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Sun Y, Zhao H, Chen Z, Chen H, Li B, Wang C, Lin X, Cai Y, Zhou D, Ouyang L, Zhu C, He H, Peng X. Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice. PLANTS (BASEL, SWITZERLAND) 2022; 12:156. [PMID: 36616286 PMCID: PMC9824520 DOI: 10.3390/plants12010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.
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Affiliation(s)
- Yue Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huan Zhao
- Jiangxi Biotech Vocational College, JAU, Nanchang 330200, China
| | - Zhongkai Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Huizhen Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Bai Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Chunlei Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaoli Lin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Yicong Cai
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, JAU, Nanchang 330045, China
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Chen K, Shi Z, Zhang S, Wang Y, Xia X, Jiang Y, Gull S, Chen L, Guo H, Wu T, Zhang H, Liu J, Kong W. Methylation and Expression of Rice NLR Genes after Low Temperature Stress. Gene 2022; 845:146830. [PMID: 35995119 DOI: 10.1016/j.gene.2022.146830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/17/2022] [Accepted: 08/16/2022] [Indexed: 11/04/2022]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) are included in most plant disease resistance proteins. Some NLR proteins have been revealed to be induced by the invasion of plant pathogens. DNA methylation is required for adaption to adversity and proper regulation of gene expression in plants. Low temperature stress (LTS) is a restriction factor in rice growth, development and production. Here, we report the methylation and expression of NLR genes in two rice cultivars, i.e., 9311 (an indica rice cultivar sensitive to LTS), and P427 (a japonica cultivar, tolerant to LTS), after LTS. We found that the rice NLR genes were heavily methylated within CG sites at room temperature and low temperature in 9311 and P427, and many rice NLR genes showed DNA methylation alteration after LTS. A great number of rice NLR genes were observed to be responsive to LTS at the transcriptional level. Our observation suggests that the alteration of expression of rice NLR genes was similar but their change in DNA methylation was dynamic between the two rice cultivars after LTS. We identified that more P427 NLR genes reacted to LTS than those of 9311 at the methylation and transcriptional level. The results in this study will be useful for further understanding the transcriptional regulation and potential functions of rice NLR genes.
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Affiliation(s)
- Kun Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Zuqi Shi
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shengwei Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yanxin Wang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xue Xia
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yan Jiang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Sadia Gull
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Lin Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hui Guo
- Rice Research Institute, Guizhou Provincial Academy of Agriculture Sciences, Guiyang, 550006, China
| | - Tingkai Wu
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Hongyu Zhang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jinglan Liu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
| | - Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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3
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Pang H, Chen Q, Li Y, Wang Z, Wu L, Yang Q, Zheng X. Comparative analysis of the transcriptomes of two rice subspecies during domestication. Sci Rep 2021; 11:3660. [PMID: 33574456 PMCID: PMC7878495 DOI: 10.1038/s41598-021-83162-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/28/2021] [Indexed: 11/11/2022] Open
Abstract
Two subspecies of rice, Oryza sativa ssp. indica and O. sativa ssp. japonica, with reproductive isolation and differences in morphology and phenotypic differences, were established during the process of rice domestication. To understand how domestication has changed the transcriptomes of the two rice subspecies and given rise to the phenotypic differences, we obtained approximately 700 Gb RNA-Seq data from 26 indica and 25 japonica accessions, and identified 97,005 transcribed fragments and 4579 novel transcriptionally active regions. The two rice subspecies had significantly different gene expression profiles, we identified 1,357 (3.3% in all genes) differentially expressed genes (DEGs) between indica and japonica rice. Combining existing gene function studies, it is found that some of these differential genes are related to the differentiation of the two subspecies, such as grain shape and cold tolerance, etc. Functional annotation of these DEGs indicates that they are involved in cell wall biosynthesis and reproductive processes. Furthermore, compared with the non-DEGs, the DEGs from both subspecies had more 5'flanking regions with low polymorphism to divergence ratios, indicating a stronger positive selection pressure on the regulation of the DEGs. This study improves our understanding of the rice genome by comparatively analyzing the transcriptomes of indica and japonica rice and identifies DEGs those may be responsible for the reproductive isolation and phenotypic differences between the two rice subspecies.
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Affiliation(s)
- Hongbo Pang
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qiang Chen
- Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Yueying Li
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Ze Wang
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Longkun Wu
- College of Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Qingwen Yang
- Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoming Zheng
- Center for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Tian D, Chen Z, Lin Y, Chen Z, Bui KT, Wang Z, Wang F. Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice. RICE (NEW YORK, N.Y.) 2020; 13:81. [PMID: 33306159 PMCID: PMC7732884 DOI: 10.1186/s12284-020-00439-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Rice blast, caused by the ascomycete fungus M. oryzae, is one of the most important diseases of rice. Although many blast resistance (R) genes have been identified and deployed in rice varieties, the molecular mechanisms responsible for the R gene-mediated defense responses are yet not fully understood. RESULTS In this study, we used comparative transcriptomic analysis to explore the molecular mechanism involved in Piz-t-mediated resistance in a transgenic line containing Piz-t (NPB-Piz-t) compared to Nipponbare (NPB). Clustering and principal component analysis (PCA) revealed that the time-point at 24-h post inoculation (hpi) was the most important factor distinguishing the four time-points, which consisted of four genes of mitogen-activated protein kinases (MAPKs) signaling pathway, one gene related to WRKY DNA-binding domain containing protein, five pathogenesis-related protein (OsPR1s) genes, and three genes of R proteins involving in the most significant protein-protein interaction (PPI) pathway. Using weighted gene co-expression network analysis (WGCNA) to investigate RNA-seq data across 0, 24, 48, and 72 hpi, nine modules with similar patterns expression pattern (SEP) and three modules with differential expression pattern (DEP) between NPB-Piz-t and NPB across 0, 24, 48, and 72 hpi with KJ201 (referred to as Piz-t-KJ201 and NPB-KJ201) were identified. Among these the most representative SEP green-yellow module is associated with photosynthesis, and DEP pink module comprised of two specific expressed nucleotide-binding domain and leucine-rich repeat (NLR) genes of LOC_Os06g17900 and LOC_Os06g17920 of Pi2/9 homologous, three NLR genes of LOC_Os11g11810, LOC_Os11g11770, and LOC_Os11g11920 which are putatively associated with important agronomic traits, and a B3 DNA binding domain containing protein related genes (LOC_Os10g39190). Knockout of LOC_Os10g39190 via CRISPR-Cas9 resulted in plant death at the seedling stage. CONCLUSIONS The research suggested that Piz-t and multiple NLR network might play important roles in the regulation of the resistance response in the Piz-t-KJ201 interaction system. The identified genes provide an NLR repository to study the rice-M. oryzae interaction system and facilitate the breeding of blast-resistant cultivars in the future.
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Affiliation(s)
- Dagang Tian
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zaijie Chen
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Yan Lin
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Ziqiang Chen
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Khuynh The Bui
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Feng Wang
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.
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5
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Liu Q, Yang X, Tzin V, Peng Y, Romeis J, Li Y. Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2236-2249. [PMID: 32593184 PMCID: PMC7540705 DOI: 10.1111/tpj.14895] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 05/09/2023]
Abstract
Advancements in -omics techniques provide powerful tools to assess the potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering (GE) causes changes in plants that go beyond the changes introduced by conventional plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis genes developed by GE and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines were. Metabolome profiling analysis found several new metabolites in GE rice lines when compared with the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both GE and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and high-performance liquid chromatography mass spectrometry technology to assess the unintended changes in new rice varieties, and the results suggest that GE does not cause unintended effects that go beyond conventional cross-breeding in rice.
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Affiliation(s)
- Qingsong Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
- College of Life SciencesXinyang Normal UniversityXinyang464000People’s Republic of China
| | - Xiaowei Yang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of DrylandsJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevSede Boqer CampusMidreseht Ben Gurion8499000Israel
| | - Yufa Peng
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
| | - Jörg Romeis
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
- Agroscope, Research Division Agroecology and EnvironmentZurich8046Switzerland
| | - Yunhe Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193People’s Republic of China
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6
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Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H. Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). BMC Genomics 2020; 21:394. [PMID: 32513103 PMCID: PMC7278148 DOI: 10.1186/s12864-020-06786-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/19/2020] [Indexed: 01/24/2023] Open
Abstract
Background Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). Results The transcriptomes of the two subspecies of rice are highly divergent. Japonica have significantly lower expression and genetic diversity relative to Indica, which is likely a consequence of a population bottleneck during Japonica domestication. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. Conclusions Using RNA sequencing data for 91diverse rice accessions and high-density genotypic data, we show that the two species are highly divergent with respect to gene expression levels, as well as the genetic regulation of expression. The data generated by this study provide, to date, the largest collection of genome-wide transcriptional levels for rice, and provides a community resource to accelerate functional genomic studies in rice.
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Affiliation(s)
- Malachy T Campbell
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, 1825 N 38th St., Lincoln, 68583, NE, USA. .,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Drive, Blacksburg, 24060, VA, USA.
| | - Qian Du
- School of Biological Sciences, University of Nebraska Lincoln, 1901 Vine St., Lincoln, 68503, NE, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska Lincoln, 1901 Vine St., Lincoln, 68503, NE, USA
| | - Sandeep Sharma
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, 1825 N 38th St., Lincoln, 68583, NE, USA.,Marine Biotechnology and Ecology Division, CSIR-CSMCRI, Bhavnagar, Gujarat, India
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska Lincoln, 1901 Vine St., Lincoln, 68503, NE, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, 1825 N 38th St., Lincoln, 68583, NE, USA.
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7
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Zhao N, Sheng M, Zhao J, Ma X, Wei Q, Song Q, Zhang K, Xu W, Sun C, Liu F, Su Z. Over-Expression of HDA710 Delays Leaf Senescence in Rice ( Oryza sativa L.). Front Bioeng Biotechnol 2020; 8:471. [PMID: 32509751 PMCID: PMC7248171 DOI: 10.3389/fbioe.2020.00471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/22/2020] [Indexed: 11/13/2022] Open
Abstract
Histone deacetylases (HDACs) influence chromatin state and gene expression. Eighteen HDAC genes with important biological functions have been identified in rice. In this study, we surveyed the gene presence frequency of all 18 rice HDAC genes in 3,010 rice accessions. HDA710/OsHDAC2 showed insertion/deletion (InDel) polymorphisms in almost 98.8% japonica accessions but only 1% indica accessions. InDel polymorphism association analysis showed that accessions with partial deletions in HDA710 tended to display early leaf senescence. Further transgenic results confirmed that HDA710 delayed leaf senescence in rice. The over-expression of HDA710 delayed leaf senescence, and the knock-down of HDA710 accelerated leaf senescence. Transcriptome analysis showed that photosynthesis and chlorophyll biosynthesis related genes were up-regulated in HDA710 over-expression lines, while some programmed cell death and disease resistance related genes were down-regulated. Co-expression network analysis with gene expression view revealed that HDA710 was co-expressed with multiple genes, particularly OsGSTU12, which was significantly up-regulated in 35S::HDA710-sense lines. InDels in the promoter region of OsGSTU12 and in the gene region of HDA710 occurred coincidentally among more than 90% accessions, and we identified multiple W-box motifs at the InDel position of OsGSTU12. Over-expression of OsGSTU12 also delayed leaf senescence in rice. Taken together, our results suggest that both HDA710 and OsGSTU12 are involved in regulating the process of leaf senescence in rice.
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Affiliation(s)
- Nannan Zhao
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Minghao Sheng
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jie Zhao
- Beijing Key Laboratory of Crop, Ministry of Education (MOE) Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing, China.,Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xuelian Ma
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qiang Wei
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qian Song
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kang Zhang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chuanqing Sun
- Beijing Key Laboratory of Crop, Ministry of Education (MOE) Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing, China.,Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Fengxia Liu
- Beijing Key Laboratory of Crop, Ministry of Education (MOE) Laboratory of Crop Heterosis and Utilization, National Center for Evaluation of Agricultural Wild Plants (Rice), Beijing, China.,Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, Beijing, China
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8
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Zhou Q, Fu H, Yang D, Ye C, Zhu S, Lin J, Ye W, Ji G, Ye X, Wu X, Li QQ. Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:260-276. [PMID: 30570805 DOI: 10.1111/tpj.14209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 05/25/2023]
Abstract
Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3' untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Dewei Yang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Sheng Zhu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Wenbin Ye
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xinfu Ye
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China
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9
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Chen J, Hu L, Sun L, Lin B, Huang K, Zhuo K, Liao J. A novel Meloidogyne graminicola effector, MgMO237, interacts with multiple host defence-related proteins to manipulate plant basal immunity and promote parasitism. MOLECULAR PLANT PATHOLOGY 2018; 19:1942-1955. [PMID: 29485753 PMCID: PMC6638000 DOI: 10.1111/mpp.12671] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 05/04/2023]
Abstract
Plant-parasitic nematodes can secrete effector proteins into the host tissue to facilitate their parasitism. In this study, we report a novel effector protein, MgMO237, from Meloidogyne graminicola, which is exclusively expressed within the dorsal oesophageal gland cell and markedly up-regulated in parasitic third-/fourth-stage juveniles of M. graminicola. Transient expression of MgMO237 in protoplasts from rice roots showed that MgMO237 was localized in the cytoplasm and nucleus of the host cells. Rice plants overexpressing MgMO237 showed an increased susceptibility to M. graminicola. In contrast, rice plants expressing RNA interference vectors targeting MgMO237 showed an increased resistance to M. graminicola. In addition, yeast two-hybrid and co-immunoprecipitation assays showed that MgMO237 interacted specifically with three rice endogenous proteins, i.e. 1,3-β-glucan synthase component (OsGSC), cysteine-rich repeat secretory protein 55 (OsCRRSP55) and pathogenesis-related BetvI family protein (OsBetvI), which are all related to host defences. Moreover, MgMO237 can suppress host defence responses, including the expression of host defence-related genes, cell wall callose deposition and the burst of reactive oxygen species. These results demonstrate that the effector MgMO237 probably promotes the parasitism of M. graminicola by interacting with multiple host defence-related proteins and suppressing plant basal immunity in the later parasitic stages of nematodes.
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Affiliation(s)
- Jiansong Chen
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Lili Hu
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Longhua Sun
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Borong Lin
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Kun Huang
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
| | - Kan Zhuo
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
| | - Jinling Liao
- Laboratory of Plant NematologySouth China Agricultural UniversityGuangzhou510642China
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlSouth China Agricultural UniversityGuangzhou510642China
- Department of Eco‐engineering, Guangdong Eco‐Engineering PolytechnicGuangzhou510520China
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10
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Chandran AKN, Bhatnagar N, Yoo YH, Moon S, Park SA, Hong WJ, Kim BG, An G, Jung KH. Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles. PLANT MOLECULAR BIOLOGY 2018; 96:17-34. [PMID: 29086189 DOI: 10.1007/s11103-017-0675-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
This work suggests 2020 potential candidates in rice for the functional annotation of unannotated genes using meta-analysis of anatomical samples derived from microarray and RNA-seq technologies and this information will be useful to identify novel morphological agronomic traits. Although the genome of rice (Oryza sativa) has been sequenced, 14,365 genes are considered unannotated because they lack putative annotation information. According to the Rice Genome Annotation Project Database ( http://rice.plantbiology.msu.edu/ ), the proportion of functionally characterized unannotated genes (0.35%) is quite limited when compared with the approximately 3.9% of annotated genes with assigned putative functions. Researchers require additional information to help them investigate the molecular mechanisms associated with those unannotated genes. To determine which of them might regulate morphological or physiological traits in the rice genome, we conducted a meta-analysis of expression data that covered a wide range of tissue/organ samples. Overall, 2020 genes showed cultivar-, tissue-, or organ-preferential patterns of expression. Representative candidates from featured groups were validated by RT-PCR, and the GUS reporter system was used to validate the expression of genes that were clustered according to their leaf or root preference. Taking a molecular and genetics approach, we examined meta-expression data and found that 127 genes were differentially expressed between japonica and indica rice cultivars. This is potentially significant for future agronomic applications. We also used a T-DNA insertional mutant and performed a co-expression network analysis of Sword shape dwarf1 (SSD1), a gene that regulates cell division. This network was refined via RT-PCR analysis. Our results suggested that SSD1 represses the expression of four genes related to the processes of DNA replication or cell division and provides insight into possible molecular mechanisms. Together, these strategies present a valuable tool for in-depth characterization of currently unannotated genes.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Nikita Bhatnagar
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sun-Ah Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Beom-Gi Kim
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 54875, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
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11
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De Schutter K, Tsaneva M, Kulkarni SR, Rougé P, Vandepoele K, Van Damme EJM. Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa). RICE (NEW YORK, N.Y.) 2017; 10:26. [PMID: 28560587 PMCID: PMC5449364 DOI: 10.1186/s12284-017-0164-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Lectins, defined as 'Proteins that can recognize and bind specific carbohydrate structures', are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins. RESULTS Despite the availability of multiple completely sequenced rice genomes, little is known on the occurrence of lectins in rice. We identified 329 putative lectin genes in the genome of Oryza sativa subsp. japonica belonging to nine out of 12 plant lectin families. In this paper, an in-depth molecular characterization of the EUL family of rice was performed. In addition, analyses of the promoter sequences and investigation of the transcript levels for these EUL genes enabled retrieval of important information related to the function and stress responsiveness of these lectins. Finally, a comparative analysis between rice cultivars and several monocot and dicot species revealed a high degree of sequence conservation within the EUL domain as well as in the domain organization of these lectins. CONCLUSIONS The presence of EULs throughout the plant kingdom and the high degree of sequence conservation in the EUL domain suggest that these proteins serve an important function in the plant cell. Analysis of the promoter region of the rice EUL genes revealed a diversity of stress responsive elements. Furthermore analysis of the expression profiles of the EUL genes confirmed that they are differentially regulated in response to several types of stress. These data suggest a potential role for the EULs in plant stress signaling and defense.
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Affiliation(s)
- Kristof De Schutter
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Mariya Tsaneva
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Pierre Rougé
- UMR 152 PHARMA-DEV, Université de Toulouse, IRD, UPS, Chemin des Maraîchers 35, 31400, Toulouse, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
| | - Els J M Van Damme
- Laboratory Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, B-9000, Ghent, Belgium.
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12
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Zhang J, Chen K, Pang Y, Naveed SA, Zhao X, Wang X, Wang Y, Dingkuhn M, Pasuquin J, Li Z, Xu J. QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study. BMC Genomics 2017; 18:828. [PMID: 29078746 PMCID: PMC5658907 DOI: 10.1186/s12864-017-4221-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/17/2017] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population. RESULTS A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe or SZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a, qSdw3b, qSdw12 and qSFe5 / qSZn5) were detected in the same genomic regions under the two stress conditions and 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses. CONCLUSION Rice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidate genes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information for future functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assisted selection or designed QTL pyramiding.
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Affiliation(s)
- Jian Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Kai Chen
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Yunlong Pang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaoqian Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yun Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Michael Dingkuhn
- Cirad, Umr AGAP (Dept. BIOS) and Upr AIDA (Dept. ES), F-34398 Montpellier, France
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | - Julie Pasuquin
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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13
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Horiuchi Y, Harushima Y, Fujisawa H, Mochizuki T, Fujita M, Ohyanagi H, Kurata N. Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. BMC Genomics 2015; 16:1099. [PMID: 26699716 PMCID: PMC4690246 DOI: 10.1186/s12864-015-2319-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. RESULTS We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis-eQTLs. Expression evolution of changed-tissues DE genes was rapid in tissue specifically expressed genes and those rapidly evolved changed-tissues DE genes were regulated not by cis-eQTLs, but by complicated trans-eQTLs. CONCLUSIONS Global DE genes and changed-tissues DE genes had contrasting characteristics. The two contrasting types of DE genes provide possible explanations for the previous controversial conclusions about the relationships between molecular evolution and expression evolution of genes in different species, and the relationship between expression breadth and expression conservation in evolution.
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Affiliation(s)
- Youko Horiuchi
- Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Hulic Kamiyacho 2 F, 4-3-13 Toranomon, Minatoku, Tokyo, 105-0001, Japan.
| | - Yoshiaki Harushima
- Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Hulic Kamiyacho 2 F, 4-3-13 Toranomon, Minatoku, Tokyo, 105-0001, Japan.
| | - Hironori Fujisawa
- Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, 10-3 Midori-cho, Tachikawa, Tokyo, 190-8562, Japan.
- SOKENDAI (The Graduate University for Advanced Studies), 1560-35 Kamiyamaguchi, Hayama, Miura District, Kanagawa Prefecture, 240-0115, Japan.
| | - Takako Mochizuki
- Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- Present address: Genome Informatics Laboratory, Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
| | - Masahiro Fujita
- Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
| | - Hajime Ohyanagi
- Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- Mitsubishi Space Software Co Ltd, Tsukuba Mitsui Building 14 F, 1-6-1 Takezono, Tsukuba, Ibaraki, 305-0032, Japan.
- Present address: Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Nori Kurata
- Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan.
- SOKENDAI (The Graduate University for Advanced Studies), 1560-35 Kamiyamaguchi, Hayama, Miura District, Kanagawa Prefecture, 240-0115, Japan.
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14
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Giong HK, Moon S, Jung KH. A systematic view of the rice calcineurin B-like protein interacting protein kinase family. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0229-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Thavamanikumar S, Southerton S, Thumma B. RNA-Seq using two populations reveals genes and alleles controlling wood traits and growth in Eucalyptus nitens. PLoS One 2014; 9:e101104. [PMID: 24967893 PMCID: PMC4072731 DOI: 10.1371/journal.pone.0101104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/02/2014] [Indexed: 11/17/2022] Open
Abstract
Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in biotic and abiotic stress response reflecting the low growth among low KPY trees. Genes down-regulated in low KPY trees mainly belonged to gene categories involved in wood formation and growth. Differential allelic expression was observed in 2103 SNPs (in 1068 genes) and of these 640 SNPs (30%) occurred in 313 unique genes that were also differentially expressed. These SNPs may represent the cis-acting regulatory variants that influence total gene expression. In addition we also identified 196 genes which had Ka/Ks ratios greater than 1.5, suggesting that these genes are under positive selection. Candidate genes and alleles identified in this study will provide a valuable resource for future association studies aimed at identifying molecular markers for KPY and growth.
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Affiliation(s)
- Saravanan Thavamanikumar
- Department of Forest and Ecosystem Science, University of Melbourne, Creswick, Victoria, Australia
| | | | - Bala Thumma
- CSIRO Plant Industry, Acton, ACT, Australia
- * E-mail:
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16
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Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet 2014; 46:714-21. [PMID: 24908251 DOI: 10.1038/ng.3007] [Citation(s) in RCA: 433] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/15/2014] [Indexed: 12/21/2022]
Abstract
Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.
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17
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Lim JH, Yang HJ, Jung KH, Yoo SC, Paek NC. Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice. Mol Cells 2014; 37:149-60. [PMID: 24599000 PMCID: PMC3935628 DOI: 10.14348/molcells.2014.2336] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022] Open
Abstract
Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line 'SNUSG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.
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Affiliation(s)
- Jung-Hyun Lim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Hyun-Jung Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 446-701,
Korea
| | - Soo-Cheul Yoo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
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