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Zhang G, Yang Z, Zhou S, Zhu J, Liu X, Luo J. Cellulose synthase-like OsCSLD4: a key regulator of agronomic traits, disease resistance, and metabolic indices in rice. PLANT CELL REPORTS 2024; 43:264. [PMID: 39414689 DOI: 10.1007/s00299-024-03356-y] [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: 04/26/2024] [Accepted: 10/03/2024] [Indexed: 10/18/2024]
Abstract
KEY MESSAGE Cellulose synthase-like OsCSLD4 plays a pivotal role in regulating diverse agronomic traits, enhancing resistance against bacterial leaf blight, and modulating metabolite indices based on the multi-omics analysis in rice. To delve deeper into this complex network between agronomic traits and metabolites in rice, we have compiled a dataset encompassing genome, phenome, and metabolome, including 524 diverse accessions, 11 agronomic traits, and 841 metabolites, enabling us to pinpoint eight hotspots through GWAS. We later discovered four distinct metabolite categories, encompassing 15 metabolites that are concurrently present on the QTL qC12.1, associated with leaf angle of flag and spikelet length, and finally focused the cellulose synthase-like OsCSLD4, which was pinpointed through a rigorous process encompassing sequence variation, haplotype, ATAC, and differential expression across diverse tissues. Compared to the wild type, csld4 exhibited significant reductions in the plant height, flag leaf length, leaf width, spikelet length, 1000-grain weight, grain width, grain thickness, fertility, yield per plant, and bacterial blight resistance. However, there were significant increase in tiller numbers, degree of leaf rolling, flowering period, growth period, grain length, and empty kernel rate. Furthermore, the content of four polyphenol metabolites, excluding metabolite N-feruloyltyramine (mr1268), notably rose, whereas the levels of the other three polyphenol metabolites, smiglaside C (mr1498), 4-coumaric acid (mr1622), and smiglaside A (mr1925) decreased significantly in mutant csld4. The content of amino acid L-tyramine (mr1446) exhibited a notable increase, whereas the alkaloid trigonelline (mr1188) displayed a substantial decrease among the mutants. This study offered a comprehensive multi-omics perspective to analyze the genetic mechanism of OsCSLD4, and breeders can potentially enhance rice's yield, bacterial leaf blight resistance, and metabolite content, leading to more sustainable and profitable rice production.
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Affiliation(s)
- Guofang Zhang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
- School of Breeding and Multiplication, Hainan University, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zhuang Yang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
- School of Breeding and Multiplication, Hainan University, Sanya, 572025, China
| | - Shen Zhou
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
- School of Breeding and Multiplication, Hainan University, Sanya, 572025, China
| | - Jinjin Zhu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
- School of Breeding and Multiplication, Hainan University, Sanya, 572025, China
| | - Xianqing Liu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
- School of Breeding and Multiplication, Hainan University, Sanya, 572025, China
| | - Jie Luo
- School of Breeding and Multiplication, Hainan University, Sanya, 572025, China.
- Yazhou Bay National Laboratory, Sanya, 572025, China.
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Chen N, Ma T, Xia S, Li C, Liu Y, Wang J, Qu G, Liu H, Zheng H, Yang L, Zou D, Wang J, Xin W. Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage. Genes (Basel) 2024; 15:327. [PMID: 38540386 PMCID: PMC10970145 DOI: 10.3390/genes15030327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 06/14/2024] Open
Abstract
Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.
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Affiliation(s)
- Ning Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Tianze Ma
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Sijia Xia
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Chengxin Li
- Harbin Academy of Agricultural Sciences, Harbin 150030, China;
| | - Yinuo Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Jiaqi Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Guize Qu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Luomiao Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
| | - Wei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (N.C.); (T.M.); (S.X.); (Y.L.); (J.W.); (G.Q.); (H.L.); (H.Z.); (L.Y.); (D.Z.)
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
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Liu S, Luo S, Yang D, Huang J, Jiang X, Yu S, Fu J, Zhou D, Chen X, He H, Fu H. Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq. BMC PLANT BIOLOGY 2024; 24:145. [PMID: 38413866 PMCID: PMC10900630 DOI: 10.1186/s12870-024-04839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. RESULTS In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. CONCLUSION Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.
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Affiliation(s)
- Shaochun Liu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shuqi Luo
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dewei Yang
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Junying Huang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinlei Jiang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shangwei Yu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
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Zhang A, Zhang H, Wang R, He H, Song B, Song R. Bactericidal bissulfone B 7 targets bacterial pyruvate kinase to impair bacterial biology and pathogenicity in plants. SCIENCE CHINA. LIFE SCIENCES 2024; 67:391-402. [PMID: 37987940 DOI: 10.1007/s11427-023-2449-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/11/2023] [Indexed: 11/22/2023]
Abstract
The prevention and control of rice bacterial leaf blight (BLB) disease has not yet been achieved due to the lack of effective agrochemicals and available targets. Herein, we develop a series of novel bissulfones and a novel target with a unique mechanism to address this challenge. The developed bissulfones can control Xanthomonas oryzae pv. oryzae (Xoo), and 2-(bis(methylsulfonyl)methylene)-N-(4-chlorophenyl) hydrazine-1-carboxamide (B7) is more effective than the commercial drugs thiodiazole copper (TC) and bismerthiazol (BT). Pyruvate kinase (PYK) in Xoo has been identified for the first time as the target protein of our bissulfone B7. PYK modulates bacterial virulence via a CRP-like protein (Clp)/two-component system regulatory protein (regR) axis. The elucidation of this pathway facilitates the use of B7 to reduce PYK expression at the transcriptional level, block PYK activity at the protein level, and impair the interaction within the PYK-Clp-regR complex via competitive inhibition, thereby attenuating bacterial biology and pathogenicity. This study offers insights into the molecular and mechanistic aspects underlying anti-Xoo strategies that target PYK. We believe that these valuable discoveries will be used for bacterial disease control in the future.
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Affiliation(s)
- Awei Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Haizhen Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Ronghua Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Hongfu He
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Runjiang Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
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Luo H, Wang Q, Dong C, Shi Z, He C, Guo Z, Shi J, Li C, Gao W, Li J. Establishment of Functional PCR-Based Markers against Bacterial Leaf Blight Disease in Rice Landraces of Yunnan Province of China. Life (Basel) 2023; 13:2101. [PMID: 37895481 PMCID: PMC10608166 DOI: 10.3390/life13102101] [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: 09/06/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Bacterial leaf blight is a devastating disease of rice worldwide. The resistant genes are routinely transferred from landraces to cultivated varieties through backcross breeding along with marker-assisted selection. In the present study, we use the gene-specific markers to screen the rice landraces in Yunnan Province of China. We collected 404 representative samples of 24 different rice landraces from Yunnan Province of China. The initial PCR-based screening suggested that the leaf blight resistance was not evenly distributed in Yunnan Province. Our results indicate that there is a complete loss of resistance for landraces based on xa5 and xa13 genes. On the other hand, landraces harboring Xa7 and Xa21 showed a high level of resistance. Using gene-specific PCR-based data, we were able to identify the resistant, susceptible and heterozygous populations across Yunnan Province. The widely used Xa21 gene alone showed a remarkable level of resistance throughout the province, indicating its potential to develop broad-spectrum resistance in rice germplasm. The key aspects of bacterial blight spread according to local sites in Yunnan Province and the resistance conferred by different landraces due to the presence of different resistance genes are discussed.
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Affiliation(s)
- Hengming Luo
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Qun Wang
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Chao Dong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China;
- Yunnan Seed Laboratory, Kunming 650205, China
- Yunnan Provincial Key Lab of Agricultural Biotechnology, Kunming 650205, China
- Key Laboratory of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Kunming 650205, China
- Scientific Observation Station for Rice Germplasm Resources of Yunnan, Ministry of Agriculture and Rural Affairs, Kunming 650205, China
| | - Zhufeng Shi
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Chengxing He
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Zhixiang Guo
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Junyi Shi
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
| | - Chun Li
- Wenshan Plant Protection and Quarantine Station, Wenshan 663099, China; (C.L.); (W.G.)
| | - Wei Gao
- Wenshan Plant Protection and Quarantine Station, Wenshan 663099, China; (C.L.); (W.G.)
| | - Jinbin Li
- Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (H.L.); (Q.W.); (Z.S.); (C.H.); (Z.G.); (J.S.)
- Ministry of Agriculture and Rural Affairs International Joint Research Center for Agriculture, Kunming 650205, China
- Ministry of Agriculture and Rural Affairs Key Laboratory for Prevention and Control of Biological Invasions, Kunming 650205, China
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Kunming 650205, China
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Chen J, Sun M, Xiao G, Shi R, Zhao C, Zhang Q, Yang S, Xuan Y. Starving the enemy: how plant and microbe compete for sugar on the border. FRONTIERS IN PLANT SCIENCE 2023; 14:1230254. [PMID: 37600180 PMCID: PMC10433384 DOI: 10.3389/fpls.2023.1230254] [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: 05/28/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
As the primary energy source for a plant host and microbe to sustain life, sugar is generally exported by Sugars Will Eventually be Exported Transporters (SWEETs) to the host extracellular spaces or the apoplast. There, the host and microbes compete for hexose, sucrose, and other important nutrients. The host and microbial monosaccharide transporters (MSTs) and sucrose transporters (SUTs) play a key role in the "evolutionary arms race". The result of this competition hinges on the proportion of sugar distribution between the host and microbes. In some plants (such as Arabidopsis, corn, and rice) and their interacting pathogens, the key transporters responsible for sugar competition have been identified. However, the regulatory mechanisms of sugar transporters, especially in the microbes require further investigation. Here, the key transporters that are responsible for the sugar competition in the host and pathogen have been identified and the regulatory mechanisms of the sugar transport have been briefly analyzed. These data are of great significance to the increase of the sugar distribution in plants for improvement in the yield.
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Affiliation(s)
- Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Miao Sun
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Rujie Shi
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Chanjuan Zhao
- Chongqing Three Gorges Vocational College, Wanzhou, China
| | - Qianqian Zhang
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Shuo Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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He Y, Zhang K, Li S, Lu X, Zhao H, Guan C, Huang X, Shi Y, Kang Z, Fan Y, Li W, Chen C, Li G, Long O, Chen Y, Hu M, Cheng J, Xu B, Chapman MA, Georgiev MI, Fernie AR, Zhou M. Multiomics analysis reveals the molecular mechanisms underlying virulence in Rhizoctonia and jasmonic acid-mediated resistance in Tartary buckwheat (Fagopyrum tataricum). THE PLANT CELL 2023; 35:2773-2798. [PMID: 37119263 PMCID: PMC10396374 DOI: 10.1093/plcell/koad118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 06/19/2023]
Abstract
Rhizoctonia solani is a devastating soil-borne pathogen that seriously threatens the cultivation of economically important crops. Multiple strains with a very broad host range have been identified, but only 1 (AG1-IA, which causes rice sheath blight disease) has been examined in detail. Here, we analyzed AG4-HGI 3 originally isolated from Tartary buckwheat (Fagopyrum tataricum), but with a host range comparable to AG1-IA. Genome comparison reveals abundant pathogenicity genes in this strain. We used multiomic approaches to improve the efficiency of screening for disease resistance genes. Transcriptomes of the plant-fungi interaction identified differentially expressed genes associated with virulence in Rhizoctonia and resistance in Tartary buckwheat. Integration with jasmonate-mediated transcriptome and metabolome changes revealed a negative regulator of jasmonate signaling, cytochrome P450 (FtCYP94C1), as increasing disease resistance probably via accumulation of resistance-related flavonoids. The integration of resistance data for 320 Tartary buckwheat accessions identified a gene homolog to aspartic proteinase (FtASP), with peak expression following R. solani inoculation. FtASP exhibits no proteinase activity but functions as an antibacterial peptide that slows fungal growth. This work reveals a potential mechanism behind pathogen virulence and host resistance, which should accelerate the molecular breeding of resistant varieties in economically essential crops.
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Affiliation(s)
- Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Shijuan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Chaonan Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xu Huang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Yaliang Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Zhen Kang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Wei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Cheng Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Guangsheng Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Ou Long
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Yuanyuan Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Mang Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Milen I Georgiev
- Laboratory of Metabolomics, Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv 4000, Bulgaria
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Gene Bank Building, Beijing 100081, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
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9
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
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10
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Ma L, Yu Y, Li C, Wang P, Liu K, Ma W, Wang W, Fan Y, Xiong Z, Jiang T, Zhang J, Wang Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene Pb3 Encoding NLR Protein. Int J Mol Sci 2022; 23:ijms232214032. [PMID: 36430507 PMCID: PMC9698523 DOI: 10.3390/ijms232214032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rice blast is a worldwide fungal disease that seriously affects the yield and quality of rice. Identification of resistance genes against rice blast disease is one of the effective ways to control this disease. However, panicle blast resistance genes, which are useful in the fields, have rarely been studied due to the difficulty in phenotypic identification and the environmental influences. Here, panicle blast resistance-3 (Pb3) was identified by a genome-wide association study (GWAS) based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel I (RDP-I) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A total of 16 panicle blast resistance loci (PBRLs) within three years including one repeated locus PBRL3 located in chromosome 11 were identified. In addition, 7 genes in PBRL3 were identified as candidate genes by haplotype analysis, which showed significant differences between resistant and susceptible varieties. Among them, one nucleotide-binding domain and Leucine-rich Repeat (NLR) gene Pb3 was highly conserved in multiple resistant rice cultivars, and its expression was significantly induced after rice blast inoculation. Evolutionary analysis showed that Pb3 was a typical disease resistance gene containing coiled-coil, NB-ARC, and LRR domains. T-DNA insertion mutants and CRISPR lines of Pb3 showed significantly reduced panicle blast resistance. These results indicate that Pb3 is a panicle blast resistance gene and GWAS is a rapid method for identifying panicle blast resistance in rice.
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Affiliation(s)
- Lu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changqing Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Panting Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kunquan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunxin Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziwei Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingran Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhixue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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11
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Mohd Hanafiah N, Cheng A, Lim PE, Sethuraman G, Mohd Zain NA, Baisakh N, Mispan MS. Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice. Life (Basel) 2022; 12:1542. [PMID: 36294977 PMCID: PMC9604669 DOI: 10.3390/life12101542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (Oryza sativa) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.
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Affiliation(s)
- Noraikim Mohd Hanafiah
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Gomathy Sethuraman
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Nurul Amalina Mohd Zain
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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12
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Wang A, Ma L, Shu X, Jiang Y, Liang J, Zheng A. Rice (Oryza sativa L.) cytochrome P450 protein 716A subfamily CYP716A16 regulates disease resistance. BMC Genomics 2022; 23:343. [PMID: 35505282 PMCID: PMC9066777 DOI: 10.1186/s12864-022-08568-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/19/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The sustainable development of rice production is facing severe threats by a variety of pathogens, such as necrotrophic Rhizoctonia solani and hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo). Mining and applying resistance genes to increase the durable resistance of rice is an effective method that can be used to control these diseases. RESULTS In this research, we isolated and characterized CYP716A16, which is a positive regulator of rice to R. solani AG1-IA and Xoo, and belongs to the cytochrome P450 (CYP450) protein 716A subfamily. Overexpression (OE) of CYP716A16 resulted in enhanced resistance to R. solani AG1-IA and Xoo, while RNA interference (RNAi) of CYP716A16 resulted in increased susceptibility compared with wild-type (WT) plants. Additionally, jasmonic acid (JA)-dependent defense responses and reactive oxygen species (ROS) were activated in the CYP716A16-OE lines after R. solani AG1-IA inoculation. The comparative transcriptomic and metabolomics analysis of CYP716A16-OE and the WT lines showed that OE of CYP716A16 activated the biosynthesis of flavonoids and increased the amounts of narcissoside, methylophiopogonanone A, oroxin A, and amentoflavone in plants. CONCLUSION Based on these results, we suggest that JA-dependent response, ROS level, multiple resistance-related proteins, and flavonoid contents play an important role in CYP716A16-regulated R. solani AG1-IA and Xoo resistance. Our results broaden our knowledge regarding the function of a P450 protein 716A subfamily in disease resistance and provide new insight into the molecular mechanism of rice immune response.
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Affiliation(s)
- Aijun Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Li Ma
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Xinyue Shu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuqi Jiang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Juan Liang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Aiping Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China.
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13
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Zhang J, Feng X, Wu Q, Yang G, Tao M, Yang Y, He Y. Rice bacterial blight resistant cultivar selection based on visible/near-infrared spectrum and deep learning. PLANT METHODS 2022; 18:49. [PMID: 35428329 PMCID: PMC9013134 DOI: 10.1186/s13007-022-00882-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/31/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rice bacterial blight (BB) has caused serious damage in rice yield and quality leading to huge economic loss and food safety problems. Breeding disease resistant cultivar becomes the eco-friendliest and most effective alternative to regulate its outburst, since the propagation of pathogenic bacteria is restrained. However, the BB resistance cultivar selection suffers tremendous labor cost, low efficiency, and subjective human error. And dynamic rice BB phenotyping study is absent from exploring the pattern of BB growth with different genotypes. RESULTS In this paper, with the aim of alleviating the labor burden of plant breeding experts in the resistant cultivar screening processing and exploring the disease resistance phenotyping variation pattern, visible/near-infrared (VIS-NIR) hyperspectral images of rice leaves from three varieties after inoculation were collected and sent into a self-built deep learning model LPnet for disease severity assessment. The growth status of BB lesion at the time scale was fully revealed. On the strength of the attention mechanism inside LPnet, the most informative spectral features related to lesion proportion were further extracted and combined into a novel and refined leaf spectral index. The effectiveness and feasibility of the proposed wavelength combination were verified by identifying the resistant cultivar, assessing the resistant ability, and spectral image visualization. CONCLUSIONS This study illustrated that informative VIS-NIR spectrums coupled with attention deep learning had great potential to not only directly assess disease severity but also excavate spectral characteristics for rapid screening disease resistant cultivars in high-throughput phenotyping.
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Affiliation(s)
- Jinnuo Zhang
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Xuping Feng
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Qingguan Wu
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Guofeng Yang
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Mingzhu Tao
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China.
| | - Yong He
- College of Biosystems Engineering and Food Science, Key Laboratory of Spectroscopy, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, 310058, China.
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