Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Gene Mining and Germplasm Innovation for the Important Traits in Rice

Special Issue Editors
Special Issue Information
Keywords
Published Papers

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: 25 August 2024 | Viewed by 7074

Share This Special Issue

Special Issue Editors

Prof. Dr. Yongmei Bao

E-Mail Website
Guest Editor

College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: rice disease resistance; seed health
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Shimin Zuo

E-Mail Website
Guest Editor

Department of Crop Genetics and Breeding, Agricultural College of Yangzhou University, Yangzhou, China
Interests: rice sheath blight; host disease resistance; host pathogen; breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rice is one of the most important crops, feeding half of the population worldwide, but diseases caused by fungi, bacteria, or viruses can seriously affect its yield and quality. Moreover, with the steady increase in population, a further increase in the rice yield is of particular importance. Breeding new rice varieties with a high yield and strong disease resistance is the simplest and most effective management strategy for diseases.

In recent years, rice has been recognized as a genetic model for molecular biology research aimed toward understanding high-quality mechanisms with a high yield and disease resistance. To date, significant progress has been achieved in the molecular genetics of rice yield and disease resistance. At least 2000 genes controlling important agronomic traits and disease resistance have been isolated, and their molecular biological mechanisms have also been partially characterized. IJMS, the International Journal of Molecular Science, has had increasing influence on the molecular genetics of rice important traits. This Special Issue of IJMS aims to highlight the new findings or the utilization of molecular research on the following areas:

The screening and development of rice disease-resistant germplasm;
The breeding of high-yield and disease-resistant rice cultivar through marker assisted selection and genome editing;
Inoculation methods and investigations;
The mapping and cloning of genes controlling rice with economically important traits (GWAS, etc.);
Molecular biology research on resistance and yield-associated traits;
Mechanisms of the rice–pathogen interaction.

Prof. Dr. Yongmei Bao
Prof. Dr. Shimin Zuo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

rice
gene mining
disease resistance
molecular design
gene editing
germplasm innovation

Published Papers (7 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

15 pages, 7273 KiB

Open AccessArticle

Genome-Wide Association Study Identifies Rice Panicle Blast-Resistant Gene Pb4 Encoding a Wall-Associated Kinase

by Yunxin Fan, Lu Ma, Xiaoqian Pan, Pujiang Tian, Wei Wang, Kunquan Liu, Ziwei Xiong, Changqing Li, Zhixue Wang, Jianfei Wang, Hongsheng Zhang and Yongmei Bao

Int. J. Mol. Sci. 2024, 25(2), 830; https://doi.org/10.3390/ijms25020830 - 09 Jan 2024

Viewed by 884

Abstract

Rice blast is one of the most devastating diseases, causing a significant reduction in global rice production. Developing and utilizing resistant varieties has proven to be the most efficient and cost-effective approach to control blasts. However, due to environmental pressure and intense pathogenic selection, resistance has rapidly broken down, and more durable resistance genes are being discovered. In this paper, a novel wall-associated kinase (WAK) gene, Pb4, which confers resistance to rice blast, was identified through a genome-wide association study (GWAS) utilizing 249 rice accessions. Pb4 comprises an N-terminal signal peptide, extracellular GUB domain, EGF domain, EGF-Ca²⁺ domain, and intracellular Ser/Thr protein kinase domain. The extracellular domain (GUB domain, EGF domain, and EGF-Ca²⁺ domain) of Pb4 can interact with the extracellular domain of CEBiP. Additionally, its expression is induced by chitin and polygalacturonic acid. Furthermore, transgenic plants overexpressing Pb4 enhance resistance to rice blast. In summary, this study identified a novel rice blast-resistant gene, Pb4, and provides a theoretical basis for understanding the role of WAKs in mediating rice resistance against rice blast disease. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Figure 1

21 pages, 5580 KiB

Open AccessArticle

The RING-Type Domain-Containing Protein GNL44 Is Essential for Grain Size and Quality in Rice (Oryza sativa L.)

by Lei He, Tao Chen, Wenhua Liang, Chunfang Zhao, Ling Zhao, Shu Yao, Lihui Zhou, Zhen Zhu, Qingyong Zhao, Kai Lu, Cailin Wang, Li Zhu and Yadong Zhang

Int. J. Mol. Sci. 2024, 25(1), 589; https://doi.org/10.3390/ijms25010589 - 02 Jan 2024

Viewed by 846

Abstract

Grain size in rice (Oryza sativa L.) shapes yield and quality, but the underlying molecular mechanism is not fully understood. We functionally characterized GRAIN NUMBER AND LARGE GRAIN SIZE 44 (GNL44), encoding a RING-type protein that localizes to the cytoplasm. The gnl44 mutant has fewer but enlarged grains compared to the wild type. GNL44 is mainly expressed in panicles and developing grains. Grain chalkiness was higher in the gnl44 mutant than in the wild type, short-chain amylopectin content was lower, middle-chain amylopectin content was higher, and appearance quality was worse. The amylose content and gel consistency of gnl44 were lower, and protein content was higher compared to the wild type. Rapid Visco Analyzer results showed that the texture of cooked gnl44 rice changed, and that the taste value of gnl44 was lower, making the eating and cooking quality of gnl44 worse than that of the wild type. We used gnl44, qgl3, and gs3 monogenic and two-gene near-isogenic lines to study the effects of different combinations of genes affecting grain size on rice quality-related traits. Our results revealed additive effects for these three genes on grain quality. These findings enrich the genetic resources available for rice breeders. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Figure 1

15 pages, 4627 KiB

Open AccessArticle

Conserved Residues Lys64 and Glu78 at the Subunit Surface of Tau Glutathione Transferase in Rice Affect Structure and Enzymatic Properties

by Xue Yang, Zhe Zhang, Lei Wu, Meiying Yang, Siyuan Li and Jie Gao

Int. J. Mol. Sci. 2024, 25(1), 398; https://doi.org/10.3390/ijms25010398 - 28 Dec 2023

Viewed by 559

Abstract

Glutathione transferases (GSTs) are a superfamily of dimeric proteins associated with the detoxification of various reactive electrophiles and responsive to a multitude of stressors. We individually substituted Lys64 and Glu78 with Ala using site-directed mutagenesis to understand the role of subunit interactions in the structure and enzymatic properties of a rice GST (OsGSTU17). The wild-type OsGSTU17 lost the conserved hydrogen bond between subunits in tau class GSTs due to conserved Tyr92 replaced with Phe92, but still exhibited high substrate activities, and thermal stability remained in its dimeric structure. The significant decrease in thermal stability and obvious changes in the structure of mutant K64A implied that conserved Lys64 might play an essential role in the structural stability of tau class GSTs. The mutant E78A, supposed to be deprived of hydrogen and salt bonds between subunits, appeared in the soluble form of dimers, even though its tertiary structure altered and stability declined dramatically. These results suggest that the hydrogen and ionic bonds provided by conserved residues are not as important for OsGSTU17 dimerization and enzymatic properties. These results further supplement our understanding of the relationship between the structure and function of GSTs and provide a theoretical basis for improving crop resistance through targeted modification of GSTs. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Figure 1

15 pages, 4119 KiB

Open AccessArticle

Overexpression of an ART1-Interacting Gene OsNAC016 Improves Al Tolerance in Rice

by Fuhang Liu, Dan Ma, Jinyu Yu, Ran Meng, Zhigang Wang, Baolei Zhang, Xingxiang Chen, Lin Zhang, Liyun Peng and Jixing Xia

Int. J. Mol. Sci. 2023, 24(23), 17036; https://doi.org/10.3390/ijms242317036 - 01 Dec 2023

Viewed by 1069

Abstract

Rice (Oryza sativa) exhibits tremendous aluminum (Al)-tolerance. The C2H2-transcription factor (TF) ART1 critically regulates rice Al tolerance via modulation of specific gene expression. However, little is known about the posttranscriptional ART1 regulation. Here, we identified an ART1-interacted gene OsNAC016 via a yeast two-hybrid (Y2H) assay. OsNAC016 was primarily expressed in roots and weakly induced by Al. Immunostaining showed that OsNAC016 was a nuclear protein and localized in all root cells. Knockout of OsNAC016 did not alter Al sensitivity. Overexpression of OsNAC016 resulted in less Al aggregation within roots and enhanced Al tolerance in rice. Based on transcriptomic and qRT-PCR evaluations, certain cell-wall-related or ART-regulated gene expressions such as OsMYB30 and OsFRDL4 were altered in OsNAC016-overexpressing plants. These results indicated that OsNAC016 interacts with ART1 to cooperatively regulate some Al-tolerance genes and is a critical regulatory factor in rice Al tolerance. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Figure 1

17 pages, 2785 KiB

Open AccessArticle

Insertion of Transposable Elements in AVR-Pib of Magnaporthe oryzae Leading to LOSS of the Avirulent Function

by Jinbin Li, Lin Lu, Chengyun Li, Qun Wang and Zhufeng Shi

Int. J. Mol. Sci. 2023, 24(21), 15542; https://doi.org/10.3390/ijms242115542 - 24 Oct 2023

Cited by 1 | Viewed by 841

Abstract

Rice blast is a very serious disease caused by Magnaporthe oryzae, which threatens rice production and food supply throughout the world. The avirulence (AVR) genes of rice blast are perceived by the corresponding rice blast resistance (R) genes and prompt specific resistance. A mutation in AVR is a major force for new virulence. Exploring mutations in AVR among M. oryzae isolates from rice production fields could aid assessment of the efficacy and durability of R genes. We studied the probable molecular-evolutionary patterns of AVR-Pib alleles by assaying their DNA-sequence diversification and examining their avirulence to the corresponding Pib resistance gene under natural conditions in the extremely genetically diverse of rice resources of Yunnan, China. PCRs detected results from M. oryzae genomic DNA and revealed that 162 out of 366 isolates collected from Yunnan Province contained AVR-Pib alleles. Among them, 36.1–73.3% isolates from six different rice production areas of Yunnan contained AVR-Pib alleles. Furthermore, 36 (28.6%) out of 126 isolates had a transposable element (TE) insertion in AVR-Pib, which resulted in altered virulence. The TE insertion was identified in isolates from rice rather than from Musa nana Lour. Twelve AVR-Pib haplotypes encoding three novel AVR-Pib variants were identified among the remaining 90 isolates. AVR-Pib alleles evolved to virulent forms from avirulent forms by base substitution and TE insertion of Pot2 and Pot3 in the 5′ untranslated region of AVR-Pib. These findings support the hypothesis that functional AVR-Pib possesses varied sequence structures and can escape surveillance by hosts via multiple variation manners. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Figure 1

16 pages, 3565 KiB

Open AccessArticle

Knocking Out OsAAP11 to Improve Rice Grain Quality Using CRISPR/Cas9 System

by Yihao Yang, Yi Zhang, Zixing Sun, Ziyan Shen, Youguang Li, Yifan Guo, Yuntong Feng, Shengyuan Sun, Min Guo, Zhi Hu and Changjie Yan

Int. J. Mol. Sci. 2023, 24(18), 14360; https://doi.org/10.3390/ijms241814360 - 21 Sep 2023

Cited by 1 | Viewed by 1043

Abstract

The demand for rice grain quality, particularly in terms of eating and cooking quality, is increasingly concerning at present. However, the limited availability of rice-quality-related gene resources and time-consuming and inefficient traditional breeding methods have severely hindered the pace of rice grain quality improvement. Exploring novel methods for improving rice grain quality and creating new germplasms is an urgent problem that needs to be addressed. In this study, an amino-acid-transporter-encoding gene OsAAP11 (Os11g0195600) mainly expressed in endosperm was selected as the target for gene editing using the CRISPR/Cas9 system in three japonica genetic backgrounds (Wuyungeng30, Nangeng9108, and Yanggeng158, hereafter referred to as WYG30, NG9108, and YG158). We successfully obtained homozygous osaap11 mutants without transgenic insertion. Subsequently, we conducted comprehensive investigations on the agronomic traits, rice grain quality traits, and transcriptomic analysis of these mutants. The results demonstrate that loss of OsAAP11 function led to a reduced amino acid content and total protein content in grains without affecting the agronomic traits of the plants; meanwhile, it significantly increased the peak viscosity, holding viscosity, and final viscosity values during the cooking process, thereby enhancing the eating and cooking quality. This study not only provides valuable genetic resources and fundamental materials for improving rice grain quality but also provides novel technical support for the rapid enhancement of rice grain quality. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Figure 1

13 pages, 3113 KiB

Open AccessArticle

Genome-Wide Association Study Identifies a Plant-Height—Associated Gene OsPG3 in a Population of Commercial Rice Varieties

by Shasha Peng, Yanchen Liu, Yuchen Xu, Jianhua Zhao, Peng Gao, Qi Liu, Shuangyong Yan, Yinghui Xiao, Shi-Min Zuo and Houxiang Kang

Int. J. Mol. Sci. 2023, 24(14), 11454; https://doi.org/10.3390/ijms241411454 - 14 Jul 2023

Viewed by 1325

Abstract

Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice’s molecular design breeding toward an ideal plant height. Full article

(This article belongs to the Special Issue Gene Mining and Germplasm Innovation for the Important Traits in Rice)

► Show Figures

Journal Menu

Journal Browser

Gene Mining and Germplasm Innovation for the Important Traits in Rice

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Published Papers (7 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI