responsible for salt tolerance in Thai rice populations. We performed a genome-wide association study with growth traits, relative water content, and cell membrane stability at the seedling stage, and predicted 25 putative genes. Eleven of them were located within previously reported salt-tolerant QTLs (ST-QTLs). OsCRN, located outside the ST-QTLs, was selected for gene characterization using the Arabidopsis mutant line with T-DNA insertion in the orthologous gene. Mutations in the AtCRN gene led to the enhancement of salt tolerance by increasing the ability to maintain photosynthetic pigment content and relative water content, while the complemented lines with ectopic expression of OsCRN showed more susceptibility to salt stress detected by photosynthesis performance. Moreover, the salt-tolerant rice varieties showed lower expression of this gene than the susceptible rice varieties under salt stress conditions. The study concludes that by acting as a negative regulator, OsCRN plays an important role in salt tolerance in rice. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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18 pages, 4337 KiB

Open AccessArticle

Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice

by Richard S. Garcia, Sapphire Coronejo, Jonathan Concepcion and Prasanta K. Subudhi

Int. J. Mol. Sci. 2022, 23(3), 1608; https://doi.org/10.3390/ijms23031608 - 30 Jan 2022

Cited by 3 | Viewed by 3056

Abstract

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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15 pages, 1057 KiB

Open AccessArticle

Control of Thousand-Grain Weight by OsMADS56 in Rice

by Zi-Wei Zuo, Zhen-Hua Zhang, De-Run Huang, Ye-Yang Fan, Si-Bin Yu, Jie-Yun Zhuang and Yu-Jun Zhu

Int. J. Mol. Sci. 2022, 23(1), 125; https://doi.org/10.3390/ijms23010125 - 23 Dec 2021

Cited by 12 | Viewed by 3035

Abstract

Grain weight and size are important traits determining grain yield and influencing grain quality in rice. In a previous study, a quantitative trait locus controlling thousand-grain weight (TGW) in rice, qTGW10-20.8, was mapped in a 70.7 kb region on chromosome 10. Validation of the candidate gene for qTGW10-20.8, OsMADS56 encoding a MADS-box transcription factor, was performed in this study. In a near-isogenic line (NIL) population segregated only at the OsMADS56 locus, NILs carrying the OsMADS56 allele of IRBB52 were 1.9% and 2.9% lower in TGW than NILs carrying the OsMADS56 allele of Teqing in 2018 and 2020, respectively. Using OsMADS56 knock-out mutants and overexpression transgenic plants, OsMADS56 was validated as the causal gene for qTGW10-20.8. Compared with the recipients, the TGW of the knock-out mutants was reduced by 6.0–15.0%. In these populations, decreased grain weight and size were associated with a reduction in the expression of OsMADS56. In transgenic populations of OsMADS56 driven by a strong constitutive promoter, grain weight and size of the positive plants were significantly higher than those of the negative plants. Haplotype analysis showed that the Teqing-type allele of OsMADS56 is the major type presented in cultivated rice and used in variety improvement. Cloning of OsMADS56 provides a new gene resource to improve grain weight and size through molecular design breeding. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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16 pages, 4846 KiB

Open AccessArticle

Identification and Characterization of Short Crown Root 8, a Temperature-Sensitive Mutant Associated with Crown Root Development in Rice

by Peng Hu, Yi Wen, Yueying Wang, Hao Wu, Junge Wang, Kaixiong Wu, Bingze Chai, Lixin Zhu, Guangheng Zhang, Zhenyu Gao, Deyong Ren, Li Zhu, Longbiao Guo, Dali Zeng, Jing Xu, Song Yan, Qian Qian, Yuchun Rao and Jiang Hu

Int. J. Mol. Sci. 2021, 22(18), 9868; https://doi.org/10.3390/ijms22189868 - 13 Sep 2021

Cited by 3 | Viewed by 2359

Abstract

Crown roots are essential for plants to obtain water and nutrients, perceive environmental changes, and synthesize plant hormones. In this study, we identified and characterized short crown root 8 (scr8), which exhibited a defective phenotype of crown root and vegetative development. Temperature treatment showed that scr8 was sensitive to temperature and that the mutant phenotypes were rescued when grown under low temperature condition (20 °C). Histological and EdU staining analysis showed that the crown root formation was hampered and that the root meristem activity was decreased in scr8. With map-based cloning strategy, the SCR8 gene was fine-mapped to an interval of 126.4 kb on chromosome 8. Sequencing analysis revealed that the sequence variations were only found in LOC_Os08g14850, which encodes a CC-NBS-LRR protein. Expression and inoculation test analysis showed that the expression level of LOC_Os08g14850 was significantly decreased under low temperature (20 °C) and that the resistance to Xanthomonas oryzae pv. Oryzae (Xoo) was enhanced in scr8. These results indicated that LOC_Os08g14850 may be the candidate of SCR8 and that its mutation activated the plant defense response, resulting in a crown root growth defect. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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17 pages, 3055 KiB

Open AccessArticle

Modulation of Rice Leaf Angle and Grain Size by Expressing OsBCL1 and OsBCL2 under the Control of OsBUL1 Promoter

by Seonghoe Jang, Jwa-Yeong Cho, Gyung-Ran Do, Yeeun Kang, Hsing-Yi Li, Jaeeun Song, Ho-Youn Kim, Beom-Gi Kim and Yue-Ie Hsing

Int. J. Mol. Sci. 2021, 22(15), 7792; https://doi.org/10.3390/ijms22157792 - 21 Jul 2021

Cited by 7 | Viewed by 2777

Abstract

Leaf angle and grain size are important agronomic traits affecting rice productivity directly and/or indirectly through modulating crop architecture. OsBC1, as a typical bHLH transcription factor, is one of the components comprising a complex formed with LO9-177 and OsBUL1 contributing to modulation of rice leaf inclination and grain size. In the current study, two homologues of OsBC1, OsBCL1 and OsBCL2 were functionally characterized by expressing them under the control of OsBUL1 promoter, which is preferentially expressed in the lamina joint and the spikelet of rice. Increased leaf angle and grain length with elongated cells in the lamina joint and the grain hull were observed in transgenic rice containing much greater gibberellin A₃ (GA₃) levels than WT, demonstrating that both OsBCL1 and OsBCL2 are positive regulators of cell elongation at least partially through increased GA biosynthesis. Moreover, the cell elongation was likely due to cell expansion rather than cell division based on the related gene expression and, the cell elongation-promoting activities of OsBCL1 and OsBCL2 were functional in a dicot species, Arabidopsis. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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Review

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11 pages, 699 KiB

Open AccessReview

Grain Size Associated Genes and the Molecular Regulatory Mechanism in Rice

by Hongzhen Jiang, Anpeng Zhang, Xintong Liu and Jingguang Chen

Int. J. Mol. Sci. 2022, 23(6), 3169; https://doi.org/10.3390/ijms23063169 - 15 Mar 2022

Cited by 25 | Viewed by 3833

Abstract

Grain size is a quantitative trait that is controlled by multiple genes. It is not only a yield trait, but also an important appearance quality of rice. In addition, grain size is easy to be selected in evolution, which is also a significant trait for studying rice evolution. In recent years, many quantitative trait loci (QTL)/genes for rice grain size were isolated by map-based cloning or genome-wide association studies, which revealed the genetic and molecular mechanism of grain size regulation in part. Here, we summarized the QTL/genes cloned for grain size and the regulation mechanism with a view to provide the theoretical basis for improving rice yield and breeding superior varieties. Full article

(This article belongs to the Special Issue Molecular Research in Rice)

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