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Ogunyemi SO, Luo J, Abdallah Y, Yu S, Wang X, Alkhalifah DHM, Hozzein WN, Wang F, Bi J, Yan C, Li B. Copper oxide nanoparticles: an effective suppression tool against bacterial leaf blight of rice and its impacts on plants. PEST MANAGEMENT SCIENCE 2024; 80:1279-1288. [PMID: 37897195 DOI: 10.1002/ps.7857] [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: 07/13/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND To address the challenges of food security for the ever-increasing population, the emergence of nanotechnology provides an alternate technology of choice for the production of safer pesticides which serves as a substitute for conventional fertilizer. The antidrug resistance of Xanthomonas oryzae pv. oryzae (Xoo) and build-up of chemicals in the environment has made it necessary to find alternative safe techniques for effective disease management. Hence, in this study, copper oxide nanoparticles (CuONPs) were produced by green synthesis using a Hibiscus rosa-sinensis L. flower extract. RESULTS The characterization of CuONPs using ultraviolet-visible spectrophotometry, scanning electron microscopy with an energy-dispersive spectrum profile, Fourier transform infrared spectroscopy, and X-ray diffraction ascertained the presence of CuONPs, which were nanorods of 28.1 nm. CuONPs significantly obstructed the growth and biofilm development of Xoo by 79.65% and 79.17% respectively. The antibacterial mechanism of CuONPs was found to result from wounding the cell membrane, giving rise to an exodus of intracellular content and generation of oxidative reactive oxygen species that invariably inhibited Xoo respiration and growth. A toxicity study under greenhouse conditions revealed that CuONPs significantly increased growth variables and the biomass of rice, and reduced bacterial leaf blight. Application of CuONPs on Arabidopsis improved the chlorophyll fluorescence parameters; the ΦPSII was significantly increased by 152.05% in comparison to the control. CONCLUSION Altogether, these results suggest that CuONPs in low concentration (200.0 μg mL-1 ) are not toxic to plants and can serve as nano-fertilizers and nano-pesticides. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai, China
| | - Yasmine Abdallah
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Plant Pathology Department, Faculty of Agriculture, Minia University, Elminya, Egypt
| | - Shanhong Yu
- Taizhou Academy of Agricultural Sciences, Taizhou, China
| | - Xiao Wang
- Ningbo Jiangbei District Agricultural Technology Extension Service Station, Ningbo, China
| | - Dalal Hussien M Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Wael N Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Fang Wang
- Crop Institute, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Ji'an Bi
- Crop Institute, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Chengqi Yan
- Crop Institute, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Abdallah Y, Nehela Y, Ogunyemi SO, Ijaz M, Ahmed T, Elashmony R, Alkhalifah DHM, Hozzein WN, Xu L, Yan C, Chen J, Li B. Bio-functionalized nickel-silica nanoparticles suppress bacterial leaf blight disease in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1216782. [PMID: 37655220 PMCID: PMC10466215 DOI: 10.3389/fpls.2023.1216782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023]
Abstract
Introduction Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastative diseases that threatens rice plants worldwide. Biosynthesized nanoparticle (NP) composite compounds have attracted attention as environmentally safe materials that possess antibacterial activity that could be used in managing plant diseases. Methods During this study, a nanocomposite of two important elements, nickel and silicon, was biosynthesized using extraction of saffron stigmas (Crocus sativus L.). Characterization of obtained nickel-silicon dioxide (Ni-SiO2) nanocomposite was investigated using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Transmission/Scanning electron microscopy (TEM/SEM), and energy-dispersive spectrum (EDS). Antibacterial activities of the biosynthesized Ni-SiO2 nanocomposite against Xoo were tested by measuring bacterial growth, biofilm formation, and dead Xoo cells. Results and discussions The bacterial growth (OD600) and biofilm formation (OD570) of Xoo treated with distilled water (control) was found to be 1.21 and 1.11, respectively. Treatment with Ni-SiO2 NPs composite, respectively, reduced the growth and biofilm formation by 89.07% and 80.40% at 200 μg/ml. The impact of obtained Ni-SiO2 nanocomposite at a concentration of 200 μg/ml was assayed on infected rice plants. Treatment of rice seedlings with Ni-SiO2 NPs composite only had a plant height of 64.8 cm while seedlings treated with distilled water reached a height of 45.20 cm. Notably, Xoo-infected seedlings treated with Ni-SiO2 NPs composite had a plant height of 57.10 cm. Furthermore, Ni-SiO2 NPs composite sprayed on inoculated seedlings had a decrease in disease leaf area from 43.83% in non-treated infected seedlings to 13.06% in treated seedlings. The FTIR spectra of biosynthesized Ni-SiO2 nanocomposite using saffron stigma extract showed different bands at 3,406, 1,643, 1,103, 600, and 470 cm-1. No impurities were found in the synthesized composite. Spherically shaped NPs were observed by using TEM and SEM. EDS revealed that Ni-SiO2 nanoparticles (NPs) have 13.26% Ni, 29.62% Si, and 57.11% O. Xoo treated with 200 µg/ml of Ni-SiO2 NPs composite drastically increased the apoptosis of bacterial cells to 99.61% in comparison with 2.23% recorded for the control. Conclusions The application of Ni-SiO2 NPs significantly improved the vitality of rice plants and reduced the severity of BLB.
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Affiliation(s)
- Yasmine Abdallah
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Department of Plant Pathology, Faculty of Agriculture, Minia University, ElMinya, Egypt
| | - Yasser Nehela
- Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Munazza Ijaz
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ranya Elashmony
- Department of Plant Pathology, Faculty of Agriculture, Minia University, ElMinya, Egypt
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Wael N. Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Lihui Xu
- Institute of Eco-Environmental Protection, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chengqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Alsamman AM, Mousa KH, Nassar AE, Faheem MM, Radwan KH, Adly MH, Hussein A, Istanbuli T, Mokhtar MM, Elakkad TA, Kehel Z, Hamwieh A, Abdelsattar M, El Allali A. Identification, characterization, and validation of NBS-encoding genes in grass pea. Front Genet 2023; 14:1187597. [PMID: 37408775 PMCID: PMC10318170 DOI: 10.3389/fgene.2023.1187597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/07/2023] Open
Abstract
Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop.
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Affiliation(s)
- Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled H. Mousa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed E. Nassar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mostafa M. Faheem
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Monica H. Adly
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Tamer Ahmed Elakkad
- Department of Genetics and Genetic Engineering, Faculty of Agriculture at Moshtohor, Benha University, Benha, Egypt
- Moshtohor Research Park, Molecular Biology Lab, Benha University, Benha, Egypt
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Liu J, Wu Y, Zhang X, Gill RA, Hu M, Bai Z, Zhao C, Zhang Y, Liu Y, Hu Q, Cheng X, Huang J, Liu L, Yan S, Liu S. Functional and evolutionary study of MLO gene family in the regulation of Sclerotinia stem rot resistance in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:86. [PMID: 37217949 DOI: 10.1186/s13068-023-02325-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Oilseed rape (Brassica napus L.) is known as one of the most important oilseed crops cultivated around the world. However, its production continuously faces a huge challenge of Sclerotinia stem rot (SSR), a destructive disease caused by the fungus Sclerotinia sclerotiorum, resulting in huge yield loss annually. The SSR resistance in B. napus is quantitative and controlled by a set of minor genes. Identification of these genes and pyramiding them into a variety are a major strategy for SSR resistance breeding in B. napus. RESULTS Here, we performed a genome-wide association study (GWAS) using a natural population of B. napus consisting of 222 accessions to identify BnaA08g25340D (BnMLO2_2) as a candidate gene that regulates the SSR resistance. BnMLO2_2 was a member of seven homolog genes of Arabidopsis Mildew Locus O 2 (MLO2) and the significantly SNPs were mainly distributed in the promoter of BnMLO2_2, suggesting a role of BnMLO2_2 expression level in the regulation of SSR resistance. We expressed BnMLO2_2 in Arabidopsis and the transgenic plants displayed an enhanced SSR resistance. Transcriptome profiling of different tissues of B. napus revealed that BnMLO2_2 had the most expression level in leaf and silique tissues among all the 7 BnMLO2 members and also expressed higher in the SSR resistant accession than in the susceptible accession. In Arabidopsis, mlo2 plants displayed reduced resistance to SSR, whereas overexpression of MLO2 conferred plants an enhanced SSR resistance. Moreover, a higher expression level of MLO2 showed a stronger SSR resistance in the transgenic plants. The regulation of MLO2 in SSR resistance may be associated with the cell death. Collinearity and phylogenetic analysis revealed a large expansion of MLO family in Brassica crops. CONCLUSION Our study revealed an important role of BnMLO2 in the regulation of SSR resistance and provided a new gene candidate for future improvement of SSR resistance in B. napus and also new insights into understanding of MLO family evolution in Brassica crops.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yupo Wu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiong Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Rafaqat Ali Gill
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zetao Bai
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | | | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Qiong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junyan Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
| | - Lijiang Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
| | - Shunping Yan
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
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Mir ZA, Chauhan D, Pradhan AK, Srivastava V, Sharma D, Budhlakoti N, Mishra DC, Jadon V, Sahu TK, Grover M, Gangwar OP, Kumar S, Bhardwaj SC, Padaria JC, Singh AK, Rai A, Singh GP, Kumar S. Comparative transcriptome profiling of near isogenic lines PBW343 and FLW29 to unravel defense related genes and pathways contributing to stripe rust resistance in wheat. Funct Integr Genomics 2023; 23:169. [PMID: 37209309 DOI: 10.1007/s10142-023-01104-1] [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: 02/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
Stripe rust (Sr), caused by Puccinia striiformis f. sp. tritici (Pst), is the most devastating disease that poses serious threat to the wheat-growing nations across the globe. Developing resistant cultivars is the most challenging aspect in wheat breeding. The function of resistance genes (R genes) and the mechanisms by which they influence plant-host interactions are poorly understood. In the present investigation, comparative transcriptome analysis was carried out by involving two near-isogenic lines (NILs) PBW343 and FLW29. The seedlings of both the genotypes were inoculated with Pst pathotype 46S119. In total, 1106 differentially expressed genes (DEGs) were identified at early stage of infection (12 hpi), whereas expressions of 877 and 1737 DEGs were observed at later stages (48 and 72 hpi) in FLW29. The identified DEGs were comprised of defense-related genes including putative R genes, 7 WRKY transcriptional factors, calcium, and hormonal signaling associated genes. Moreover, pathways involved in signaling of receptor kinases, G protein, and light showed higher expression in resistant cultivar and were common across different time points. Quantitative real-time PCR was used to further confirm the transcriptional expression of eight critical genes involved in plant defense mechanism against stripe rust. The information about genes are likely to improve our knowledge of the genetic mechanism that controls the stripe rust resistance in wheat, and data on resistance response-linked genes and pathways will be a significant resource for future research.
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Affiliation(s)
- Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Divya Chauhan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | | | - Vivek Srivastava
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | | | - Vasudha Jadon
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Monendra Grover
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal, Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal, Pradesh, 171002, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal, Pradesh, 171002, India
| | - Jasdeep C Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - G P Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
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Mbo Nkoulou LF, Ngalle HB, Cros D, Adje COA, Fassinou NVH, Bell J, Achigan-Dako EG. Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species. FRONTIERS IN PLANT SCIENCE 2022; 13:953133. [PMID: 36388523 PMCID: PMC9650417 DOI: 10.3389/fpls.2022.953133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Genomic selection (GS) in plant breeding is explored as a promising tool to solve the problems related to the biotic and abiotic threats. Polyploid plants like bananas (Musa spp.) face the problem of drought and black sigatoka disease (BSD) that restrict their production. The conventional plant breeding is experiencing difficulties, particularly phenotyping costs and long generation interval. To overcome these difficulties, GS in plant breeding is explored as an alternative with a great potential for reducing costs and time in selection process. So far, GS does not have the same success in polyploid plants as with diploid plants because of the complexity of their genome. In this review, we present the main constraints to the application of GS in polyploid plants and the prospects for overcoming these constraints. Particular emphasis is placed on breeding for BSD and drought-two major threats to banana production-used in this review as a model of polyploid plant. It emerges that the difficulty in obtaining markers of good quality in polyploids is the first challenge of GS on polyploid plants, because the main tools used were developed for diploid species. In addition to that, there is a big challenge of mastering genetic interactions such as dominance and epistasis effects as well as the genotype by environment interaction, which are very common in polyploid plants. To get around these challenges, we have presented bioinformatics tools, as well as artificial intelligence approaches, including machine learning. Furthermore, a scheme for applying GS to banana for BSD and drought has been proposed. This review is of paramount impact for breeding programs that seek to reduce the selection cycle of polyploids despite the complexity of their genome.
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Affiliation(s)
- Luther Fort Mbo Nkoulou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
- Institute of Agricultural Research for Development, Centre de Recherche Agricole de Mbalmayo (CRAM), Mbalmayo, Cameroon
| | - Hermine Bille Ngalle
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - David Cros
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR) Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Montpellier, France
- Unité Mixte de Recherche (UMR) Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, University of Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Agro, Montpellier, France
| | - Charlotte O. A. Adje
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| | - Nicodeme V. H. Fassinou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| | - Joseph Bell
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Enoch G. Achigan-Dako
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
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Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. BIOLOGY 2022; 11:biology11060821. [PMID: 35741342 PMCID: PMC9220128 DOI: 10.3390/biology11060821] [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: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Developing cultivars with resistance genes (R genes) is an effective strategy to support high yield and quality in Brassica crops. The availability of clone R gene and genomic sequences in Brassica species and Arabidopsis thaliana provide the opportunity to compare genomic regions and survey R genes across genomic databases. In this paper, we aim to identify genes related to cloned genes through sequence identity, providing a repertoire of species-wide related R genes in Brassica crops. The comprehensive list of candidate R genes can be used as a reference for functional analysis. Abstract Various diseases severely affect Brassica crops, leading to significant global yield losses and a reduction in crop quality. In this study, we used the complete protein sequences of 49 cloned resistance genes (R genes) that confer resistance to fungal and bacterial diseases known to impact species in the Brassicaceae family. Homology searches were carried out across Brassica napus, B. rapa, B. oleracea, B. nigra, B. juncea, B. carinata and Arabidopsis thaliana genomes. In total, 660 cloned disease R gene homologs (CDRHs) were identified across the seven species, including 431 resistance gene analogs (RGAs) (248 nucleotide binding site-leucine rich repeats (NLRs), 150 receptor-like protein kinases (RLKs) and 33 receptor-like proteins (RLPs)) and 229 non-RGAs. Based on the position and distribution of specific homologs in each of the species, we observed a total of 87 CDRH clusters composed of 36 NLR, 16 RLK and 3 RLP homogeneous clusters and 32 heterogeneous clusters. The CDRHs detected consistently across the seven species are candidates that can be investigated for broad-spectrum resistance, potentially providing resistance to multiple pathogens. The R genes identified in this study provide a novel resource for the future functional analysis and gene cloning of Brassicaceae R genes towards crop improvement.
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Du XX, Park JR, Wang XH, Jan R, Lee GS, Kim KM. Genotype and Phenotype Interaction between OsWKRYq6 and BLB after Xanthomonas oryzae pv. Oryzae Inoculation in the Field. PLANTS 2022; 11:plants11030287. [PMID: 35161267 PMCID: PMC8840003 DOI: 10.3390/plants11030287] [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: 10/18/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022]
Abstract
Bacterial leaf blight (BLB) is an important and devastating rice disease caused by the pathogen Xanthomonas oryzae pv. Oryzae (Xoo). In particular, in recent years, the occurrence of abnormal climate and warming phenomena has produced a good environment for the occurrence of BLB, and the rice yield due to the occurrence of BLB continues to decrease. Currently, molecular breeding is applied by searching for resistant genes to development of BLB resistance cultivar. In addition, there are many methods for screening resistant genes, and among them, phenotype analysis in the field and applied research is rarely conducted. Due to recent rapid climate change, BLB is a major problem that has a more serious negative effect on rice yield. Therefore, we suggest OsWRKYq6 to be effectively used for breeding BLB-resistant cultivars by screening BLB-resistant genes. In this study, the BLB-resistant gene was screened using the lesion length, which most definitely changes to the phenotype when Xoo is infected. OsWRKYq6 was finally selected as a BLB resistance gene by analyzing the phenotype and genotype after inoculating Xoo in 120 Cheongcheong/Nagdong double haploid (CNDH) lines in the field. After Xoo inoculation, lesion length and yield were investigated, and 120 CNDH lines were divided from BLB-resistant and susceptible lines. Moreover, when the transcription level of OsWRKYq6 was analyzed in the resistant and susceptible lines after Xoo inoculation in the field, the expression level was regulated to a high level in the resistant line. In this study, we propose OsWRKYq6 as a transcription factor involved in BLB resistance. Currently, the differentiation of various races is proceeding rapidly due to rapid climate change. In addition, screening of transcription factor genes involved in BLB resistance in the field can be effectively applied to molecular breeding to develop resistant cultivars in preparation for rapid climate change.
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Affiliation(s)
- Xiao-Xuan Du
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea
| | - Jae-Ryoung Park
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (J.-R.P.); (R.J.)
- Department of Crop Breeding, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea
| | - Xiao-Han Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54875, Korea;
| | - Rahmatullah Jan
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (J.-R.P.); (R.J.)
| | - Gang-Seob Lee
- Biosafety Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4791 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
| | - Kyung-Min Kim
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea
- Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Korea; (J.-R.P.); (R.J.)
- Correspondence: (G.-S.L.); (K.-M.K.); Tel.: +82-63-238-4791 (G.-S.L.); +82-53-950-5711 (K.-M.K.)
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Understanding Rice- Magnaporthe Oryzae Interaction in Resistant and Susceptible Cultivars of Rice under Panicle Blast Infection Using a Time-Course Transcriptome Analysis. Genes (Basel) 2021; 12:genes12020301. [PMID: 33672641 PMCID: PMC7924189 DOI: 10.3390/genes12020301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/21/2023] Open
Abstract
Rice blast is a global threat to food security with up to 50% yield losses. Panicle blast is a more severe form of rice blast and the response of rice plant to leaf and panicle blast is distinct in different genotypes. To understand the specific response of rice in panicle blast, transcriptome analysis of blast resistant cultivar Tetep, and susceptible cultivar HP2216 was carried out using RNA-Seq approach after 48, 72 and 96 h of infection with Magnaporthe oryzae along with mock inoculation. Transcriptome data analysis of infected panicle tissues revealed that 3553 genes differentially expressed in HP2216 and 2491 genes in Tetep, which must be the responsible factor behind the differential disease response. The defense responsive genes are involved mainly in defense pathways namely, hormonal regulation, synthesis of reactive oxygen species, secondary metabolites and cell wall modification. The common differentially expressed genes in both the cultivars were defense responsive transcription factors, NBS-LRR genes, kinases, pathogenesis related genes and peroxidases. In Tetep, cell wall strengthening pathway represented by PMR5, dirigent, tubulin, cell wall proteins, chitinases, and proteases was found to be specifically enriched. Additionally, many novel genes having DOMON, VWF, and PCaP1 domains which are specific to cell membrane were highly expressed only in Tetep post infection, suggesting their role in panicle blast resistance. Thus, our study shows that panicle blast resistance is a complex phenomenon contributed by early defense response through ROS production and detoxification, MAPK and LRR signaling, accumulation of antimicrobial compounds and secondary metabolites, and cell wall strengthening to prevent the entry and spread of the fungi. The present investigation provided valuable candidate genes that can unravel the mechanisms of panicle blast resistance and help in the rice blast breeding program.
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de Jesús-Pires C, Ferreira-Neto JRC, Pacifico Bezerra-Neto J, Kido EA, de Oliveira Silva RL, Pandolfi V, Wanderley-Nogueira AC, Binneck E, da Costa AF, Pio-Ribeiro G, Pereira-Andrade G, Sittolin IM, Freire-Filho F, Benko-Iseppon AM. Plant Thaumatin-like Proteins: Function, Evolution and Biotechnological Applications. Curr Protein Pept Sci 2021; 21:36-51. [PMID: 30887921 DOI: 10.2174/1389203720666190318164905] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/01/2019] [Accepted: 03/11/2019] [Indexed: 12/30/2022]
Abstract
Thaumatin-like proteins (TLPs) are a highly complex protein family associated with host defense and developmental processes in plants, animals, and fungi. They are highly diverse in angiosperms, for which they are classified as the PR-5 (Pathogenesis-Related-5) protein family. In plants, TLPs have a variety of properties associated with their structural diversity. They are mostly associated with responses to biotic stresses, in addition to some predicted activities under drought and osmotic stresses. The present review covers aspects related to the structure, evolution, gene expression, and biotechnological potential of TLPs. The efficiency of the discovery of new TLPs is below its potential, considering the availability of omics data. Furthermore, we present an exemplary bioinformatics annotation procedure that was applied to cowpea (Vigna unguiculata) transcriptome, including libraries of two tissues (root and leaf), and two stress types (biotic/abiotic) generated using different sequencing approaches. Even without using genomic sequences, the pipeline uncovered 56 TLP candidates in both tissues and stresses. Interestingly, abiotic stress (root dehydration) was associated with a high number of modulated TLP isoforms. The nomenclature used so far for TLPs was also evaluated, considering TLP structure and possible functions identified to date. It is clear that plant TLPs are promising candidates for breeding purposes and for plant transformation aiming a better performance under biotic and abiotic stresses. The development of new therapeutic drugs against human fungal pathogens also deserves attention. Despite that, applications derived from TLP molecules are still below their potential, as it is evident in our review.
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Affiliation(s)
- Carolline de Jesús-Pires
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - João Pacifico Bezerra-Neto
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Ederson Akio Kido
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Eliseu Binneck
- Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Soja, Londrina, Parana, Brazil
| | | | - Gilvan Pio-Ribeiro
- Departamento de Agronomia/Fitossanidade, Universidade Federal Rural de Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Genira Pereira-Andrade
- Departamento de Agronomia/Fitossanidade, Universidade Federal Rural de Pernambuco (UFRPE), Recife, Pernambuco, Brazil
| | - Ilza Maria Sittolin
- Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Meio-Norte, Teresina, Piaui, Brazil
| | - Francisco Freire-Filho
- Empresa Brasileira de Pesquisa Agropecuaria, Embrapa Amazonia Oriental, Belem, Para, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genetica, Centro de Biociencias, Universidade Federal de Pernambuco (UFPE), Recife, Pernambuco, Brazil
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11
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Sruthilaxmi CB, Babu S. Proteome Responses to Individual Pathogens and Abiotic Conditions in Rice Seedlings. PHYTOPATHOLOGY 2020; 110:1326-1341. [PMID: 32175828 DOI: 10.1094/phyto-11-19-0425-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice plants under field conditions experience various biotic and abiotic stresses and are adapted to survive using a molecular cross-talk of genes and their protein products based on the severity of a given stress. Seedlings of cultivated variety ASD16 (resistant to fungal disease, blast; tolerant to abiotic stress, salinity) were subjected to salt, drought, high temperature and low temperature stress as well as infection by Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (causing reemerging diseases such as sheath blight and leaf blight), respectively, the sheath blight and bacterial leaf blight pathogens. Leaf proteome was analyzed using two-dimensional electrophoresis and differentially expressed proteins were identified using mass spectrometry. In addition to many other differentially expressed proteins, acidic endochitinase was found to be upregulated during fungal infection and drought treatment, and a germin-like protein upregulated during fungal infection and high temperature stress. These two proteins were further validated at the gene expression level using reverse transcription-PCR in dual stress experiments. Pot culture plants were subjected to fungal infection followed by drought and drought followed by fungal infection to validate chitinase gene expression. Similarly, plants subjected to fungal infections followed by high temperature stress and vice versa were used to validate the expression of germin-like protein-coding gene. The results of the present study indicate that chitinase and germin-like protein are potential targets for further exploration to develop rice plants resistant or tolerant to biotic and abiotic stresses.
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Affiliation(s)
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore 632014, India
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12
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Dolatabadian A, Bayer PE, Tirnaz S, Hurgobin B, Edwards D, Batley J. Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:969-982. [PMID: 31553100 PMCID: PMC7061875 DOI: 10.1111/pbi.13262] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 05/18/2023]
Abstract
Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.
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Affiliation(s)
- Aria Dolatabadian
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Bhavna Hurgobin
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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Singh S, Mahato AK, Jayaswal PK, Singh N, Dheer M, Goel P, Raje RS, Yasin JK, Sreevathsa R, Rai V, Gaikwad K, Singh NK. A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.). Sci Rep 2020; 10:4960. [PMID: 32188919 PMCID: PMC7080765 DOI: 10.1038/s41598-020-61889-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/04/2020] [Indexed: 12/05/2022] Open
Abstract
Pigeonpea is the second most important pulse legume crop for food and nutritional security of South Asia that requires accelerated breeding using high throughput genomic tools. Single nucleotide polymorphisms (SNPs) are highly suitable markers for this purpose because of their bi-allelic nature, reproducibility and high abundance in the genome. Here we report on development and use of a pigeonpea 62 K SNP chip array ‘CcSNPnks’ for Affymetrix GeneTitan® platform. The array was designed after filtering 645,662 genic-SNPs identified by re-sequencing of 45 diverse genotypes and has 62,053 SNPs from 9629 genes belonging to five different categories, including 4314 single-copy genes unique to pigeonpea, 4328 single-copy genes conserved between soybean and pigeonpea, 156 homologs of agronomically important cloned genes, 746 disease resistance and defense response genes and 85 multi-copy genes of pigeonpea. This fully genic chip has 28.94% exonic, 33.04% intronic, 27.56% 5′UTR and 10.46% 3′UTR SNPs and incorporates multiple SNPs per gene allowing gene haplotype network analysis. It was used successfully for the analysis of genetic diversity and population structure of 95 pigeonpea varieties and high resolution mapping of 11 yield related QTLs for number of branches, pod bearing length and number of seeds per pod in a biparental RIL population. As an accurate high-density genotyping tool, ‘CcSNPnks’ chip array will be useful for high resolution fingerprinting, QTL mapping and genome wide as well as gene-based association studies in pigeonpea.
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Affiliation(s)
- Sangeeta Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Ajay K Mahato
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Pawan K Jayaswal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nisha Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Meenakshi Dheer
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Preeti Goel
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ranjeet S Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jeshima K Yasin
- ICAR-National Bureau of Plant Genetic Resources Pusa Campus, New Delhi, 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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14
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Sun X, Zhang L, Tang Z, Shi X, Ma J, Cui R. Transcriptome analysis of roots from resistant and susceptible rice varieties infected with Hirschmanniella mucronata. FEBS Open Bio 2019; 9:1968-1982. [PMID: 31571430 PMCID: PMC6823281 DOI: 10.1002/2211-5463.12737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/14/2019] [Accepted: 09/27/2019] [Indexed: 01/23/2023] Open
Abstract
Hirschmanniella mucronata is a plant-parasitic nematode that is widespread in rice production areas and causes 10-25% yield losses a year on average. Here, we investigated the mechanism of resistance to this nematode by comparing the transcriptomes of roots from resistant (Jiabali) and susceptible (Bawangbian) varieties of rice. Of 39 233 unigenes, 2243. exhibited altered total expression levels between control and infected resistant and susceptible varieties. Significant differences were observed in the expression levels of genes related to stress, peptidase regulation or inhibition, oxidoreductase activity, peroxidase activity and antioxidant activity. The up-regulated genes related to plant secondary metabolites, such as phenylpropanoid, lignin, cellulose or hemicellulose, may result in an increase in the degree of resistance of Jiabali to the H. mucronata infection compared with that of Bawangbian by affecting cell wall organization or biogenesis. Of the genes that responded similarly to H. mucronata infection, ~252 (~76.59%) showed greater changes (whether induced or suppressed) in RN155 (susceptible varieties infected by rice root nematode) than in RN51 (resistance varieties infected by rice root nematode). Nineteen pathogenesis-related genes belonging to nine pathogenesis-related gene families were significantly induced by H. mucronata in the infected roots of Jiabali and Bawangbian, and 13 differentially expressed genes showed changes in their abundance only in the susceptible Bawangbian variety. This study may help enhance our understanding of the mechanisms underlying plant resistance to nematodes.
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Affiliation(s)
- Xiaotang Sun
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lei Zhang
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ziqing Tang
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xugen Shi
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jian Ma
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ruqiang Cui
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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15
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Bayer PE, Golicz AA, Tirnaz S, Chan CK, Edwards D, Batley J. Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:789-800. [PMID: 30230187 PMCID: PMC6419861 DOI: 10.1111/pbi.13015] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/16/2018] [Accepted: 09/14/2018] [Indexed: 05/19/2023]
Abstract
Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. oleracea lines. The sequenced reference cultivar does not contain all B. oleracea genes due to gene presence/absence variation between individuals, which makes it necessary to search for RGA candidates in the B. oleracea pangenome. Here we present a comparative analysis of RGA candidates in the pangenome of B. oleracea. We show that the presence of RGA candidates differs between lines and suggests that in B. oleracea, SNPs and presence/absence variation drive RGA diversity using separate mechanisms. We identified 59 RGA candidates linked to Sclerotinia, clubroot, and Fusarium wilt resistance QTL, and these findings have implications for crop breeding in B. oleracea, which may also be applicable in other crops species.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVic.Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Chon‐Kit Kenneth Chan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
- Australian Genome Research FacilityMelbourneVic.Australia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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Bourgeois Y, Stritt C, Walser JC, Gordon SP, Vogel JP, Roulin AC. Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:438-451. [PMID: 30044522 DOI: 10.1111/tpj.14042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/20/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species, and affects different genomic regions across the two populations. Gene ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near base-perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Christoph Stritt
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH Zürich, Universitätstrasse 16, Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anne C Roulin
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
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Singh PK, Nag A, Arya P, Kapoor R, Singh A, Jaswal R, Sharma TR. Prospects of Understanding the Molecular Biology of Disease Resistance in Rice. Int J Mol Sci 2018; 19:E1141. [PMID: 29642631 PMCID: PMC5979409 DOI: 10.3390/ijms19041141] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.
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Affiliation(s)
- Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Nag
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Preeti Arya
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
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Yasmin S, Hafeez FY, Mirza MS, Rasul M, Arshad HMI, Zubair M, Iqbal M. Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3. Front Microbiol 2017; 8:1895. [PMID: 29018437 PMCID: PMC5622989 DOI: 10.3389/fmicb.2017.01895] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/15/2017] [Indexed: 01/28/2023] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is widely prevalent and causes Bacterial Leaf Blight (BLB) in Basmati rice grown in different areas of Pakistan. There is a need to use environmentally safe approaches to overcome the loss of grain yield in rice due to this disease. The present study aimed to develop inocula, based on native antagonistic bacteria for biocontrol of BLB and to increase the yield of Super Basmati rice variety. Out of 512 bacteria isolated from the rice rhizosphere and screened for plant growth promoting determinants, the isolate BRp3 was found to be the best as it solubilized 97 μg/ mL phosphorus, produced 30 μg/mL phytohormone indole acetic acid and 15 mg/ L siderophores in vitro. The isolate BRp3 was found to be a Pseudomonas aeruginosa based on 16S rRNA gene sequencing (accession no. HQ840693). This bacterium showed antagonism in vitro against different phytopathogens including Xoo and Fusarium spp. Strain BRp3 showed consistent pathogen suppression of different strains of BLB pathogen in rice. Mass spectrometric analysis detected the production of siderophores (1-hydroxy-phenazine, pyocyanin, and pyochellin), rhamnolipids and a series of already characterized 4-hydroxy-2-alkylquinolines (HAQs) as well as novel 2,3,4-trihydroxy-2-alkylquinolines and 1,2,3,4-tetrahydroxy-2-alkylquinolines in crude extract of BRp3. These secondary metabolites might be responsible for the profound antibacterial activity of BRp3 against Xoo pathogen. Another contributing factor toward the suppression of the pathogen was the induction of defense related enzymes in the rice plant by the inoculated strain BRp3. When used as an inoculant in a field trial, this strain enhanced the grain and straw yields by 51 and 55%, respectively, over non-inoculated control. Confocal Laser Scanning Microscopy (CLSM) used in combination with immunofluorescence marker confirmed P. aeruginosa BRp3 in the rice rhizosphere under sterilized as well as field conditions. The results provide evidence that novel secondary metabolites produced by BRp3 may contribute to its activity as a biological control agent against Xoo and its potential to promote the growth and yield of Super Basmati rice.
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Affiliation(s)
- Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Fauzia Y Hafeez
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad S Mirza
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Maria Rasul
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Hafiz M I Arshad
- Plant Protection Division, Nuclear Institute of Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad Zubair
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Mazhar Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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19
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Wu J, Zhu J, Wang L, Wang S. Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean. FRONTIERS IN PLANT SCIENCE 2017; 8:1398. [PMID: 28848595 PMCID: PMC5552710 DOI: 10.3389/fpls.2017.01398] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/26/2017] [Indexed: 05/03/2023]
Abstract
Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the largest and most important disease resistance genes in plants. The genome sequence of the common bean (Phaseolus vulgaris L.) provides valuable data for determining the genomic organization of NBS-LRR genes. However, data on the NBS-LRR genes in the common bean are limited. In total, 178 NBS-LRR-type genes and 145 partial genes (with or without a NBS) located on 11 common bean chromosomes were identified from genome sequences database. Furthermore, 30 NBS-LRR genes were classified into Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) types, and 148 NBS-LRR genes were classified into coiled-coil (CC)-NBS-LRR (CNL) types. Moreover, the phylogenetic tree supported the division of these PvNBS genes into two obvious groups, TNL types and CNL types. We also built expression profiles of NBS genes in response to anthracnose and common bacterial blight using qRT-PCR. Finally, we detected nine disease resistance loci for anthracnose (ANT) and seven for common bacterial blight (CBB) using the developed NBS-SSR markers. Among these loci, NSSR24, NSSR73, and NSSR265 may be located at new regions for ANT resistance, while NSSR65 and NSSR260 may be located at new regions for CBB resistance. Furthermore, we validated NSSR24, NSSR65, NSSR73, NSSR260, and NSSR265 using a new natural population. Our results provide useful information regarding the function of the NBS-LRR proteins and will accelerate the functional genomics and evolutionary studies of NBS-LRR genes in food legumes. NBS-SSR markers represent a wide-reaching resource for molecular breeding in the common bean and other food legumes. Collectively, our results should be of broad interest to bean scientists and breeders.
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Affiliation(s)
| | | | | | - Shumin Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijing, China
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20
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The draft genome of Corchorus olitorius cv. JRO-524 (Navin). GENOMICS DATA 2017; 12:151-154. [PMID: 28540183 PMCID: PMC5432662 DOI: 10.1016/j.gdata.2017.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/23/2022]
Abstract
Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).
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21
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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22
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Frazier TP, Palmer NA, Xie F, Tobias CM, Donze-Reiner TJ, Bombarely A, Childs KL, Shu S, Jenkins JW, Schmutz J, Zhang B, Sarath G, Zhao B. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. BMC Genomics 2016; 17:892. [PMID: 27821048 PMCID: PMC5100175 DOI: 10.1186/s12864-016-3201-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. RESULTS In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated. CONCLUSIONS Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.
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Affiliation(s)
| | - Nathan A. Palmer
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583-0937 USA
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | | | - Teresa J. Donze-Reiner
- Department of Biology, West Chester University of Pennsylvania, Wester Chester, PA 19382 USA
| | | | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94595 USA
| | - Jerry W. Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94595 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583-0937 USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
- 407 Latham Hall, 220 Ag Quad Lane, Blacksburg, VA 24061 USA
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23
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Wei L, Jian H, Lu K, Filardo F, Yin N, Liu L, Qu C, Li W, Du H, Li J. Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1368-80. [PMID: 26563848 DOI: 10.1111/pbi.12501] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 05/20/2023]
Abstract
Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Fiona Filardo
- Queensland Department of Agriculture and Fisheries (QDAF), Ecosciences Precinct, Brisbane, Old, Australia
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hai Du
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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24
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Sekhwal MK, Li P, Lam I, Wang X, Cloutier S, You FM. Disease Resistance Gene Analogs (RGAs) in Plants. Int J Mol Sci 2015; 16:19248-90. [PMID: 26287177 PMCID: PMC4581296 DOI: 10.3390/ijms160819248] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/01/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022] Open
Abstract
Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens' resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed.
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Affiliation(s)
- Manoj Kumar Sekhwal
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Pingchuan Li
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Irene Lam
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Xiue Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sylvie Cloutier
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Plant Science Department, University of Manitoba, Winnipeg, MB R3T 2N6, Canada.
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