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Gene Mining and Germplasm Innovation for the Important Traits in Rice

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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: 30 November 2024 | Viewed by 13629

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Prof. Dr. Yongmei Bao

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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

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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
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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

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Keywords

rice
gene mining
disease resistance
molecular design
gene editing
germplasm innovation

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Published Papers (10 papers)

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Research

20 pages, 7684 KiB

Open AccessArticle

Genome-Wide Analysis of Heat Shock Protein Family and Identification of Their Functions in Rice Quality and Yield

by Hong Wang, Sidra Charagh, Nannan Dong, Feifei Lu, Yixin Wang, Ruijie Cao, Liuyang Ma, Shiwen Wang, Guiai Jiao, Lihong Xie, Gaoneng Shao, Zhonghua Sheng, Shikai Hu, Fengli Zhao, Shaoqing Tang, Long Chen, Peisong Hu and Xiangjin Wei

Int. J. Mol. Sci. 2024, 25(22), 11931; https://doi.org/10.3390/ijms252211931 - 6 Nov 2024

Viewed by 547

Abstract

Heat shock proteins (Hsps), acting as molecular chaperones, play a pivotal role in plant responses to environmental stress. In this study, we found a total of 192 genes encoding Hsps, which are distributed across all 12 chromosomes, with higher concentrations on chromosomes 1, 2, 3, and 5. These Hsps can be divided into six subfamilies (sHsp, Hsp40, Hsp60, Hsp70, Hsp90, and Hsp100) based on molecular weight and homology. Expression pattern data indicated that these Hsp genes can be categorized into three groups: generally high expression in almost all tissues, high tissue-specific expression, and low expression in all tissues. Further analysis of 15 representative genes found that the expression of 14 Hsp genes was upregulated by high temperatures. Subcellular localization analysis revealed seven proteins localized to the endoplasmic reticulum, while others localized to the mitochondria, chloroplasts, and nucleus. We successfully obtained the knockout mutants of above 15 Hsps by the CRISPR/Cas9 gene editing system. Under natural high-temperature conditions, the mutants of eight Hsps showed reduced yield mainly due to the seed setting rate or grain weight. Moreover, the rice quality of most of these mutants also changed, including increased grain chalkiness, decreased amylose content, and elevated total protein content, and the expressions of starch metabolism-related genes in the endosperm of these mutants were disturbed compared to the wild type under natural high-temperature conditions. In conclusion, our study provided new insights into the HSP gene family and found that it plays an important role in the formation of rice quality and yield. Full article

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

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19 pages, 24465 KiB

Open AccessArticle

Identification and Characterization of Shaker Potassium Channel Gene Family and Response to Salt and Chilling Stress in Rice

by Quanxiang Tian, Tongyuan Yu, Mengyuan Dong, Yue Hu, Xiaoguang Chen, Yuan Xue, Yunxia Fang, Jian Zhang, Xiaoqin Zhang and Dawei Xue

Int. J. Mol. Sci. 2024, 25(17), 9728; https://doi.org/10.3390/ijms25179728 - 8 Sep 2024

Viewed by 794

Abstract

Shaker potassium channel proteins are a class of voltage-gated ion channels responsible for K⁺ uptake and translocation, playing a crucial role in plant growth and salt tolerance. In this study, bioinformatic analysis was performed to identify the members within the Shaker gene family. Moreover, the expression patterns of rice Shaker(OsShaker) K⁺ channel genes were analyzed in different tissues and salt treatment by RT–qPCR. The results revealed that there were eight OsShaker K⁺ channel genes distributed on chromosomes 1, 2, 5, 6 and 7 in rice, and their promoters contained a variety of cis-regulatory elements, including hormone-responsive, light-responsive, and stress-responsive elements, etc. Most of the OsShaker K⁺ channel genes were expressed in all tissues of rice, but at different levels in different tissues. In addition, the expression of OsShaker K⁺ channel genes differed in the timing, organization and intensity of response to salt and chilling stress. In conclusion, our findings provide a reference for the understanding of OsShaker K⁺ channel genes, as well as their potential functions in response to salt and chilling stress in rice. Full article

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

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14 pages, 1785 KiB

Open AccessArticle

The Waxy Gene Has Pleiotropic Effects on Hot Water-Soluble and -Insoluble Amylose Contents in Rice (Oryza sativa) Grains

by Hongkai Wu, Siyuan Wang and Min Wu

Int. J. Mol. Sci. 2024, 25(12), 6561; https://doi.org/10.3390/ijms25126561 - 14 Jun 2024

Viewed by 678

Abstract

Rice (Oryza sativa) is a cereal crop with a starchy endosperm. Starch is composed of amylose and amylopectin. Amylose content (AC) is the principal determinant of rice quality, but varieties with similar ACs can still vary substantially in their quality. In this study, we analyzed the total AC (TAC) and its constituent fractions, the hot water-soluble amylose content (SAC) and hot water-insoluble amylose content (IAC), in two sets of related chromosome segment substitution lines of rice with a common genetic background grown in two years. We searched for quantitative trait loci (QTLs) associated with SAC, IAC, and TAC and identified one common QTL (qSAC–6, qIAC–6, and qTAC–6) on chromosome 6. Map-based cloning revealed that the gene underlying the trait associated with this common QTL is Waxy (Wx). An analysis of the colors of soluble and insoluble starch–iodine complexes and their λ_max values (wavelengths at the positions of their peak absorbance values) as well as gel permeation chromatography revealed that Wx is responsible for the biosynthesis of amylose, comprising a large proportion of the soluble fractions of the SAC. Wx is also involved in the biosynthesis of long chains of amylopectin, comprising the hot water-insoluble fractions of the IAC. These findings highlight the pleiotropic effects of Wx on the SAC and IAC. This pleiotropy indicates that these traits have a positive genetic correlation. Therefore, further studies of rice quality should use rice varieties with the same Wx genotype to eliminate the pleiotropic effects of this gene, allowing the independent relationship between the SAC or IAC and rice quality to be elucidated through a multiple correlation analysis. These findings are applicable to other valuable cereal crops as well. Full article

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

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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 - 9 Jan 2024

Cited by 3 | Viewed by 1825

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)

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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 - 2 Jan 2024

Viewed by 1443

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)

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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 948

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)

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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 - 1 Dec 2023

Cited by 3 | Viewed by 1718

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)

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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 1260

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)

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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 8 | Viewed by 1661

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)

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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 1927

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)

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