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Chiwina K, Xiong H, Bhattarai G, Dickson RW, Phiri TM, Chen Y, Alatawi I, Dean D, Joshi NK, Chen Y, Riaz A, Gepts P, Brick M, Byrne PF, Schwartz H, Ogg JB, Otto K, Fall A, Gilbert J, Shi A. Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection. Int J Mol Sci 2023; 24:15300. [PMID: 37894980 PMCID: PMC10607830 DOI: 10.3390/ijms242015300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for Fop race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved Fop resistance.
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Affiliation(s)
- Kenani Chiwina
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Ryan William Dickson
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Theresa Makawa Phiri
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Ibtisam Alatawi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Derek Dean
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
| | - Neelendra K. Joshi
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Yuyan Chen
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Awais Riaz
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Paul Gepts
- Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA;
| | - Mark Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Patrick F. Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Howard Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; (H.S.); (K.O.)
| | - James B. Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Kristin Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA; (H.S.); (K.O.)
| | - Amy Fall
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Jeremy Gilbert
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.B.); (P.F.B.); (J.B.O.); (A.F.); (J.G.)
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (K.C.); (G.B.); (R.W.D.); (T.M.P.); (Y.C.); (I.A.); (D.D.)
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Pan YH, Chen L, Guo HF, Feng R, Lou QJ, Rashid MAR, Zhu XY, Qing DJ, Liang HF, Gao LJ, Huang CC, Zhao Y, Deng GF. Systematic Analysis of NB-ARC Gene Family in Rice and Functional Characterization of GNP12. Front Genet 2022; 13:887217. [PMID: 35783267 PMCID: PMC9244165 DOI: 10.3389/fgene.2022.887217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
The NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) gene family plays a critical role in plant development. However, our understanding of the mechanisms of how NB-ARC genes regulate plant development in the plant panicle is still limited. Here, we subjected 258 NB-ARC genes in rice to genome-wide analysis to characterize their structure, function, and expression patterns. The NB-ARC genes were classified into three major groups, and group II included nine subgroups. Evolutionary analysis of NB-ARC genes in a dicotyledon plant (Arabidopsis thaliana) and two monocotyledonous plants (Oryza sativa L. and Triticum aestivum) indicated that homologous genome segments were conserved in monocotyledons and subjected to weak positive selective pressure during evolution. Dispersed and proximal replication events were detected. Expression analysis showed expression of most NB-ARC genes in roots, panicles, and leaves, and regulation at the panicle development stage in rice Ce253. The GNP12 gene encodes RGH1A protein, which regulates rice yield according to panicle length, grain number of panicle, and grain length, with eight major haplotypes. Most members of NB-ARC protein family are predicted to contain P-loop conserved domains and localize on the membrane. The results of this study will provide insight into the characteristics and evolution of NB-ARC family and suggest that GNP12 positively regulates panicle development.
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Affiliation(s)
- Ying-Hua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
- *Correspondence: Ying-Hua Pan, ; Yan Zhao, ; Guo-Fu Deng,
| | - Lei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Hai-Feng Guo
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Rui Feng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Qi-Jin Lou
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | | | - Xiao-Yang Zhu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Dong-Jin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Hai-Fu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Li-Jun Gao
- Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Cheng-Cui Huang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- *Correspondence: Ying-Hua Pan, ; Yan Zhao, ; Guo-Fu Deng,
| | - Guo-Fu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
- *Correspondence: Ying-Hua Pan, ; Yan Zhao, ; Guo-Fu Deng,
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Anuragi H, Yadav R, Sheoran R. Gamma-rays and EMS induced resistance to mungbean yellow mosaic India virus in mungbean [ Vigna radiata (L.) R. Wilczek] and its validation using linked molecular markers. Int J Radiat Biol 2021; 98:69-81. [PMID: 34705607 DOI: 10.1080/09553002.2022.1998710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE Mungbean yellow mosaic India virus (MYMIV) is a serious constraint in the mungbean which is a potential source of easily digestible high-quality proteins, fibers, minerals, and vitamins in Asian countries. Developing resistant cultivars is the most cost-effective, eco-friendly, and sustainable approach to protect mungbean from MYMIV damage. Mutation breeding provides a quick and cost-effective way of developing resistance as lack of genetic variability is the biggest bottleneck for other traditional breeding tools. MATERIALS AND METHODS Outstanding but MYMIV-sensitive varieties of mungbean, viz., MH 2-15 and MH 318 were mutagenized through various individual and combined doses of gamma-rays and Ethyl methanesulfonate (EMS) and evaluated in M2 and M3 generations for the appearance of resistance reactions. This was subsequently validated through marker-assisted genotyping using previously reported Yellow Mosaic Disease (YMD) linked markers. RESULTS The phenotyping in M3 generation yielded 64 MYMIV resistant mutants whereas, marker-assisted genotyping identified the 22 mutants with true resistance. Markers YR4, CYR1, and CEDG180 were found associated with MYMIV resistance whereas, DMB-SSR158 did not show any amplification. Among identified resistant mutants, ten lines exhibited at par and two revealed a little higher seed yield over controls. CONCLUSIONS The mutagenesis created significant variability in MYMIV resistance as well as seed yield per plant. YR4, CYR1, and CEDG180 are found to be linked with the MYMIV loci in the mungbean and could be utilized for MYMIV resistance breeding. Mutant M-37 from MH 2-15 and M-104 from MH 318 exhibited more seed yield along with MYMIV resistance which upon further validation can be released as a variety. The induced mutagenesis integrated with powerful emerging molecular and next-generation sequencing (NGS) tools would be highly helpful in breeding mungbean for durable resistance against threatening MYMIV.
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Affiliation(s)
- Hirdayesh Anuragi
- ICAR-Central Agroforestry Research Institute, Jhansi, India.,Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Rajesh Yadav
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Ravika Sheoran
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
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Monino‐Lopez D, Nijenhuis M, Kodde L, Kamoun S, Salehian H, Schentsnyi K, Stam R, Lokossou A, Abd‐El‐Haliem A, Visser RG, Vossen JH. Allelic variants of the NLR protein Rpi-chc1 differentially recognize members of the Phytophthora infestans PexRD12/31 effector superfamily through the leucine-rich repeat domain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:182-197. [PMID: 33882622 PMCID: PMC8362081 DOI: 10.1111/tpj.15284] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 05/22/2023]
Abstract
Phytophthora infestans is a pathogenic oomycete that causes the infamous potato late blight disease. Resistance (R) genes from diverse Solanum species encode intracellular receptors that trigger effective defense responses upon the recognition of cognate RXLR avirulence (Avr) effector proteins. To deploy these R genes in a durable fashion in agriculture, we need to understand the mechanism of effector recognition and the way the pathogen evades recognition. In this study, we cloned 16 allelic variants of the Rpi-chc1 gene from Solanum chacoense and other Solanum species, and identified the cognate P. infestans RXLR effectors. These tools were used to study effector recognition and co-evolution. Functional and non-functional alleles of Rpi-chc1 encode coiled-coil nucleotide-binding leucine-rich repeat (CNL) proteins, being the first described representatives of the CNL16 family. These alleles have distinct patterns of RXLR effector recognition. While Rpi-chc1.1 recognized multiple PexRD12 (Avrchc1.1) proteins, Rpi-chc1.2 recognized multiple PexRD31 (Avrchc1.2) proteins, both belonging to the PexRD12/31 effector superfamily. Domain swaps between Rpi-chc1.1 and Rpi-chc1.2 revealed that overlapping subdomains in the leucine-rich repeat (LRR) domain are responsible for the difference in effector recognition. This study showed that Rpi-chc1.1 and Rpi-chc1.2 evolved to recognize distinct members of the same PexRD12/31 effector family via the LRR domain. The biased distribution of polymorphisms suggests that exchange of LRRs during host-pathogen co-evolution can lead to novel recognition specificities. These insights will guide future strategies to breed durable resistant varieties.
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Affiliation(s)
- Daniel Monino‐Lopez
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Maarten Nijenhuis
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Agrico ResearchBurchtweg 17Bant8314PPThe Netherlands
| | - Linda Kodde
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research Park, NorwichUK
| | - Hamed Salehian
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Kyrylo Schentsnyi
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Center for Plant Molecular BiologyAuf der Morgenstelle 32Tübingen2076Germany
| | - Remco Stam
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Technical University MunichMunichGermany
| | - Anoma Lokossou
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Ahmed Abd‐El‐Haliem
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
- Present address:
Rijk Zwaan Breeding B.VBurgemeester Crezéelaan 40De Lier2678KXThe Netherlands
| | - Richard G.F. Visser
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
| | - Jack H. Vossen
- Plant BreedingWageningen University & ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands
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Mishra GP, Dikshit HK, S. V. R, Tripathi K, Kumar RR, Aski M, Singh A, Roy A, Priti, Kumari N, Dasgupta U, Kumar A, Praveen S, Nair RM. Yellow Mosaic Disease (YMD) of Mungbean ( Vigna radiata (L.) Wilczek): Current Status and Management Opportunities. FRONTIERS IN PLANT SCIENCE 2020; 11:918. [PMID: 32670329 PMCID: PMC7327115 DOI: 10.3389/fpls.2020.00918] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/04/2020] [Indexed: 03/30/2024]
Abstract
Globally, yellow mosaic disease (YMD) remains a major constraint of mungbean production, and management of this deadly disease is still the biggest challenge. Thus, finding ways to manage YMD including development of varieties possessing resistance against mungbean yellow mosaic virus (MYMV) and mungbean yellow mosaic India virus (MYMIV) is a research priority for mungbean crop. Characterization of YMD resistance using various advanced molecular and biochemical approaches during plant-virus interactions has unfolded a comprehensive network of pathogen survival, disease severity, and the response of plants to pathogen attack, including mechanisms of YMD resistance in mungbean. The biggest challenge in YMD management is the effective utilization of an array of information gained so far, in an integrated manner for the development of genotypes having durable resistance against yellow mosaic virus (YMV) infection. In this backdrop, this review summarizes the role of various begomoviruses, its genomic components, and vector whiteflies, including cryptic species in the YMD expression. Also, information about the genetics of YMD in both mungbean and blackgram crops is comprehensively presented, as both the species are crossable, and same viral strains are also found affecting these crops. Also, implications of various management strategies including the use of resistance sources, the primary source of inoculums and vector management, wide-hybridization, mutation breeding, marker-assisted selection (MAS), and pathogen-derived resistance (PDR) are thoroughly discussed. Finally, the prospects of employing various powerful emerging tools like translational genomics, and gene editing using CRISPR/Cas9 are also highlighted to complete the YMD management perspective in mungbean.
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Affiliation(s)
- Gyan P. Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harsh K. Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramesh S. V.
- Division of Physiology, Biochemistry and PHT, ICAR-Central Plantation, Kasaragod, India
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet R. Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anirban Roy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priti
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nikki Kumari
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Uttarayan Dasgupta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shelly Praveen
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramakrishnan M. Nair
- World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, Hyderabad, India
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Zhang S, Ding F, Peng H, Huang Y, Lu J. Molecular cloning of a CC-NBS-LRR gene from Vitis quinquangularis and its expression pattern in response to downy mildew pathogen infection. Mol Genet Genomics 2017; 293:61-68. [PMID: 28864888 DOI: 10.1007/s00438-017-1360-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Downy mildew, caused by Plasmopara viticola, can result in a substantial decrease in grapevine productivity. Vitis vinifera is a widely cultivated grapevine species, which is susceptible to this disease. Repeated pesticide applications are harmful for both the environment and human health. Thus, it is essential to develop varieties/cultivars that are resistant to downy mildew and other diseases. In our previous studies, we investigated the natural resistance of the Chinese wild grapevine V. quinquangularis accession 'PS' against P. viticola and obtained several candidate resistance (R) genes that may play important roles in plant disease resistance. In the present study, we isolated a CC-NBS-LRR-type R gene from 'PS' and designated it VqCN. Its open reading frame is 2676 bp which encodes a protein of 891 amino acids with a predicted molecular mass of 102.12 kDa and predicted isoelectric point of 6.53. Multiple alignments with other disease resistant (R) proteins revealed a conserved phosphate-binding loop (P-loop), resistance nucleotide binding site, a hydrophobic domain (GLPL) and methionine-histidine-aspartate (MHD) motifs, which are typical components of nucleotide-binding site leucine-rich repeat proteins, as well as a coiled-coil region in the N-terminus. Quantitative real-time polymerase chain reaction analysis showed that the transcript of VqCN was rapidly and highly induced after infection with P. viticola in 'PS'. Moreover, the leaves of susceptible 'Cabernet Sauvignon' transiently expressing VqCN manifested increased resistance to P. viticola. The results indicated that VqCN might play a positive role in protecting grapevine against infection with P. viticola. Cloning and functional analysis of a putative resistance gene provide a basis for disease-resistance breeding.
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Affiliation(s)
- Shuwei Zhang
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Feng Ding
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Hongxiang Peng
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yu Huang
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jiang Lu
- Guangxi Crop Genetic Improvement and Biotechnology Key Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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Kim K, Choi D, Kim SM, Kwak DY, Choi J, Lee S, Lee BC, Hwang D, Hwang I. A systems approach for identifying resistance factors to Rice stripe virus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:534-545. [PMID: 22217248 DOI: 10.1094/mpmi-11-11-0282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Rice stripe virus (RSV) causes disease that can severely affect the productivity of rice (Oryza sativa). Several RSV-resistant cultivars have been developed. However, host factors conferring RSV resistance in these cultivars are still elusive. Here, we present a systems approach for identifying potential rice resistance factors. We developed two near-isogenic lines (NIL), RSV-resistant NIL22 and RSV-susceptible NIL37, and performed gene expression profiling of the two lines in RSV-infected and RSV-uninfected conditions. We identified 237 differentially expressed genes (DEG) between NIL22 and NIL37. By integrating with known quantitative trait loci (QTL), we selected 11 DEG located within the RSV resistance QTL as RSV resistance factor candidates. Furthermore, we identified 417 DEG between RSV-infected and RSV-uninfected conditions. Using an interaction network-based method, we selected 20 DEG highly interacting with the two sets of DEG as RSV resistance factor candidates. Among the 31 candidates, we selected the final set of 21 potential RSV resistance factors whose differential expression was confirmed in the independent samples using real-time reverse-transcription polymerase chain reaction. Finally, we reconstructed a network model delineating potential association of the 21 selected factors with resistance-related processes. In summary, our approach, based on gene expression profiling, revealed potential host resistance factors and a network model describing their relationships with resistance-related processes, which can be further validated in detailed experiments.
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Affiliation(s)
- Kangmin Kim
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
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Maiti S, Paul S, Pal A. Isolation, Characterization, and Structure Analysis of a Non-TIR-NBS-LRR Encoding Candidate Gene from MYMIV-Resistant Vigna mungo. Mol Biotechnol 2011; 52:217-33. [DOI: 10.1007/s12033-011-9488-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Liao PC, Lin KH, Ko CL, Hwang SY. Molecular evolution of a family of resistance gene analogs of nucleotide-binding site sequences in Solanum lycopersicum. Genetica 2011; 139:1229-40. [PMID: 22203213 DOI: 10.1007/s10709-011-9624-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
Nucleotide-binding site-leucine-rich repeats (NBS-LRR) gene families are one of the major plant resistance genes. Genomic NBS evolution was studied in many plant species for diverse arrays of NBS gene families. In this study, we focused on one family of NBS sequences in an attempt to understand how closely related NBS sequences evolved in the light of selection in domesticated plant species. A phylogenetic analysis revealed five major clades (A-E) and five subclades (A1-A5) within clade A of cloned NBS sequences. Positive selection was only detected in newly evolved NBS lineages in subclades of clade A. Positively selected codon sites were found among NBS sequences of clade A. A sliding-window analysis revealed that regions with Ka/Ks ratios of >1 were in the inter-motifs when paired clades were compared, but regions with Ka/Ks ratios of >1 were found across NBS sequences when subclades of clade A were compared. Our results based on a family of closely related NBS sequences showed that positive selection was first exerted on specific lineages across all NBS sequences after selective constraints. Subsequently, sequences with mutations in commonly conserved motifs were scrutinized by purifying selection. In the long term, conserved high frequency alleles in commonly conserved motifs and changes in inter-motifs were maintained in the investigated family of NBS sequences. Moreover, codons identified to be under positive selection in the inter-motifs were mainly located in regions involved in functions of ATP binding or hydrolysis.
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Affiliation(s)
- Pei-Chun Liao
- Department of Biological Science and Technology, Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC
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Molecular Marker-Assisted Genotyping of Mungbean Yellow Mosaic India Virus Resistant Germplasms of Mungbean and Urdbean. Mol Biotechnol 2010; 47:95-104. [DOI: 10.1007/s12033-010-9314-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Gayral P, Iskra-Caruana ML. Phylogeny of Banana Streak Virus reveals recent and repetitive endogenization in the genome of its banana host (Musa sp.). J Mol Evol 2009; 69:65-80. [PMID: 19517051 DOI: 10.1007/s00239-009-9253-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 05/05/2009] [Accepted: 05/26/2009] [Indexed: 12/11/2022]
Abstract
Banana streak virus (BSV) is a plant dsDNA pararetrovirus (family Caulimoviridae, genus badnavirus). Although integration is not an essential step in the BSV replication cycle, the nuclear genome of banana (Musa sp.) contains BSV endogenous pararetrovirus sequences (BSV EPRVs). Some BSV EPRVs are infectious by reconstituting a functional viral genome. Recent studies revealed a large molecular diversity of episomal BSV viruses (i.e., nonintegrated) while others focused on BSV EPRV sequences only. In this study, the evolutionary history of badnavirus integration in banana was inferred from phylogenetic relationships between BSV and BSV EPRVs. The relative evolution rates and selective pressures (d(N)/d(S) ratio) were also compared between endogenous and episomal viral sequences. At least 27 recent independent integration events occurred after the divergence of three banana species, indicating that viral integration is a recent and frequent phenomenon. Relaxation of selective pressure on badnaviral sequences that experienced neutral evolution after integration in the plant genome was recorded. Additionally, a significant decrease (35%) in the EPRV evolution rate was observed compared to BSV, reflecting the difference in the evolution rate between episomal dsDNA viruses and plant genome. The comparison of our results with the evolution rate of the Musa genome and other reverse-transcribing viruses suggests that EPRVs play an active role in episomal BSV diversity and evolution.
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Affiliation(s)
- Philippe Gayral
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, Montpellier, France
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