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Ambalavanan A, Mallikarjuna MG, Bansal S, Bashyal BM, Subramanian S, Kumar A, Prakash G. Genome-wide characterization of the NBLRR gene family provides evolutionary and functional insights into blast resistance in pearl millet (Cenchrus americanus (L.) Morrone). PLANTA 2024; 259:143. [PMID: 38704489 DOI: 10.1007/s00425-024-04413-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/14/2024] [Indexed: 05/06/2024]
Abstract
MAIN CONCLUSION The investigation is the first report on genome-wide identification and characterization of NBLRR genes in pearl millet. We have shown the role of gene loss and purifying selection in the divergence of NBLRRs in Poaceae lineage and candidate CaNBLRR genes for resistance to Magnaporthe grisea infection. Plants have evolved multiple integral mechanisms to counteract the pathogens' infection, among which plant immunity through NBLRR (nucleotide-binding site, leucine-rich repeat) genes is at the forefront. The genome-wide mining in pearl millet (Cenchrus americanus (L.) Morrone) revealed 146 CaNBLRRs. The variation in the branch length of NBLRRs showed the dynamic nature of NBLRRs in response to evolving pathogen races. The orthology of NBLRRs showed a predominance of many-to-one orthologs, indicating the divergence of NBLRRs in the pearl millet lineage mainly through gene loss events followed by gene gain through single-copy duplications. Further, the purifying selection (Ka/Ks < 1) shaped the expansion of NBLRRs within the lineage of pear millet and other members of Poaceae. Presence of cis-acting elements, viz. TCA element, G-box, MYB, SARE, ABRE and conserved motifs annotated with P-loop, kinase 2, RNBS-A, RNBS-D, GLPL, MHD, Rx-CC and LRR suggests their putative role in disease resistance and stress regulation. The qRT-PCR analysis in pearl millet lines showing contrasting responses to Magnaporthe grisea infection identified CaNBLRR20, CaNBLRR33, CaNBLRR46 CaNBLRR51, CaNBLRR78 and CaNBLRR146 as putative candidates. Molecular docking showed the involvement of three and two amino acid residues of LRR domains forming hydrogen bonds (histidine, arginine and threonine) and salt bridges (arginine and lysine) with effectors. Whereas 14 and 20 amino acid residues of CaNBLRR78 and CaNBLRR20 showed hydrophobic interactions with 11 and 9 amino acid residues of effectors, Mg.00g064570.m01 and Mg.00g006570.m01, respectively. The present investigation gives a comprehensive overview of CaNBLRRs and paves the foundation for their utility in pearl millet resistance breeding through understanding of host-pathogen interactions.
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Affiliation(s)
- Aruljothi Ambalavanan
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shilpi Bansal
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Science and Humanities, SRM Institute of Science and Technology, Modinagar, Uttar Pradesh, 201204, India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sabtharishi Subramanian
- Division of Entomology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ganesan Prakash
- Division of Plant Pathology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India.
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Zhang Y, Lin XF, Li L, Piao RH, Wu S, Song A, Gao M, Jin YM. CRISPR/Cas9-mediated knockout of Bsr-d1 enhances the blast resistance of rice in Northeast China. PLANT CELL REPORTS 2024; 43:100. [PMID: 38498220 DOI: 10.1007/s00299-024-03192-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
KEY MESSAGE The blast resistance allele of OsBsr-d1 does not exist in most japonica rice varieties of Jilin Province in China. The development of Bsr-d1 knockout mutants via CRISPR/Cas9 enhances broad-spectrum resistance to rice blast in Northeast China. Rice blast is a global disease that has a significant negative impact on rice yield and quality. Due to the complexity and variability of the physiological races of rice blast, controlling rice blast is challenging in agricultural production. Bsr-d1, a negative transcription factor that confers broad-spectrum resistance to rice blast, was identified in the indica rice cultivar Digu; however, its biological function in japonica rice varieties is still unclear. In this study, we analyzed the blast resistance allele of Bsr-d1 in a total of 256 japonica rice varieties from Jilin Province in Northeast China and found that this allele was not present in these varieties. Therefore, we generated Bsr-d1 knockout mutants via the CRISPR/Cas9 system using the japonica rice variety Jigeng88 (JG88) as a recipient variety. Compared with those of the wild-type JG88, the homozygous Bsr-d1 mutant lines KO#1 and KO#2 showed enhanced leaf blast resistance at the seedling stage to several Magnaporthe oryzae (M. oryzae) races collected from Jilin Province in Northeast China. Physiological and biochemical indices revealed that the homozygous mutant lines produced more hydrogen peroxide than did JG88 plants when infected with M. oryzae. Comparative RNA-seq revealed that the DEGs were mainly involved in the synthesis of amide compounds, zinc finger proteins, transmembrane transporters, etc. In summary, our results indicate that the development of Bsr-d1 knockout mutants through CRISPR/Cas9 can enhance the broad-spectrum resistance of rice in Northeast China to rice blast. This study not only provides a theoretical basis for disease resistance breeding involving the Bsr-d1 gene in Northeast China, but also provides new germplasm resources for disease-resistance rice breeding.
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Affiliation(s)
- Ying Zhang
- Research Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, People's Republic of China
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, People's Republic of China
| | - Xiu-Feng Lin
- Research Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, People's Republic of China
| | - Li Li
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences/Jilin Key Laboratory of Agricultural Microbiology/Key Laboratory of Integrated Pest Management On Crops in Northeast China, Ministry of Agriculture and Rural Affairs, Gongzhuling, 136100, People's Republic of China
| | - Ri-Hua Piao
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, People's Republic of China
| | - Songquan Wu
- College of Agricultural Sciences, Yanbian University, Yanji, 133000, People's Republic of China
| | - Anqi Song
- Research Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, People's Republic of China
- College of Agricultural Sciences, Yanbian University, Yanji, 133000, People's Republic of China
| | - Mengmeng Gao
- Research Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, People's Republic of China
- College of Agricultural Sciences, Yanbian University, Yanji, 133000, People's Republic of China
| | - Yong-Mei Jin
- Research Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, People's Republic of China.
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Fan Y, Ma L, Pan X, Tian P, Wang W, Liu K, Xiong Z, Li C, Wang Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies Rice Panicle Blast-Resistant Gene Pb4 Encoding a Wall-Associated Kinase. Int J Mol Sci 2024; 25:830. [PMID: 38255904 PMCID: PMC10815793 DOI: 10.3390/ijms25020830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Rice blast is one of the most devastating diseases, causing a significant reduction in global rice production. Developing and utilizing resistant varieties has proven to be the most efficient and cost-effective approach to control blasts. However, due to environmental pressure and intense pathogenic selection, resistance has rapidly broken down, and more durable resistance genes are being discovered. In this paper, a novel wall-associated kinase (WAK) gene, Pb4, which confers resistance to rice blast, was identified through a genome-wide association study (GWAS) utilizing 249 rice accessions. Pb4 comprises an N-terminal signal peptide, extracellular GUB domain, EGF domain, EGF-Ca2+ domain, and intracellular Ser/Thr protein kinase domain. The extracellular domain (GUB domain, EGF domain, and EGF-Ca2+ domain) of Pb4 can interact with the extracellular domain of CEBiP. Additionally, its expression is induced by chitin and polygalacturonic acid. Furthermore, transgenic plants overexpressing Pb4 enhance resistance to rice blast. In summary, this study identified a novel rice blast-resistant gene, Pb4, and provides a theoretical basis for understanding the role of WAKs in mediating rice resistance against rice blast disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China (X.P.); (P.T.); (C.L.); (H.Z.)
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Simon EV, Hechanova SL, Hernandez JE, Li CP, Tülek A, Ahn EK, Jairin J, Choi IR, Sundaram RM, Jena KK, Kim SR. Available cloned genes and markers for genetic improvement of biotic stress resistance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1247014. [PMID: 37731986 PMCID: PMC10507716 DOI: 10.3389/fpls.2023.1247014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.
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Affiliation(s)
- Eliza Vie Simon
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Sherry Lou Hechanova
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
| | - Jose E. Hernandez
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Charng-Pei Li
- Taiwan Agricultural Research Institute (TARI), Council of Agriculture, Taiwan
| | - Adnan Tülek
- Trakya Agricultural Research Institute, Edirne, Türkiye
| | - Eok-Keun Ahn
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Jirapong Jairin
- Division of Rice Research and Development, Rice Department, Bangkok, Thailand
| | - Il-Ryong Choi
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Raman M. Sundaram
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Kshirod K. Jena
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, Odisha, India
| | - Sung-Ryul Kim
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
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Liang X, Dong J. Comparative-genomic analysis reveals dynamic NLR gene loss and gain across Apiaceae species. Front Genet 2023; 14:1141194. [PMID: 36936422 PMCID: PMC10017999 DOI: 10.3389/fgene.2023.1141194] [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: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction: Nucleotide-binding leucine-rich repeat (NLR) genes play a crucial role in green plants' responding to various pathogens. Genome-scale evolutionary studies of NLR genes are important for discovering and applying functional NLR genes. However, little is known about the evolution of NLR genes in the Apiaceae family including agricultural and medical plants. Methods: In this study, comparative genomic analysis was performed in four Apiaceae species to trace the dynamic evolutionary patterns of NLR genes during speciation in this family. Results: The results revealed different number of NLR genes in these four Apiaceae species, namely, Angelica sinensis (95), Coriandrum sativum (183), Apium graveolens (153) and Daucus carota (149). Phylogenetic analysis demonstrated that NLR genes in these four species were derived from 183 ancestral NLR lineages and experienced different levels of gene-loss and gain events. The contraction pattern of the ancestral NLR lineages was discovered during the evolution of D. carota, whereas a different pattern of contraction after first expansion of NLR genes was observed for A. sinensis, C. sativum and A. graveolens. Discussion: Taken together, rapid and dynamic gene content variation has shaped evolutionary history of NLR genes in Apiaceae species.
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