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Liu JJ, Sniezko RA, Houston S, Krakowski J, Alger G, Benowicz A, Sissons R, Zamany A, Williams H, Kegley A, Rancourt B. Genome-Wide Association Study Reveals Polygenic Architecture for Limber Pine Quantitative Disease Resistance to White Pine Blister Rust. PHYTOPATHOLOGY 2024:PHYTO09230338R. [PMID: 38489164 DOI: 10.1094/phyto-09-23-0338-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Development of durable resistance effective against a broad range of pathotypes is crucial for restoration of pathogen-damaged ecosystems. This study dissected the complex genetic architecture for limber pine quantitative disease resistance (QDR) to Cronartium ribicola using a genome-wide association study. Eighteen-month-old seedlings were inoculated for resistance screening under controlled conditions. Disease development was quantitatively assessed for QDR-related traits over 4 years postinoculation. To reveal the genomic architecture contributing to QDR-related traits, a set of genes related to disease resistance with genome-wide distribution was selected for targeted sequencing for genotyping of single-nucleotide polymorphisms (SNPs). The genome-wide association study revealed a set of SNPs significantly associated with quantitative traits for limber pine QDR to white pine blister rust, including number of needle spots and stem cankers, as well as survival 4 years postinoculation. The peaks of marker-trait associations displayed a polygenic pattern, with genomic regions as potential resistant quantitative trait loci, distributed over 10 of the 12 linkage groups (LGs) of Pinus. None of them was linked to the Cr4-controlled major gene resistance previously mapped on LG08. Both normal canker and bole infection were mapped on LG05, and the associated SNPs explained their phenotypic variance up to 52%, tagging a major resistant quantitative trait locus. Candidate genes containing phenotypically associated SNPs encoded putative nucleotide-binding site leucine-rich repeat proteins, leucine-rich repeat-receptor-like kinase, cytochrome P450 superfamily protein, heat shock cognate protein 70, glutamate receptor, RNA-binding family protein, and unknown protein. The confirmation of resistant quantitative trait loci broadens the genetic pool of limber pine resistance germplasm for resistance breeding.
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Affiliation(s)
- Jun-Jun Liu
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Richard A Sniezko
- U.S. Department of Agriculture Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Drive, Cottage Grove, OR 97424, U.S.A
| | - Sydney Houston
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Jodie Krakowski
- Independent Consultant, Box 774, Coleman, AB, T0K 0M0, Canada
| | - Genoa Alger
- Parks Canada, Waterton Lakes National Park, Alberta, T0K 2M0, Canada
| | - Andy Benowicz
- Alberta Forestry and Parks, Government of Alberta, Edmonton, T6H 5T6, Canada
| | - Robert Sissons
- Parks Canada, Waterton Lakes National Park, Alberta, T0K 2M0, Canada
| | - Arezoo Zamany
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Holly Williams
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
| | - Angelia Kegley
- U.S. Department of Agriculture Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Drive, Cottage Grove, OR 97424, U.S.A
| | - Benjamin Rancourt
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada
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Figueroa‐Corona L, Moreno‐Letelier A, Ortega‐Del Vecchyo D, Peláez P, Gernandt DS, Eguiarte LE, Wegrzyn J, Piñero D. Changes in demography and geographic distribution in the weeping pinyon pine ( Pinus pinceana) during the Pleistocene. Ecol Evol 2022; 12:e9369. [PMID: 36225821 PMCID: PMC9534753 DOI: 10.1002/ece3.9369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/12/2022] Open
Abstract
Climate changes, together with geographical barriers imposed by the Sierra Madre Oriental and the Chihuahuan Desert, have shaped the genetic diversity and spatial distribution of different species in northern Mexico. Pinus pinceana Gordon & Glend. tolerates extremely arid conditions. Northern Mexico became more arid during the Quaternary, modifying ecological communities. Here, we try to identify the processes underlying the demographic history of P. pinceana and characterize its genetic diversity using 3100 SNPs from genotyping by sequencing 90 adult individuals from 10 natural populations covering the species' entire geographic distribution. We inferred its population history and contrasted possible demographic scenarios of divergence that modeled the genetic diversity present in this restricted pinyon pine; in support, the past distribution was reconstructed using climate from the Last Glacial Maximum (LGM, 22 kya). We inferred that P. pinceana diverged into two lineages ~2.49 Ma (95% CI 3.28-1.62), colonizing two regions: the Sierra Madre Oriental (SMO) and the Chihuahuan Desert (ChD). Our results of population genomic analyses reveal the presence of heterozygous SNPs in all populations. In addition, low migration rates across regions are probably related to glacial-interglacial cycles, followed by the gradual aridification of the Chihuahuan Desert during the Holocene.
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Affiliation(s)
- Laura Figueroa‐Corona
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico,Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | | | - Diego Ortega‐Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de MéxicoJuriquillaMexico
| | - Pablo Peláez
- Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavacaMorelosMexico
| | - David S. Gernandt
- Departamento de BotánicaInstituto de Biología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Luis E. Eguiarte
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Daniel Piñero
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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SNP Detection in Pinus pinaster Transcriptome and Association with Resistance to Pinewood Nematode. FORESTS 2022. [DOI: 10.3390/f13060946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pinewood nematode (PWN, Bursaphelenchus xylophilus) is the causal agent of pine wilt disease (PWD), which severely affects Pinus pinaster stands in southwestern Europe. Despite the high susceptibility of P. pinaster, individuals of selected half-sib families have shown genetic variability in survival after PWN inoculation, indicating that breeding for resistance can be a valuable strategy to control PWD. In this work, RNA-seq data from susceptible and resistant plants inoculated with PWN were used for SNP discovery and analysis. A total of 186,506 SNPs were identified, of which 31 were highly differentiated between resistant and susceptible plants, including SNPs in genes involved in cell wall lignification, a process previously linked to PWN resistance. Fifteen of these SNPs were selected for validation through Sanger sequencing and 14 were validated. To evaluate SNP-phenotype associations, 40 half-sib plants were genotyped for six validated SNPs. Associations with phenotype after PWN inoculation were found for two SNPs in two different genes (MEE12 and PCMP-E91), as well as two haplotypes of HIPP41, although significance was not maintained following Bonferroni correction. SNPs here detected may be useful for the development of molecular markers for PWD resistance and should be further investigated in future association studies.
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Liu JJ, Fernandes H, Zamany A, Sikorski M, Jaskolski M, Sniezko RA. In-vitro anti-fungal assay and association analysis reveal a role for the Pinus monticola PR10 gene (PmPR10-3.1) in quantitative disease resistance to white pine blister rust. Genome 2021; 64:693-704. [PMID: 33464999 DOI: 10.1139/gen-2020-0080] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pathogenesis-related (PR) proteins play important roles in plant defense response. However, functional investigation of PR10 genes is still limited and their physiological roles have not been conclusively characterized in biological processes of conifer trees. Here, we identified multiple novel members in the western white pine (Pinus monticola) PmPR10 family by bioinformatic mining available transcriptomic data. Phylogenetic analysis of protein sequences revealed four PR10 and two PR10-like clusters with a high synteny across different species of five-needle pines. Of 10 PmPR10 genes, PmPR10-3.1 was selected and expressed in Escherichia coli. The purified recombinant protein exhibited inhibitory effects on spore hyphal growth of fungal pathogens Cronartium ribicola, Phoma exigua, and Phoma argillacea by in-vitro anti-fungal analysis. Genetic variation analysis detected a total of 21 single nucleotide polymorphisms (SNPs) within PmPR10-3.1 in a collection of P. monticola seed families. A nonsynonymous SNP (t178g) showed significant association with relative levels of quantitative disease resistance (QDR), explaining about 8.7% of phenotypic variation as the peak value across all SNPs. Our results provide valuable insight into the genetic architecture underlying P. monticola QDR and imply that PmPR10-3.1 may function as an important component in conifer basal immunity for non-specific resistance to a wide spectrum of pathogens.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Humberto Fernandes
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada
| | - Michal Sikorski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Richard A Sniezko
- United States Department of Agriculture Forest Service, Dorena Genetic Resource Center, Cottage Grove, OR, USA
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Liu J, Sun Z, Mao X, Gerken H, Wang X, Yang W. Multiomics analysis reveals a distinct mechanism of oleaginousness in the emerging model alga Chromochloris zofingiensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:745-758. [PMID: 30828893 DOI: 10.1111/tpj.14270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 12/24/2018] [Accepted: 01/28/2019] [Indexed: 05/03/2023]
Abstract
Chromochloris zofingiensis, featured due to its capability to simultaneously synthesize triacylglycerol (TAG) and astaxanthin, is emerging as a leading candidate alga for production uses. To better understand the oleaginous mechanism of this alga, we conducted a multiomics analysis by systematically integrating time-resolved transcriptomes, lipidomes and metabolomes in response to nitrogen deprivation. The data analysis unraveled the distinct mechanism of TAG accumulation, which involved coordinated stimulation of multiple biological processes including supply of energy and reductants, carbon reallocation from protein and starch, and 'pushing' and 'pulling' carbon to TAG synthesis. Unlike the model alga Chlamydomonas, de novo fatty acid synthesis in C. zofingiensis was promoted, together with enhanced turnover of both glycolipids and phospholipids, supporting the drastic need of acyls for TAG assembly. Moreover, genomewide analysis identified many key functional enzymes and transcription factors that had engineering potential for TAG modulation. Two genes encoding glycerol-3-phosphate acyltransferase (GPAT), the first committed enzyme for TAG assembly, were found in the C. zofingiensis genome; in vivo functional characterization revealed that extrachloroplastic GPAT instead of chloroplastic GPAT played a central role in TAG synthesis. These findings illuminate distinct oleaginousness mechanisms in C. zofingiensis and pave the way towards rational manipulation of this alga to becone an emerging model for trait improvements.
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Affiliation(s)
- Jin Liu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Zheng Sun
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Xuemei Mao
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Henri Gerken
- School of Sustainable Engineering and the Built Environment, Arizona State University Polytechnic campus, Mesa, AZ, 85212, USA
| | - Xiaofei Wang
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Wenqiang Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Lea MV, Syring J, Jennings T, Cronn R, Bruederle LP, Neale JR, Tomback DF. Development of nuclear microsatellite loci for Pinus albicaulis Engelm. (Pinaceae), a conifer of conservation concern. PLoS One 2018; 13:e0205423. [PMID: 30335779 PMCID: PMC6193661 DOI: 10.1371/journal.pone.0205423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022] Open
Abstract
Pinus albicaulis (whitebark pine) is a widely-distributed but rapidly declining high elevation western North American tree and a candidate for listing under the U.S. Endangered Species Act. Our objectives were to develop reliable nuclear microsatellite markers that can be used to assess within-population genetic diversity as well as seed and pollen migration dynamics, and to validate markers using two geographically proximal P. albicaulis populations. We identified 1,667 microsatellite-containing sequences from shotgun DNA libraries of P. albicaulis. Primer pairs were designed for 308 unique microsatellite-containing loci, and these were evaluated for PCR amplification success and segregation in a panel of diploid needle tissue. DNA was extracted with an SDS protocol, and primers were screened through gel electrophoresis. Microsatellites were genotyped through fluorescent primer fragment analysis. Ten novel and 13 transferred loci were found to be reproducible in analyses based on 20 foliage samples from each of two locations: Henderson Mountain, Custer Gallatin National Forest, Montana, and Mt. Washburn, Yellowstone National Park, Wyoming (USA). Transferred loci had higher numbers of alleles and expected heterozygosities than novel loci, but also revealed evidence for a higher frequency of null alleles. Eight of the 13 transferred loci deviated significantly from Hardy-Weinberg Equilibrium, and showed large positive FIS values that were likely inflated by null alleles. Mantel’s tests of transferred and novel markers showed no correlation between genetic and geographic distances within or among the two sampled populations. AMOVA suggests that 91% of genetic variability occurs within populations and 9% between the two populations. Studies assessing genetic diversity using these microsatellite loci can help guide future management and restoration activities for P. albicaulis.
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Affiliation(s)
- Marian V. Lea
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | - John Syring
- Department of Biology, Linfield College, McMinnville, Oregon, United States of America
| | - Tara Jennings
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, Corvallis, Oregon, United States of America
| | - Leo P. Bruederle
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
| | | | - Diana F. Tomback
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America
- * E-mail:
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7
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Growth Response of Whitebark Pine (Pinus albicaulis Engelm) Regeneration to Thinning and Prescribed Burn Treatments. FORESTS 2018. [DOI: 10.3390/f9060311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Whitebark Pine in the Northern Cascades: Tracking the Effects of Blister Rust on Population Health in North Cascades National Park Service Complex and Mount Rainier National Park. FORESTS 2018. [DOI: 10.3390/f9050244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Shih KM, Chang CT, Chung JD, Chiang YC, Hwang SY. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir ( Keteleeria davidiana var. formosana). FRONTIERS IN PLANT SCIENCE 2018; 9:92. [PMID: 29449860 PMCID: PMC5799944 DOI: 10.3389/fpls.2018.00092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 05/05/2023]
Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.
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Affiliation(s)
- Kai-Ming Shih
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Bullington LS, Lekberg Y, Sniezko R, Larkin B. The influence of genetics, defensive chemistry and the fungal microbiome on disease outcome in whitebark pine trees. MOLECULAR PLANT PATHOLOGY 2018; 19:1847-1858. [PMID: 29388309 PMCID: PMC6638087 DOI: 10.1111/mpp.12663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/02/2018] [Accepted: 01/26/2018] [Indexed: 05/23/2023]
Abstract
The invasive fungal pathogen Cronartium ribicola infects and kills whitebark pine (Pinus albicaulis) throughout western North America. Whitebark pine has been proposed for listing under the Endangered Species Act in the USA, and the loss of this species is predicted to have severe impacts on ecosystem composition and function in high-elevation forests. Numerous fungal endophytes live inside whitebark pine tissues and may influence the severity of C. ribicola infection, either directly by inhibition of pathogen growth or indirectly by the induction of chemical defensive pathways in the tree. Terpenes, a form of chemical defence in pine trees, can also influence disease. In this study, we characterized fungal endophyte communities in whitebark pine seedlings before and after experimental inoculation with C. ribicola, monitored disease progression and compared fungal community composition in susceptible vs. resistant seedlings in a common garden. We analysed the terpene composition of these same seedlings. Seed family identity or maternal genetics influenced both terpenes and endophyte communities. Terpene and endophyte composition correlated with disease severity, and terpene concentrations differed in resistant vs. susceptible seedlings. These results suggest that the resistance to C. ribicola observed in natural whitebark pine populations is caused by the combined effects of genetics, endophytes and terpenes within needle tissue, in which initial interactions between microbes and hosts take place. Tree genotype, terpene and microbiome combinations associated with healthy trees could help to predict or reduce disease severity and improve outcomes of future tree breeding programmes.
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Affiliation(s)
- Lorinda S. Bullington
- MPG RanchFlorenceMT 59833USA
- Interdisciplinary Sciences, University of MontanaMissoulaMT 59801USA
| | - Ylva Lekberg
- MPG RanchFlorenceMT 59833USA
- College of Forestry and ConservationUniversity of MontanaMissoulaMT 59801USA
| | - Richard Sniezko
- USDA Forest Service, Dorena Genetic Resource CenterCottage GroveOR 97424USA
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Liu JJ, Williams H, Li XR, Schoettle AW, Sniezko RA, Murray M, Zamany A, Roke G, Chen H. Profiling methyl jasmonate-responsive transcriptome for understanding induced systemic resistance in whitebark pine (Pinus albicaulis). PLANT MOLECULAR BIOLOGY 2017; 95:359-374. [PMID: 28861810 DOI: 10.1007/s11103-017-0655-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/23/2017] [Indexed: 06/07/2023]
Abstract
RNA-seq analysis on whitebark pine needles demonstrated that methyl jasmonate (MeJA)-triggered transcriptome re-programming substantially overlapped with defense responses against insects and fungal pathogens in Pinus species, increasing current knowledge regarding induced systemic resistance (ISR) to pathogens and pests in whitebark pine. Many whitebark pine populations are in steep decline due to high susceptibility to mountain pine beetle and the non-native white pine blister rust (WPBR). Resistance, including induced systemic resistance (ISR), is not well characterized in whitebark pine, narrowing the current options for increasing the success of restoration and breeding programs. Exogenous jasmonates are known to trigger ISR by activating the plant's immune system through regulation of gene expression to produce chemical defense compounds. This study reports profiles of whitebark pine needle transcriptomes, following methyl jasmonate (MeJA) treatment using RNA-seq. A MeJA-responsive transcriptome was de novo assembled and transcriptome profiling identified a set of differentially expressed genes (DEGs), revealing 1422 up- and 999 down-regulated transcripts with at least twofold change (FDR corrected p < 0.05) in needle tissues in response to MeJA application. GO analysis revealed that these DEGs have putative functions in plant defense signalling, transcription regulation, biosyntheses of secondary metabolites, and other biological processes. Lineage-specific expression of defense-related genes was characterized through comparison with MeJA signalling in model plants. In particular, MeJA-triggered transcriptome re-programming substantially overlapped with defense responses against WPBR and insects in related Pinus species, suggesting that MeJA may be used to improve whitebark pine resistance to pathogens/pests. Our study provides new insights into molecular mechanisms and metabolic pathways involved in whitebark pine ISR. DEGs identified in this study can be used as candidates to facilitate identification of genomic variation contributing to host resistance and aid in breeding selection of elite genotypes with better adaptive fitness to environmental stressors in this endangered tree species.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada.
| | - Holly Williams
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
| | - Xiao Rui Li
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
| | - Anna W Schoettle
- USDA Forest Service, Rocky Mountain Research Station, 240 West Prospect Road, Fort Collins, CO, 80526, USA
| | - Richard A Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA
| | - Michael Murray
- Ministry of Forests, Lands and Natural Resource Operations, 333 Victoria St., Nelson, BC, V1L 4K3, Canada
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
| | - Gary Roke
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
| | - Hao Chen
- Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1M5, Canada
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Liu J, Sniezko RA, Zamany A, Williams H, Wang N, Kegley A, Savin DP, Chen H, Sturrock RN. Saturated genic SNP mapping identified functional candidates and selection tools for the Pinus monticola Cr2 locus controlling resistance to white pine blister rust. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1149-1162. [PMID: 28176454 PMCID: PMC5552481 DOI: 10.1111/pbi.12705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 01/11/2017] [Accepted: 02/02/2017] [Indexed: 05/17/2023]
Abstract
Molecular breeding incorporates efficient tools to increase rust resistance in five-needle pines. Susceptibility of native five-needle pines to white pine blister rust (WPBR), caused by the non-native invasive fungus Cronartium ribicola (J.C. Fisch.), has significantly reduced wild populations of these conifers in North America. Major resistance (R) genes against specific avirulent pathotypes have been found in several five-needle pine species. In this study, we screened genic SNP markers by comparative transcriptome and genetic association analyses and constructed saturated linkage maps for the western white pine (Pinus monticola) R locus (Cr2). Phenotypic segregation was measured by a hypersensitive reaction (HR)-like response on the needles and disease symptoms of cankered stems post inoculation by the C. ribicola avcr2 race. SNP genotypes were determined by HRM- and TaqMan-based SNP genotyping. Saturated maps of the Cr2-linkage group (LG) were constructed in three seed families using a total of 34 SNP markers within 21 unique genes. Cr2 was consistently flanked by contig_2142 (encoding a ruvb-like protein) and contig_3772 (encoding a delta-fatty acid desaturase) across the three seed families. Cr2 was anchored to the Pinus consensus LG-1, which differs from LGs where other R loci of Pinus species were mapped. GO annotation identified a set of NBS-LRR and other resistance-related genes as R candidates in the Cr2 region. Association of one nonsynonymous SNP locus of an NBS-LRR gene with Cr2-mediated phenotypes provides a valuable tool for marker-assisted selection (MAS), which will shorten the breeding cycle of resistance screening and aid in the restoration of WPBR-disturbed forest ecosystems.
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Affiliation(s)
- Jun‐Jun Liu
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | | | - Arezoo Zamany
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | - Holly Williams
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
| | - Ning Wang
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
- Academy of Agriculture and Forestry ScienceQinghai UniversityXiningChina
| | - Angelia Kegley
- Dorena Genetic Resource CenterUSDA Forest ServiceCottage GroveORUSA
| | - Douglas P. Savin
- Dorena Genetic Resource CenterUSDA Forest ServiceCottage GroveORUSA
| | - Hao Chen
- Canadian Forest ServiceNatural Resources CanadaVictoriaCanada
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