Research

12 pages, 3831 KiB

Open AccessArticle

Blocking Rice Shoot Gravitropism by Altering One Amino Acid in LAZY1

by Shuifu Chen, Yuqun Huang, Jingluan Han, Shijuan Zhang, Qiaoyu Yang, Zhijie Li, Ya Zhang, Runyuan Mao, Ling Fan, Yaoguang Liu, Yuanling Chen and Xianrong Xie

Int. J. Mol. Sci. 2022, 23(16), 9452; https://doi.org/10.3390/ijms23169452 - 21 Aug 2022

Cited by 3 | Viewed by 1744

Abstract

Tiller angle is an important trait that determines plant architecture and yield in cereal crops. Tiller angle is partially controlled during gravistimulation by the dynamic re-allocation of LAZY1 (LA1) protein between the nucleus and plasma membrane, but the underlying mechanism remains unclear. In [...] Read more.

Tiller angle is an important trait that determines plant architecture and yield in cereal crops. Tiller angle is partially controlled during gravistimulation by the dynamic re-allocation of LAZY1 (LA1) protein between the nucleus and plasma membrane, but the underlying mechanism remains unclear. In this study, we identified and characterized a new allele of LA1 based on analysis of a rice (Oryza sativa L.) spreading-tiller mutant la1^G74V, which harbors a non-synonymous mutation in the predicted transmembrane (TM) domain-encoding region of this gene. The mutation causes complete loss of shoot gravitropism, leading to prostrate growth of plants. Our results showed that LA1 localizes not only to the nucleus and plasma membrane but also to the endoplasmic reticulum. Removal of the TM domain in LA1 showed spreading-tiller phenotype of plants similar to la1^G74V but did not affect the plasma membrane localization; thus, making it distinct from its ortholog ZmLA1 in Zea mays. Therefore, we propose that the TM domain is indispensable for the biological function of LA1, but this domain does not determine the localization of the protein to the plasma membrane. Our study provides new insights into the LA1-mediated regulation of shoot gravitropism. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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15 pages, 3840 KiB

Open AccessArticle

Fine Mapping of qTGW7b, a Minor Effect QTL for Grain Weight in Rice (Oryza sativa L.)

by Houwen Gu, Kunming Zhang, Sadia Gull, Chuyan Chen, Jinhui Ran, Bingyin Zou, Ping Wang and Guohua Liang

Int. J. Mol. Sci. 2022, 23(15), 8296; https://doi.org/10.3390/ijms23158296 - 27 Jul 2022

Cited by 3 | Viewed by 1507

Abstract

Grain weight is a key trait that determines rice quality and yield, and it is primarily controlled by quantitative trait loci (QTL). Recently, attention has been paid to minor QTLs. A minor effect QTL qTGW7 that controls grain weight was previously identified in [...] Read more.

Grain weight is a key trait that determines rice quality and yield, and it is primarily controlled by quantitative trait loci (QTL). Recently, attention has been paid to minor QTLs. A minor effect QTL qTGW7 that controls grain weight was previously identified in a set of chromosomal fragment substitution lines (CSSLs) derived from Nipponbare (NPB)/93-11. Compared to NPB, the single segment substitution line (SSSL) N83 carrying the qTGW7 introgression exhibited an increase in grain length and width and a 4.5% increase in grain weight. Meanwhile, N83 was backcrossed to NPB to create a separating population, qTGW7b, a QTL distinct from qTGW7, which was detected between markers G31 and G32. Twelve near-isogenic lines (NILs) from the BC₉F₃ population and progeny of five NILs from the BC₉F_3:4 population were genotyped and phenotyped, resulting in the fine mapping of the minor effect QTL qTGW7b to the approximately 86.2-kb region between markers G72 and G32. Further sequence comparisons and expression analysis confirmed that five genes, including Os07g39370, Os07g39430, Os07g39440, Os07g39450, and Os07g39480, were considered as the candidate genes underlying qTGW7b. These results provide a crucial foundation for further cloning of qTGW7b and molecular breeding design in rice. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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14 pages, 3773 KiB

Open AccessArticle

Disruption of LLM9428/OsCATC Represses Starch Metabolism and Confers Enhanced Blast Resistance in Rice

by Yongxiang Liao, Asif Ali, Zhenzhen Xue, Xia Zhou, Wenwei Ye, Daiming Guo, Yingxiu Liao, Pengfei Jiang, Tingkai Wu, Hongyu Zhang, Peizhou Xu, Xiaoqiong Chen, Hao Zhou, Yutong Liu, Wenming Wang and Xianjun Wu

Int. J. Mol. Sci. 2022, 23(7), 3827; https://doi.org/10.3390/ijms23073827 - 30 Mar 2022

Cited by 2 | Viewed by 2411

Abstract

Catalases (CATs) are important self-originating enzymes and are involved in many of the biological functions of plants. Multiple forms of CATs suggest their versatile role in lesion mimic mutants (LMMs), H₂O₂ homeostasis and abiotic and biotic stress tolerance. In the [...] Read more.

Catalases (CATs) are important self-originating enzymes and are involved in many of the biological functions of plants. Multiple forms of CATs suggest their versatile role in lesion mimic mutants (LMMs), H₂O₂ homeostasis and abiotic and biotic stress tolerance. In the current study, we identified a large lesion mimic mutant9428 (llm9428) from Ethyl-methane-sulfonate (EMS) mutagenized population. The llm9428 showed a typical phenotype of LMMs including decreased agronomic yield traits. The histochemical assays showed decreased cell viability and increased reactive oxygen species (ROS) in the leaves of llm9428 compared to its wild type (WT). The llm9428 showed enhanced blast disease resistance and increased relative expression of pathogenesis-related (PR) genes. Studies of the sub-cellular structure of the leaf and quantification of starch contents revealed a significant decrease in starch granule formation in llm9428. Genetic analysis revealed a single nucleotide change (C > T) that altered an amino acid (Ala > Val) in the candidate gene (Os03g0131200) encoding a CATALASE C in llm9428. CRISPR-Cas9 targetted knockout lines of LLM9428/OsCATC showed the phenotype of LMMs and reduced starch metabolism. Taken together, the current study results revealed a novel role of OsCATC in starch metabolism in addition to validating previously studied functions of CATs. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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21 pages, 6976 KiB

Open AccessArticle

Global Identification and Characterization of C2 Domain-Containing Proteins Associated with Abiotic Stress Response in Rice (Oryza sativa L.)

by Hongjia Zhang, Yuting Zeng, Jeonghwan Seo, Yu-Jin Kim, Sun Tae Kim and Soon-Wook Kwon

Int. J. Mol. Sci. 2022, 23(4), 2221; https://doi.org/10.3390/ijms23042221 - 17 Feb 2022

Cited by 2 | Viewed by 2149

Abstract

C2 domain-containing proteins (C2DPs) have been identified in different genomes that contain single or multiple C2 domains in their C- or N-terminal. It possesses higher functional activity in the transmembrane regions. The identification of C2 domains were reported in a previous study, such [...] Read more.

C2 domain-containing proteins (C2DPs) have been identified in different genomes that contain single or multiple C2 domains in their C- or N-terminal. It possesses higher functional activity in the transmembrane regions. The identification of C2 domains were reported in a previous study, such as multiple C2 domains and transmembrane-region proteins (MCTPs) and N-terminal-TM-C2 domain proteins (NTMC2s) of rice, Arabidopsis thaliana, and cotton, whereas the C2DP gene family in rice has not been comprehensively studied, and the role of the C2DP gene in rice in response to abiotic stress is not yet fully understood. In this study, we identified 82 C2DPs in the rice genome and divided them into seven groups through phylogenetic analysis. The synteny analysis revealed that duplication events were either exhibited within the genome of rice or between the genomes of rice and other species. Through the analysis of cis-acting elements in promoters, expression profiles, and qRT-PCR results, the functions of OsC2DPs were found to be widely distributed in diverse tissues and were extensively involved in phytohormones-related and abiotic stresses response in rice. The prediction of the microRNA (miRNA) targets of OsC2DPs revealed the possibility of regulation by consistent miRNAs. Notably, OsC2DP50/51/52 as a co-tandem duplication exhibited similar expression variations and involved the coincident miRNA-regulation pathway. Moreover, the results of the genotypic variation and haplotype analysis revealed that OsC2DP17, OsC2DP29, and OsC2DP49 were associated with cold stress responses. These findings provided comprehensive insights for characterizations of OsC2DPs in rice as well as for their roles for abiotic stress. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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14 pages, 2608 KiB

Open AccessArticle

Molecular Insights into Salinity Responsiveness in Contrasting Genotypes of Rice at the Seedling Stage

by Jingjing Zhang, Tingting Xu, Yiran Liu, Tong Chen, Qiuxin Zhang, Weiyan Li, Hongkai Zhou, Yuexiong Zhang and Zemin Zhang

Int. J. Mol. Sci. 2022, 23(3), 1624; https://doi.org/10.3390/ijms23031624 - 30 Jan 2022

Cited by 11 | Viewed by 2878

Abstract

Salinity is one of the most common unfavorable environmental conditions that limits plant growth and development, ultimately reducing crop productivity. To investigate the underlying molecular mechanism involved in the salinity response in rice, we initially screened 238 rice cultivars after salt treatment at [...] Read more.

Salinity is one of the most common unfavorable environmental conditions that limits plant growth and development, ultimately reducing crop productivity. To investigate the underlying molecular mechanism involved in the salinity response in rice, we initially screened 238 rice cultivars after salt treatment at the seedling stage and identified two highly salt-tolerant cultivars determined by the relative damage rate parameter. The majority of cultivars (94.1%) were ranked as salt-sensitive and highly salt-sensitive. Transcriptome profiling was completed in highly salt-tolerant, moderately salt-tolerant, and salt-sensitive under water and salinity treatments at the seedling stage. Principal component analysis displayed a clear distinction among the three cultivars under control and salinity stress conditions. Several starch and sucrose metabolism-related genes were induced after salt treatment in all genotypes at the seedling stage. The results from the present study enable the identification of the ascorbate glutathione pathway, potentially participating in the process of plant response to salinity in the early growth stage. Our findings also highlight the significance of high-affinity K⁺ uptake transporters (HAKs) and high-affinity K⁺ transporters (HKTs) during salt stress responses in rice seedlings. Collectively, the cultivar-specific stress-responsive genes and pathways identified in the present study act as a useful resource for researchers interested in plant responses to salinity at the seedling stage. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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20 pages, 4474 KiB

Open AccessArticle

Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study

by Bingxin Meng, Tao Wang, Yi Luo, Ying Guo, Deze Xu, Chunhai Liu, Juan Zou, Lanzhi Li, Ying Diao, Zhiyong Gao, Zhongli Hu and Xingfei Zheng

Int. J. Mol. Sci. 2022, 23(3), 1065; https://doi.org/10.3390/ijms23031065 - 19 Jan 2022

Cited by 5 | Viewed by 3100

Abstract

Grain shape is an important agronomic character of rice, which affects the appearance, processing, and the edible quality. Screening and identifying more new genes associated with grain shape is beneficial to further understanding the genetic basis of grain shape and provides more gene [...] Read more.

Grain shape is an important agronomic character of rice, which affects the appearance, processing, and the edible quality. Screening and identifying more new genes associated with grain shape is beneficial to further understanding the genetic basis of grain shape and provides more gene resources for genetic breeding. This study has a natural population containing 623 indica rice cultivars. Genome-wide association studies/GWAS of several traits related to grain shape (grain length/GL, grain width/GW, grain length to width ratio/GLWR, grain circumferences/GC, and grain size/grain area/GS) were conducted by combining phenotypic data from four environments and the second-generation resequencing data, which have identified 39 important Quantitative trait locus/QTLs. We analyzed the 39 QTLs using three methods: gene-based association analysis, haplotype analysis, and functional annotation and identified three cloned genes (GS3, GW5, OsDER1) and seven new candidate genes in the candidate interval. At the same time, to effectively utilize the genes in the grain shape-related gene bank, we have also analyzed the allelic combinations of the three cloned genes. Finally, the extreme allele combination corresponding to each trait was found through statistical analysis. This study’s novel candidate genes and allele combinations will provide a valuable reference for future breeding work. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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31 pages, 39681 KiB

Open AccessArticle

RNA-Seq and Electrical Penetration Graph Revealed the Role of Grh1-Mediated Activation of Defense Mechanisms towards Green Rice Leafhopper (Nephotettix cincticeps Uhler) Resistance in Rice (Oryza sativa L.)

by Youngho Kwon, Nkulu Rolly Kabange, Ji-Yoon Lee, Bo Yoon Seo, Dongjin Shin, So-Myeong Lee, Jin-Kyung Cha, Jun-Hyeon Cho, Ju-Won Kang, Dong-Soo Park, Jong-Min Ko and Jong-Hee Lee

Int. J. Mol. Sci. 2021, 22(19), 10696; https://doi.org/10.3390/ijms221910696 - 02 Oct 2021

Cited by 6 | Viewed by 2883

Abstract

The green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is one of the most important insect pests causing serious damage to rice production and yield loss in East Asia. Prior to performing RNA-Seq analysis, we conducted an electrical penetration graph (EPG) test to investigate [...] Read more.

The green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is one of the most important insect pests causing serious damage to rice production and yield loss in East Asia. Prior to performing RNA-Seq analysis, we conducted an electrical penetration graph (EPG) test to investigate the feeding behavior of GRH on Ilpum (recurrent parent, GRH-susceptible cultivar), a near-isogenic line (NIL carrying Grh1) compared to the Grh1 donor parent (Shingwang). Then, we conducted a transcriptome-wide analysis of GRH-responsive genes in Ilpum and NIL, which was followed by the validation of RNA-Seq data by qPCR. On the one hand, EPG results showed differential feeding behaviors of GRH between Ilpum and NIL. The phloem-like feeding pattern was detected in Ilpum, whereas the EPG test indicated a xylem-like feeding habit of GRH on NIL. In addition, we observed a high death rate of GRH on NIL (92%) compared to Ilpum (28%) 72 h post infestation, attributed to GRH failure to suck the phloem sap of NIL. On the other hand, RNA-Seq data revealed that Ilpum and NIL GRH-treated plants generated 1,766,347 and 3,676,765 counts per million mapped (CPM) reads, respectively. The alignment of reads indicated that more than 75% of reads were mapped to the reference genome, and 8859 genes and 15,815,400 transcripts were obtained. Of this number, 3424 differentially expressed genes (DEGs, 1605 upregulated in Ilpum and downregulated in NIL; 1819 genes upregulated in NIL and downregulated in Ilpum) were identified. According to the quantile normalization of the fragments per kilobase of transcript per million mapped reads (FPKM) values, followed by the Student’s t-test (p < 0.05), we identified 3283 DEGs in Ilpum (1935 upregulated and 1348 downregulated) and 2599 DEGs in NIL (1621 upregulated and 978 downregulated) with at least a log₂ (logarithm base 2) twofold change (Log₂FC ≥2) in the expression level upon GRH infestation. Upregulated genes in NIL exceeded by 13.3% those recorded in Ilpum. The majority of genes associated with the metabolism of carbohydrates, amino acids, lipids, nucleotides, the activity of coenzymes, the action of phytohormones, protein modification, homeostasis, the transport of solutes, and the uptake of nutrients, among others, were abundantly upregulated in NIL (carrying Grh1). However, a high number of upregulated genes involved in photosynthesis, cellular respiration, secondary metabolism, redox homeostasis, protein biosynthesis, protein translocation, and external stimuli response related genes were found in Ilpum. Therefore, all data suggest that Grh1-mediated resistance against GRH in rice would involve a transcriptome-wide reprogramming, resulting in the activation of bZIP, MYB, NAC, bHLH, WRKY, and GRAS transcription factors, coupled with the induction of the pathogen-pattern triggered immunity (PTI), systemic acquired resistance (SAR), symbiotic signaling pathway, and the activation of genes associated with the response mechanisms against viruses. This comprehensive transcriptome profile of GRH-responsive genes gives new insights into the molecular response mechanisms underlying GRH (insect pest)–rice (plant) interaction. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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12 pages, 3812 KiB

Open AccessArticle

Rice OsWRKY50 Mediates ABA-Dependent Seed Germination and Seedling Growth, and ABA-Independent Salt Stress Tolerance

by Shuangzhan Huang, Lanjuan Hu, Shihan Zhang, Mingxing Zhang, Wenzhu Jiang, Tao Wu and Xinglin Du

Int. J. Mol. Sci. 2021, 22(16), 8625; https://doi.org/10.3390/ijms22168625 - 11 Aug 2021

Cited by 29 | Viewed by 3836

Abstract

Plant WRKY transcription factors play crucial roles in plant growth and development, as well as plant responses to biotic and abiotic stresses. In this study, we identified and characterized a WRKY transcription factor in rice, OsWRKY50. OsWRKY50 functions as a transcriptional repressor in [...] Read more.

Plant WRKY transcription factors play crucial roles in plant growth and development, as well as plant responses to biotic and abiotic stresses. In this study, we identified and characterized a WRKY transcription factor in rice, OsWRKY50. OsWRKY50 functions as a transcriptional repressor in the nucleus. The transcription of OsWRKY50 was repressed under salt stress conditions, but activated after abscisic acid (ABA) treatment. OsWRKY50-overexpression (OsWRKY50-OX) plants displayed increased tolerance to salt stress compared to wild type and control plants. The expression of OsLEA3, OsRAB21, OsHKT1;5, and OsP5CS1 in OsWRKY50-OX were much higher than wild type and control plants under salt stress. Furthermore, OsWRKY50-OX displayed hyposensitivity to ABA-regulated seed germination and seedling establishment. The protoplast-based transient expression system and yeast hybrid assay demonstrated that OsWRKY50 directly binds to the promoter of OsNCED5, and thus further inhibits its transcription. Taken together, our results demonstrate that rice transcription repressor OsWRKY50 mediates ABA-dependent seed germination and seedling growth and enhances salt stress tolerance via an ABA-independent pathway. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Genetics and Breeding)

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