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Younessi-Hamzekhanlu M, Gailing O. Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection. Int J Mol Sci 2022; 23:ijms232012315. [PMID: 36293169 PMCID: PMC9604372 DOI: 10.3390/ijms232012315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/30/2022] Open
Abstract
The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.
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Affiliation(s)
- Mehdi Younessi-Hamzekhanlu
- Department of Forestry and Medicinal Plants, Ahar Faculty of Agriculture and Natural Resources, University of Tabriz, 29 Bahman Blvd., Tabriz P.O. Box 5166616471, Iran
- Correspondence: (M.Y.-H.); (O.G.)
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Correspondence: (M.Y.-H.); (O.G.)
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Malik N, George JK. Resistance Genes in Piper colubrinum: In Silico Survey From Leaf Transcriptome and Expression Studies Upon Challenge Inoculation with Phytophthora capsici. Appl Biochem Biotechnol 2017; 184:987-1008. [PMID: 28933036 DOI: 10.1007/s12010-017-2600-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 09/08/2017] [Indexed: 12/24/2022]
Abstract
The oomycetes, Phytophthora capsici, cause foot rot disease in black pepper. Piper colubrinum Link, a distant relative of cultivated black pepper, is highly resistant to this destructive pathogen. Identification of resistance (R) genes in P. colubrinum and the study of its expression profile during interaction with the pathogen can help in understanding the resistance mechanism involved. In the present study, 1289 R gene-related transcripts were mined from P. colubrinum transcriptome, clustered, and classified according to the conserved motifs and domains. Transcripts belonging to four major R gene classes were identified in P. colubrinum, but TIR-NBS-LRR-type R genes were absent. The relative expression of 12 selected R genes was studied using two virulent isolates of P. capsici, and these were found to be upregulated in the initial hours of plant pathogen interaction. The R genes studied were expressed even in aseptically maintained tissue-cultured plants and uninoculated greenhouse-grown plants at basal level suggesting that the plants are geared up with the R gene all the time and are under continuous surveillance for the pathogen and basal level of R gene expression do not require a pathogen trigger. ACT, ATUB, and EIF3E were identified as the most stable reference genes that can be used for real-time PCR study. The present study identified promising R genes in P. colubrinum which can be used in developing Phytophthora-resistant black pepper.
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Affiliation(s)
- Neema Malik
- ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, 673012, India
| | - Johnson K George
- ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, 673012, India.
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Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, Sanusi NSNM, Jayanthi N, Ponomarenko P, Triska M, Solovyev V, Firdaus-Raih M, Sambanthamurthi R, Murphy D, Low ETL. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biol Direct 2017; 12:21. [PMID: 28886750 PMCID: PMC5591544 DOI: 10.1186/s13062-017-0191-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Background Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Results Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. Conclusions We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops. Reviewers This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, California, 91750, USA.,Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Petr Ponomarenko
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Martin Triska
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90089, USA
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Mohd Firdaus-Raih
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Denis Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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Resistance gene analogs involved in tolerant cassava--geminivirus interaction that shows a recovery phenotype. Virus Genes 2015; 51:393-407. [PMID: 26370397 DOI: 10.1007/s11262-015-1246-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022]
Abstract
The current literature describes recovery from virus-induced symptoms as a RNA silencing defense, but immunity-related genes, including the structurally specific resistance gene analogs (RGAs) that may play a key role in tolerance and recovery is not yet reported. In this study, the transcriptome data of tolerant cassava TME3 (which exhibits a recovery phenotype) and susceptible cassava T200 infected with South African cassava mosaic virus were explored for RGAs. Putative resistance protein analogs (RPAs) with amide-like indole-3-acetic acid-Ile-Leu-Arg (IAA-ILR) and leucine-rich repeat (LRR)-kinase conserved domains were unique to TME3. Common responsive RPAs in TME3 and T200 were the dirigent-like protein, coil-coil nucleotide-binding site (NBS) and toll-interleukin-resistance, disease resistance zinc finger chromosome condensation-like protein (DZC), and NBS-apoptosis repressor with caspase recruitment (ARC)-LRR domains. Mutations in RPAs in the MHD motif of the NBS-ARC2 subdomain associated with the recovery phase in TME3 were observed. Additionally, a cohort of 25 RGAs mined solely during the recovery process in TME3 was identified. Phylogenetic and expression analyses support that diverse RGAs are differentially expressed during tolerance and recovery. This study reveals that in cassava, a perennial crop, RGAs participate in tolerance and differentially accumulate during recovery as a complementary defense mechanism to natural occurring RNA silencing to impair viral replication.
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Singh S, Chand S, Singh NK, Sharma TR. Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species. PLoS One 2015; 10:e0125964. [PMID: 25902056 PMCID: PMC4406684 DOI: 10.1371/journal.pone.0125964] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 03/28/2015] [Indexed: 11/19/2022] Open
Abstract
The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species.
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Affiliation(s)
- Sangeeta Singh
- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- School of Life Sciences, Devi Ahilya University, Khandwa Road, Indore, 452017, India
| | - Suresh Chand
- School of Life Sciences, Devi Ahilya University, Khandwa Road, Indore, 452017, India
| | - N. K. Singh
- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- * E-mail:
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Low ETL, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R. Analyses of hypomethylated oil palm gene space. PLoS One 2014; 9:e86728. [PMID: 24497974 PMCID: PMC3907425 DOI: 10.1371/journal.pone.0086728] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 12/15/2013] [Indexed: 12/21/2022] Open
Abstract
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
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Affiliation(s)
- Eng-Ti L. Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Ab Halim Mohd-Amin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Paul Maclean
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Rudi Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Alan McCulloch
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Roger Moraga
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
- * E-mail:
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Wanderley-Nogueira AC, Belarmino LC, Soares-Cavalcanti NDM, Bezerra-Neto JP, Kido EA, Pandolfi V, Abdelnoor RV, Binneck E, Carazzole MF, Benko-Iseppon AM. An overall evaluation of the Resistance (R) and Pathogenesis-Related (PR) superfamilies in soybean, as compared with Medicago and Arabidopsis. Genet Mol Biol 2012; 35:260-71. [PMID: 22802711 PMCID: PMC3392878 DOI: 10.1590/s1415-47572012000200007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Plants have the ability to recognize and respond to a multitude of pathogens, resulting in a massive reprogramming of the plant to activate defense responses including Resistance (R) and Pathogenesis-Related (PR) genes. Abiotic stresses can also activate PR genes and enhance pathogen resistance, representing valuable genes for breeding purposes. The present work offers an overview of soybean R and PR genes present in the GENOSOJA (Brazilian Soybean Genome Consortium) platform, regarding their structure, abundance, evolution and role in the plant-pathogen metabolic pathway, as compared with Medicago and Arabidopsis. Searches revealed 3,065 R candidates (756 in Soybean, 1,142 in Medicago and 1,167 in Arabidopsis), and PR candidates matching to 1,261 sequences (310, 585 and 366 for the three species, respectively). The identified transcripts were also evaluated regarding their expression pattern in 65 libraries, showing prevalence in seeds and developing tissues. Upon consulting the SuperSAGE libraries, 1,072 R and 481 PR tags were identified in association with the different libraries. Multiple alignments were generated for Xa21 and PR-2 genes, allowing inferences about their evolution. The results revealed interesting insights regarding the variability and complexity of defense genes in soybean, as compared with Medicago and Arabidopsis.
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Affiliation(s)
- Ana C. Wanderley-Nogueira
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Luis C. Belarmino
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - João P. Bezerra-Neto
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Ederson A. Kido
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | - Marcelo F. Carazzole
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Ana M. Benko-Iseppon
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, PE, Brazil
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Abstract
Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616, USA.
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Moon DH, Salvatierra GR, Caldas DGG, Gallo de Carvalho MCC, Carneiro RT, Franceschini LM, Oda S, Labate CA. Comparison of the expression profiles of susceptible and resistant Eucalyptus grandis exposed to Puccinia psidii Winter using SAGE. FUNCTIONAL PLANT BIOLOGY : FPB 2007; 34:1010-1018. [PMID: 32689429 DOI: 10.1071/fp07094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 09/18/2007] [Indexed: 05/02/2023]
Abstract
Eucalyptus grandis Hill ex Maiden and its hybrids are commonly planted by the Brazilian pulp and paper industry, but they are the most susceptible to the neotropical rust disease caused by Puccinia psidii Winter. In an initial attempt to understand the mechanisms of resistance, we constructed two contrasting Serial Analysis of Gene Expression (SAGE) libraries using susceptible and resistant individuals from a segregating half-sibling E. grandis population. Using the Z-test we identified tags differentially expressed between the libraries, preferentially 239 in the susceptible and 232 in the resistant type individuals. Using public (Expressed Sequence Tags) EST databases, 40 of the susceptible and 70 of the resistant tags matched ESTs and were annotated. By comparing the type of genes and their expression levels, distinct differences between the libraries were observed. Susceptible plants showed gene expression linked to leaf senescence, generalised stress responses and detoxification, and are apparently incapable of inducing a competent host defence response. On the other hand, resistant plants showed genes upregulated for cellular polarisation, cytoskeleton restructuring, vesicle transport, and cellulose and lignin biosynthesis. In the resistant individuals, evidence for systemic resistance, anti-oxidative responses and a hypersensitive response was also observed, although no R gene was identified.
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Affiliation(s)
- David H Moon
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
| | - Guillermo R Salvatierra
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
| | - Danielle G G Caldas
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
| | - Mayra C C Gallo de Carvalho
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
| | - Raphael T Carneiro
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
| | - Lívia M Franceschini
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
| | - Shinitiro Oda
- Suzano Papel e Celulose, Av. Brigadeiro Faria Lima n° 1355, 8° andar, CEP 01452-919, São Paulo-SP, Brasil
| | - Carlos A Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba-SP, Brasil
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