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Wang X, Cheng R, Xu D, Huang R, Li H, Jin L, Wu Y, Tang J, Sun C, Peng D, Chu C, Guo X. MG1 interacts with a protease inhibitor and confers resistance to rice root-knot nematode. Nat Commun 2023; 14:3354. [PMID: 37291108 PMCID: PMC10250356 DOI: 10.1038/s41467-023-39080-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
The rice root-knot nematode (Meloidogyne graminicola) is one of the most destructive pests threatening rice (Oryza sativa L.) production in Asia; however, no rice resistance genes have been cloned. Here, we demonstrate that M. GRAMINICOLA-RESISTANCE GENE 1 (MG1), an R gene highly expressed at the site of nematode invasion, determines resistance against the nematode in several rice varieties. Introgressing MG1 into susceptible varieties increases resistance comparable to resistant varieties, for which the leucine-rich repeat domain is critical for recognizing root-knot nematode invasion. We also report transcriptome and cytological changes that are correlated with a rapid and robust response during the incompatible interaction that occurs in resistant rice upon nematode invasion. Furthermore, we identified a putative protease inhibitor that directly interacts with MG1 during MG1-mediated resistance. Our findings provide insight into the molecular basis of nematode resistance as well as valuable resources for developing rice varieties with improved nematode resistance.
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Affiliation(s)
- Xiaomin Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daochao Xu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Renliang Huang
- Nanchang Subcenter of Rice National Engineering Laboratory, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Haoxing Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Jin
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, 625014, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoli Guo
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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2
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Sun H, Yuan Z, Li F, Zhang Q, Peng T, Li J, Du Y. Mapping of qChalk1 controlling grain chalkiness in japonica rice. Mol Biol Rep 2023:10.1007/s11033-023-08537-8. [PMID: 37231212 DOI: 10.1007/s11033-023-08537-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice grain chalkiness is an undesirable characteristic that affects grain quality. The aim of this study was to map QTLs controlling grain chalkiness in japonica rice. METHODS AND RESULTS In this study, two japonica rice cultivars with similar grain shapes but different grain chalkiness rates were crossed and the F2 and BC1F2 populations were subjected to QTL-seq analysis to map the QTLs controlling the grain chalkiness rate. QTL-seq analysis revealed SNP index differences on chromosome 1 in both of the segregating populations. Using polymorphic markers between the two parents, QTL mapping was conducted on 213 individual plants in the BC1F2 population. QTL mapping confined a QTL controlling grain chalkiness, qChalk1, to a 1.1 Mb genomic region on chromosome 1. qChalk1 explained 19.7% of the phenotypic variation. CONCLUSION A QTL controlling grain chalkiness qChalk1 was detected in both F2 and BC1F2 segregating populations by QTL-Seq and QTL mapping methods. This result would be helpful for further cloning of the genes controlling grain chalkiness in japonica rice.
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Affiliation(s)
- Hongzheng Sun
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Zeke Yuan
- Henan Zhumadian Agricultural School, Zhumadian, 463000, People's Republic of China
| | - Fuhao Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Qianqian Zhang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453004, People's Republic of China
| | - Ting Peng
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Junzhou Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Yanxiu Du
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China.
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3
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Zhang L, Li S, Shan C, Liu Y, Zhang Y, Ye L, Lin Y, Xiong G, Ma J, Adnan M, Shi X, Sun X, Kuang W, Cui R. Integrated transcriptome and metabolome analysis revealed that flavonoids enhanced the resistance of Oryza sativa against Meloidogyne graminicola. FRONTIERS IN PLANT SCIENCE 2023; 14:1137299. [PMID: 37063174 PMCID: PMC10102519 DOI: 10.3389/fpls.2023.1137299] [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: 01/04/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Rice is a crucial food crop worldwide, but its yield and quality are significantly affected by Meloidogyne graminicola is a root knot nematode. No rice variety is entirely immune to this nematode disease in agricultural production. Thus, the fundamental strategy to combat this disease is to utilize rice resistance genes. In this study, we conducted transcriptome and metabolome analyses on two rice varieties, ZH11 and IR64. The results indicated that ZH11 showed stronger resistance than IR64. Transcriptome analysis revealed that the change in gene expression in ZH11 was more substantial than that in IR64 after M. graminicola infection. Moreover, GO and KEGG enrichment analysis of the upregulated genes in ZH11 showed that they were primarily associated with rice cell wall construction, carbohydrate metabolism, and secondary metabolism relating to disease resistance, which effectively enhanced the resistance of ZH11. However, in rice IR64, the number of genes enriched in disease resistance pathways was significantly lower than that in ZH11, which further explained susceptibility to IR64. Metabolome analysis revealed that the metabolites detected in ZH11 were enriched in flavonoid metabolism and the pentose phosphate pathway, compared to IR64, after M. graminicola infection. The comprehensive analysis of transcriptome and metabolome data indicated that flavonoid metabolism plays a crucial role in rice resistance to M. graminicola infection. The content of kaempferin, apigenin, and quercetin in ZH11 significantly increased after M. graminicola infection, and the expression of genes involved in the synthetic pathway of flavonoids also significantly increased in ZH11. Our study provides theoretical guidance for the precise analysis of rice resistance and disease resistance breeding in further research.
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Affiliation(s)
- Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Songyan Li
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Chonglei Shan
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yankun Liu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yifan Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Lifang Ye
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Yachun Lin
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Guihong Xiong
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Jian Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Muhammad Adnan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xugen Shi
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Xiaotang Sun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
| | - Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China
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4
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Huang Q, Lin B, Cao Y, Zhang Y, Song H, Huang C, Sun T, Long C, Liao J, Zhuo K. CRISPR/Cas9-mediated mutagenesis of the susceptibility gene OsHPP04 in rice confers enhanced resistance to rice root-knot nematode. FRONTIERS IN PLANT SCIENCE 2023; 14:1134653. [PMID: 36998699 PMCID: PMC10043372 DOI: 10.3389/fpls.2023.1134653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/28/2023] [Indexed: 06/17/2023]
Abstract
CRISPR crops carrying a mutation in susceptibility (S) genes provide an effective strategy for controlling plant disease, because they could be 'transgene-free' and commonly have more broad-spectrum and durable type of resistance. Despite their importance, CRISPR/Cas9-mediated editing of S genes for engineering resistance to plant-parasitic nematode (PPN) disease has not been reported. In this study, we employed the CRISPR/Cas9 system to specifically induce targeted mutagenesis of the S gene rice copper metallochaperone heavy metal-associated plant protein 04 (OsHPP04), and successfully obtained genetically stable homozygous rice mutants with or without transgenic elements. These mutants confer enhanced resistance to the rice root-knot nematode (Meloidogyne graminicola), a major plant pathogenic nematode in rice agriculture. Moreover, the plant immune responses triggered by flg22, including reactive oxygen species burst, defence-related genes expression and callose deposition, were enhanced in the 'transgene-free' homozygous mutants. Analysis of rice growth and agronomic traits of two independent mutants showed that there are no obvious differences between wild-type plants and mutants. These findings suggest that OsHPP04 may be an S gene as a negative regulator of host immunity and genetic modification of S genes through the CRISPR/Cas9 technology can be used as a powerful tool to generate PPN resistant plant varieties.
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Affiliation(s)
- Qiuling Huang
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Borong Lin
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yuqing Cao
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yu Zhang
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Handa Song
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Chunhui Huang
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Tianling Sun
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Changwen Long
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Jinling Liao
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Kan Zhuo
- Laboratory of Plant Nematology, College of Plant Protection, South China Agricultural University, Guangzhou, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
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5
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Kaur G, Yadav IS, Bhatia D, Vikal Y, Neelam K, Dhillon NK, Praba UP, Mangat GS, Singh K. BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima. Front Genet 2022; 13:871833. [PMID: 35774507 PMCID: PMC9237506 DOI: 10.3389/fgene.2022.871833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC1F1 population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.
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Affiliation(s)
- Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Yogesh Vikal,
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Umesh Preethi Praba
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gurjit Singh Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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6
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Nguyen HT, Mantelin S, Ha CV, Lorieux M, Jones JT, Mai CD, Bellafiore S. Insights Into the Genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and Its Molecular Determinism in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:854961. [PMID: 35599898 PMCID: PMC9116194 DOI: 10.3389/fpls.2022.854961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F2 hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.
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Affiliation(s)
- Hue Thi Nguyen
- LMI RICE-2, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
- Department of Life Sciences, University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam
| | - Sophie Mantelin
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) UMR 1355 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Cuong Viet Ha
- Research Center of Tropical Plant Disease, Vietnam National University of Agriculture (VNUA), Hanoi, Vietnam
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - John T. Jones
- The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Chung Duc Mai
- LMI RICE-2, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Stéphane Bellafiore
- PHIM Plant Health Institute, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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7
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Zhang J, Panthee DR. Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes. G3 GENES|GENOMES|GENETICS 2022; 12:6449447. [PMID: 34864988 PMCID: PMC9210294 DOI: 10.1093/g3journal/jkab400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/07/2021] [Indexed: 11/12/2022]
Abstract
Genomic regions that control traits of interest can be rapidly identified using BSA-Seq, a technology in which next-generation sequencing is applied to bulked segregant analysis (BSA). We recently developed the significant structural variant method for BSA-Seq data analysis that exhibits higher detection power than standard BSA-Seq analysis methods. Our original algorithm was developed to analyze BSA-Seq data in which genome sequences of one parent served as the reference sequences in genotype calling and, thus, required the availability of high-quality assembled parental genome sequences. Here, we modified the original script to effectively detect the genomic region–trait associations using only bulk genome sequences. We analyzed two public BSA-Seq datasets using our modified method and the standard allele frequency and G-statistic methods with and without the aid of the parental genome sequences. Our results demonstrate that the genomic region(s) associated with the trait of interest could be reliably identified via the significant structural variant method without using the parental genome sequences.
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Affiliation(s)
- Jianbo Zhang
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC 28759, USA
| | - Dilip R Panthee
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Center, Mills River, NC 28759, USA
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8
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Huang L, Tang W, Wu W. Optimization of BSA-seq experiment for QTL mapping. G3 GENES|GENOMES|GENETICS 2022; 12:6428533. [PMID: 34791194 PMCID: PMC8727994 DOI: 10.1093/g3journal/jkab370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/12/2022]
Abstract
Abstract
Deep sequencing-based bulked segregant analysis (BSA-seq) has become a popular approach for quantitative trait loci (QTL) mapping in recent years. Effective statistical methods for BSA-seq have been developed, but how to design a suitable experiment for BSA-seq remains unclear. In this paper, we show in theory how the major experimental factors (including population size, pool proportion, pool balance, and generation) and the intrinsic factors of a QTL (including heritability and degree of dominance) affect the power of QTL detection and the precision of QTL mapping in BSA-seq. Increasing population size can improve the power and precision, depending on the QTL heritability. The best proportion of each pool in the population is around 0.25. So, 0.25 is generally applicable in BSA-seq. Small pool proportion can greatly reduce the power and precision. Imbalance of pool pair in size also causes decrease of the power and precision. Additive effect is more important than dominance effect for QTL mapping. Increasing the generation of filial population produced by selfing can significantly increase the power and precision, especially from F2 to F3. These findings enable researchers to optimize the experimental design for BSA-seq. A web-based program named BSA-seq Design Tool is available at http://124.71.74.135/BSA-seqDesignTool/ and https://github.com/huanglikun/BSA-seqDesignTool.
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Affiliation(s)
- Likun Huang
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Weiqi Tang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, Fujian 350108, China
| | - Weiren Wu
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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9
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Somvanshi VS, Dash M, Bhat CG, Budhwar R, Godwin J, Shukla RN, Patrignani A, Schlapbach R, Rao U. An improved draft genome assembly of Meloidogyne graminicola IARI strain using long-read sequencing. Gene 2021; 793:145748. [PMID: 34077775 DOI: 10.1016/j.gene.2021.145748] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 01/10/2023]
Abstract
The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola.
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Affiliation(s)
- Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India
| | - Manoranjan Dash
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India
| | - Chaitra G Bhat
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India
| | - Roli Budhwar
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043, India
| | - Jeffrey Godwin
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043, India
| | - Rohit N Shukla
- Bionivid Technology Private Limited, 209, 4th Cross Rd, B Channasandra, Kasturi Nagar, Bengaluru, Karnataka 560043, India
| | - Andrea Patrignani
- Functional Genomics Center Zurich, Winterthurerstr. 190, Y32H52, 8057 Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, Winterthurerstr. 190, Y32H52, 8057 Zurich, Switzerland
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi 110012, India.
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10
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Dash M, Somvanshi VS, Budhwar R, Godwin J, Shukla RN, Rao U. A rice root-knot nematode Meloidogyne graminicola-resistant mutant rice line shows early expression of plant-defence genes. PLANTA 2021; 253:108. [PMID: 33866432 DOI: 10.1007/s00425-021-03625-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Resistance to rice root-knot nematode Meloidogyne graminicola in a mutant rice line is suggested to be conferred by higher expression of several genes putatively involved in damage-associated molecular pattern recognition, secondary metabolite biosynthesis including phytoalexins, and defence-related genes. Meloidogyne graminicola has emerged as the most destructive plant-parasitic nematode disease of rice (Oryza sativa L.). Genetic resistance to M. graminicola is one of the most effective methods for its management. A M. graminicola-resistant O. sativa ssp. indica mutant line-9 was previously identified through a forward genetic screen (Hatzade et al. Biologia 74:1197-1217, 2019). In the present study, we used RNA-Sequencing to investigate the molecular mechanisms conferring nematode resistance to the mutant line-9 compared to the susceptible parent JBT 36/14 at 24 h post-infection. A total of 674 transcripts were differentially expressed in line-9. Early regulation of genes putatively related to nematode damage-associated molecular pattern recognition (e.g., wall-associated receptor kinases), signalling [Nucleotide-binding, Leucine-Rich Repeat (NLRs)], pathogenesis-related (PR) genes (PR1, PR10a), defence-related genes (NB-ARC domain-containing genes), as well as a large number of genes involved in secondary metabolites including diterpenoid biosynthesis (CPS2, OsKSL4, OsKSL10, Oscyp71Z2, oryzalexin synthase, and momilactone A synthase) was observed in M. graminicola-resistant mutant line-9. It may be suggested that after the nematode juveniles penetrate the roots of line-9, early recognition of invading nematodes triggers plant immune responses mediated by phytoalexins, and other defence proteins such as PR proteins inhibit nematode growth and reproduction. Our study provides the first transcriptomic comparison of nematode-resistant and susceptible rice plants in the same genetic background and adds to the understanding of mechanisms underlying plant-nematode resistance in rice.
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Affiliation(s)
- Manoranjan Dash
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Roli Budhwar
- Bionivid Technology Private Limited, 209, 4th Cross, Kasturi Nagar, Bangalore, 560043, India
| | - Jeffrey Godwin
- Bionivid Technology Private Limited, 209, 4th Cross, Kasturi Nagar, Bangalore, 560043, India
| | - Rohit N Shukla
- Bionivid Technology Private Limited, 209, 4th Cross, Kasturi Nagar, Bangalore, 560043, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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11
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Zeng W, Shi J, Qiu C, Wang Y, Rehman S, Yu S, Huang S, He C, Wang W, Chen H, Chen C, Wang C, Tao Z, Li P. Identification of a genomic region controlling thermotolerance at flowering in maize using a combination of whole genomic re-sequencing and bulked segregant analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2797-2810. [PMID: 32535640 DOI: 10.1007/s00122-020-03632-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
A novel genomic region controlling thermotolerance at flowering was identified by the combination of whole genomic re-sequencing and bulked segregant analysis in maize. The increasing frequency of extreme high temperature has brought a great threat to the development of maize throughout its life cycle, especially during the flowering phase. However, the genetic basis of thermotolerance at flowering in maize remains poorly understood. Here, we characterized a thermotolerant maize ecotype Abe2 and dissected its genetic basis using a F2:8 recombinant inbred line (RIL) population generated from a cross between Abe2 and B73. After continuous high temperature stress above 35 °C for 17 days, Abe2 and B73 show distinct leaf scorching phenotype under field conditions. To identify the genomic regions associated with the phenotypic variation, we applied a combination of whole genomic re-sequencing and bulked segregant analysis, and revealed 10,316,744 SNPs and 1,488,302 InDels between the two parental lines, and 2,693,054 SNPs and 313,757 InDels between the two DNA pools generated from the thermos-tolerant and the sensitive individuals of the RIL, of which, 108,655 and 17,853 SNPs may cause nonsynonymous variations. Finally, a 7.41 Mb genomic region on chromosome 1 was identified, and 7 candidate genes were annotated to participate in high temperature-related stress response. A candidate gene Zm00001d033339 encoding a serine/threonine protein kinase was proposed to be the most likely causative gene contributing to the thermotolerance at flowering by involving in stomatal movement (GO: 0010119) via Abscisic acid (ABA) pathway (KO04075). This work could provide an opportunity for gene cloning and pyramiding breeding to improve thermotolerance at flowering in maize.
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Affiliation(s)
- Wei Zeng
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jian Shi
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chunhong Qiu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunhe Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shamsur Rehman
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shuaishuai Yu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shijie Huang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chen He
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wanyi Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hongyi Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chen Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chuanhong Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Tao
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Peijin Li
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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12
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Hada A, Dutta TK, Singh N, Singh B, Rai V, Singh NK, Rao U. A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola. PLoS One 2020; 15:e0239085. [PMID: 32960916 PMCID: PMC7508375 DOI: 10.1371/journal.pone.0239085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022] Open
Abstract
Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.
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Affiliation(s)
- Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Tushar K. Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nisha Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Balwant Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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13
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Lahari Z, Nkurunziza R, Bauters L, Gheysen G. Analysis of Asian Rice ( Oryza sativa) Genotypes Reveals a New Source of Resistance to the Root-Knot Nematode Meloidogyne javanica and the Root-Lesion Nematode Pratylenchus zeae. PHYTOPATHOLOGY 2020; 110:1572-1577. [PMID: 32314949 DOI: 10.1094/phyto-11-19-0433-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The sedentary root-knot nematodes, Meloidogyne spp., and the migratory root-lesion nematodes, Pratylenchus spp., cause significant yield losses, particularly in aerobic and upland rice production systems. Recently, the Asian rice Oryza sativa accessions LD 24 and Khao Pahk Maw (KPM) were shown to be highly resistant to M. graminicola. In this study, we have analyzed the responses and broadness of resistance of these two rice genotypes to another root-knot nematode M. javanica and a root-lesion nematode P. zeae. The penetration as well as post-penetration development and reproduction of nematodes were compared including known susceptible and resistant genotypes. Our results indicate that the genotype KPM confers strong resistance to both M. javanica and P. zeae, while LD 24 was resistant to M. javanica and susceptible to P. zeae. Detailed observations revealed that similar numbers of M. javanica or P. zeae penetrated the resistant and susceptible hosts during early infection stages. However, the development and reproduction of both nematodes were arrested or reduced in resistant genotypes, implying that resistance occurs at the post-penetration stage.
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Affiliation(s)
- Zobaida Lahari
- Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | | | - Lander Bauters
- Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
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