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Clare SJ, Alhashel AF, Li M, Effertz KM, Poudel RS, Zhang J, Brueggeman RS. High resolution mapping of a novel non-transgressive hybrid susceptibility locus in barley exploited by P. teres f. maculata. BMC PLANT BIOLOGY 2024; 24:622. [PMID: 38951756 PMCID: PMC11218204 DOI: 10.1186/s12870-024-05303-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
Hybrid genotypes can provide significant yield gains over conventional inbred varieties due to heterosis or hybrid vigor. However, hybrids can also display unintended negative attributes or phenotypes such as extreme pathogen susceptibility. The necrotrophic pathogen Pyrenophora teres f. maculata (Ptm) causes spot form net blotch, which has caused significant yield losses to barley worldwide. Here, we report on a non-transgressive hybrid susceptibility locus in barley identified between the three parental lines CI5791, Tifang and Golden Promise that are resistant to Ptm isolate 13IM.3. However, F2 progeny from CI5791 × Tifang and CI5791 × Golden Promise crosses exhibited extreme susceptibility. The susceptible phenotype segregated in a ratio of 1 resistant:1 susceptible representing a genetic segregation ratio of 1 parental (res):2 heterozygous (sus):1 parental (res) suggesting a single hybrid susceptibility locus. Genetic mapping using a total of 715 CI5791 × Tifang F2 individuals (1430 recombinant gametes) and 149 targeted SNPs delimited the hybrid susceptibility locus designated Susceptibility to Pyrenophora teres 2 (Spt2) to an ~ 198 kb region on chromosome 5H of the Morex V3 reference assembly. This single locus was independently mapped with 83 CI5791 × Golden Promise F2 individuals (166 recombinant gametes) and 180 genome wide SNPs that colocalized to the same Spt2 locus. The CI5791 genome was sequenced using PacBio Continuous Long Read technology and comparative analysis between CI5791 and the publicly available Golden Promise genome assembly determined that the delimited region contained a single high confidence Spt2 candidate gene predicted to encode a pentatricopeptide repeat-containing protein.
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Affiliation(s)
- Shaun J Clare
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Abdullah F Alhashel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mengyuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Karl M Effertz
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Dewey Scientific, Pullman, WA, 99163, USA
| | - Roshan Sharma Poudel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
- Syngenta Seed Inc, Durham, NC, 27709, USA
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Robert S Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
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Feau N, Dhillon BD, Sakalidis M, Dale AL, Søndreli KL, Goodwin SB, LeBoldus JM, Hamelin RC. Forest health in the Anthropocene: the emergence of a novel tree disease is associated with poplar cultivation. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220008. [PMID: 36744569 PMCID: PMC9900707 DOI: 10.1098/rstb.2022.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/11/2022] [Indexed: 02/07/2023] Open
Abstract
Plant domestication and movement are large contributors to the success of new diseases. The introduction of new host species can result in accelerated evolutionary changes in pathogens, affecting long-established coevolutionary dynamics. This has been observed in poplars where severe epidemics of pathogens that were innocuous in their natural pathosystems occurred following host domestication. The North American fungus Sphaerulina musiva is responsible for endemic leaf spots on Populus deltoides. We show that the expansion of poplar cultivation resulted in the emergence of a new lineage of this pathogen that causes stem infections on a new host, P. balsamifera. This suggests a host shift since this is not a known host. Genome analysis of this emerging lineage reveals a mosaic pattern with islands of diversity separated by fixed genome regions, which is consistent with a homoploid hybridization event between two individuals that produced a hybrid swarm. Genome regions of extreme divergence and low diversity are enriched in genes involved in host-pathogen interactions. The specialization of this emerging lineage to a new host and its clonal propagation represents a serious threat to poplars and could affect both natural and planted forests. This work provides a clear example of the changes created by the intensification of tree cultivation that facilitate the emergence of specialized pathogens, jeopardizing the natural equilibrium between hosts and pathogens. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
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Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada, V8Z 1M5
| | - Braham D. Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4
- Department of Plant Pathology, University of Florida - Fort Lauderdale Research and Education Center, Davie, FL 33314, USA
| | - Monique Sakalidis
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4
- GC-New Construction Materials, FPInnovations, Vancouver, BC, Canada, V6T 1Z4
| | - Kelsey L. Søndreli
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Jared M. LeBoldus
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
- Forest Engineering, Resources and Management Department, Oregon State University, Corvallis, OR 97331, USA
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada, G1V 0A6
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Toniutti L, Breitler JC, Etienne H, Campa C, Doulbeau S, Urban L, Lambot C, Pinilla JCH, Bertrand B. Influence of Environmental Conditions and Genetic Background of Arabica Coffee ( C. arabica L) on Leaf Rust ( Hemileia vastatrix) Pathogenesis. FRONTIERS IN PLANT SCIENCE 2017; 8:2025. [PMID: 29234340 PMCID: PMC5712408 DOI: 10.3389/fpls.2017.02025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/14/2017] [Indexed: 05/20/2023]
Abstract
Global warming is a major threat to agriculture worldwide. Between 2008 and 2013, some coffee producing countries in South and Central America suffered from severe epidemics of coffee leaf rust (CLR), resulting in high economic losses with social implications for coffee growers. The climatic events not only favored the development of the pathogen but also affected the physiological status of the coffee plant. The main objectives of the study were to evaluate how the physiological status of the coffee plant modified by different environmental conditions impact on the pathogenesis of CLR and to identify indicators of the physiological status able to predict rust incidence. Three rust susceptible genotypes (one inbred line and two hybrids) were grown in controlled conditions with a combination of thermal regime (TR), nitrogen and light intensity close to the field situation before being inoculated with the rust fungus Hemileia vastatrix. It has been demonstrated that a TR of 27-22°C resulted in 2000 times higher sporulation than with a TR of 23-18°C. It has been also shown that high light intensity combined with low nitrogen fertilization modified the CLR pathogenesis resulting in huge sporulation. CLR sporulation was significantly lower in the F1 hybrids than in the inbred line. The hybrid vigor may have reduced disease incidence. Among the many parameters studied, parameters related to photosystem II and photosynthetic electron transport chain components appeared as indicators of the physiological status of the coffee plant able to predict rust sporulation intensity. Taken together, these results show that CLR sporulation not only depends on the TR but also on the physiological status of the coffee plant, which itself depends on agronomic conditions. Our work suggests that vigorous varieties combined with a shaded system and appropriate nitrogen fertilization should be part of an agro-ecological approach to disease control.
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Affiliation(s)
- Lucile Toniutti
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR IPME, Montpellier, France
- Nestlé R&D Tours, Tours, France
| | - Jean-Christophe Breitler
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR IPME, Montpellier, France
| | - Hervé Etienne
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR IPME, Montpellier, France
| | - Claudine Campa
- Institut de Recherche pour le Développement, UMR IPME, Montpellier, France
| | - Sylvie Doulbeau
- Institut de Recherche pour le Développement, UMR IPME, Montpellier, France
| | - Laurent Urban
- UMR QualiSud, Université d’Avignon et des Pays du Vaucluse, Avignon, France
| | | | | | - Benoît Bertrand
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR IPME, Montpellier, France
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Anthropogenic signature in the incidence and distribution of an emerging pathogen of poplars. Biol Invasions 2016. [DOI: 10.1007/s10530-015-1051-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Floate KD, Godbout J, Lau MK, Isabel N, Whitham TG. Plant-herbivore interactions in a trispecific hybrid swarm of Populus: assessing support for hypotheses of hybrid bridges, evolutionary novelty and genetic similarity. THE NEW PHYTOLOGIST 2016; 209:832-844. [PMID: 26346922 DOI: 10.1111/nph.13622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/28/2015] [Indexed: 06/05/2023]
Abstract
UNLABELLED Natural systems of hybridizing plants are powerful tools with which to assess evolutionary processes between parental species and their associated arthropods. Here we report on these processes in a trispecific hybrid swarm of Populus trees. Using field observations, common garden experiments and genetic markers, we tested the hypothesis that genetic similarities among hosts underlie the distributions of 10 species of gall-forming arthropods and their ability to adapt to new host genotypes. KEY FINDINGS the degree of genetic relatedness among parental species determines whether hybridization is primarily bidirectional or unidirectional; host genotype and genetic similarity strongly affect the distributions of gall-forming species, individually and as a community. These effects were detected observationally in the wild and experimentally in common gardens; correlations between the diversity of host genotypes and their associated arthropods identify hybrid zones as centres of biodiversity and potential species interactions with important ecological and evolutionary consequences. These findings support both hybrid bridge and evolutionary novelty hypotheses. However, the lack of parallel genetic studies on gall-forming arthropods limits our ability to define the host of origin with their subsequent shift to other host species or their evolution on hybrids as their final destination.
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Affiliation(s)
- Kevin D Floate
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, T1J 4B1, Canada
| | - Julie Godbout
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec (Sainte-Foy), QC, G1V 4C7, Canada
| | - Matthew K Lau
- Merriam-Powell Center for Environmental Research and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec (Sainte-Foy), QC, G1V 4C7, Canada
| | - Thomas G Whitham
- Merriam-Powell Center for Environmental Research and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
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Groszmann M, Gonzalez-Bayon R, Lyons RL, Greaves IK, Kazan K, Peacock WJ, Dennis ES. Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A 2015; 112:E6397-406. [PMID: 26527659 PMCID: PMC4655576 DOI: 10.1073/pnas.1519926112] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant hybrids are extensively used in agriculture to deliver increases in yields, yet the molecular basis of their superior performance (heterosis) is not well understood. Our transcriptome analysis of a number of Arabidopsis F1 hybrids identified changes to defense and stress response gene expression consistent with a reduction in basal defense levels. Given the reported antagonism between plant immunity and growth, we suggest that these altered patterns of expression contribute to the greater growth of the hybrids. The altered patterns of expression in the hybrids indicate decreases to the salicylic acid (SA) biosynthesis pathway and increases in the auxin [indole-3-acetic acid (IAA)] biosynthesis pathway. SA and IAA are hormones known to control stress and defense responses as well as plant growth. We found that IAA-targeted gene activity is frequently increased in hybrids, correlating with a common heterotic phenotype of greater leaf cell numbers. Reduced SA concentration and target gene responses occur in the larger hybrids and promote increased leaf cell size. We demonstrated the importance of SA action to the hybrid phenotype by manipulating endogenous SA concentrations. Increasing SA diminished heterosis in SA-reduced hybrids, whereas decreasing SA promoted growth in some hybrids and phenocopied aspects of hybrid vigor in parental lines. Pseudomonas syringae infection of hybrids demonstrated that the reductions in basal defense gene activity in these hybrids does not necessarily compromise their ability to mount a defense response comparable to the parents.
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Affiliation(s)
| | | | - Rebecca L Lyons
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, QLD 4069, Australia
| | | | - Kemal Kazan
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, QLD 4069, Australia
| | - W James Peacock
- CSIRO Agriculture, Canberra, ACT 2601, Australia; University of Technology, Sydney, NSW 2007, Australia
| | - Elizabeth S Dennis
- CSIRO Agriculture, Canberra, ACT 2601, Australia; University of Technology, Sydney, NSW 2007, Australia
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Roe AD, MacQuarrie CJK, Gros-Louis MC, Simpson JD, Lamarche J, Beardmore T, Thompson SL, Tanguay P, Isabel N. Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand. Ecol Evol 2014; 4:1629-47. [PMID: 24967081 PMCID: PMC4063464 DOI: 10.1002/ece3.1029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/20/2013] [Accepted: 12/31/2013] [Indexed: 01/30/2023] Open
Abstract
Hybridization and introgression are pervasive evolutionary phenomena that provide insight into the selective forces that maintain species boundaries, permit gene flow, and control the direction of evolutionary change. Poplar trees (Populus L.) are well known for their ability to form viable hybrids and maintain their distinct species boundaries despite this interspecific gene flow. We sought to quantify the hybridization dynamics and postzygotic fitness within a hybrid stand of balsam poplar (Populus balsamifera L.), eastern cottonwood (P. deltoides Marsh.), and their natural hybrids to gain insight into the barriers maintaining this stable hybrid zone. We observed asymmetrical hybrid formation with P. deltoides acting as the seed parent, but with subsequent introgression biased toward P. balsamifera. Native hybrids expressed fitness traits intermediate to the parental species and were not universally unfit. That said, native hybrid seedlings were absent from the seedling population, which may indicate additional selective pressures controlling their recruitment. It is imperative that we understand the selective forces maintaining this native hybrid zone in order to quantify the impact of exotic poplar hybrids on this native system.
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Affiliation(s)
- Amanda D Roe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, Québec, Canada
- Natural Resources Canada, Canadian Forestry Centre, Great Lakes Forestry CentreSault Ste. Marie, Ontario, Canada
| | - Chris J K MacQuarrie
- Natural Resources Canada, Canadian Forestry Centre, Great Lakes Forestry CentreSault Ste. Marie, Ontario, Canada
| | - Marie-Claude Gros-Louis
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, Québec, Canada
| | - J Dale Simpson
- Natural Resources Canada, Canadian Forest Service, Atlantic Forestry CentreFredericton, New Brunswick, Canada
| | - Josyanne Lamarche
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, Québec, Canada
| | - Tannis Beardmore
- Natural Resources Canada, Canadian Forest Service, Atlantic Forestry CentreFredericton, New Brunswick, Canada
| | - Stacey L Thompson
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, Québec, Canada
- Umeå University, Ecology and Environmental Sciences, Umeå Plant Science CentreUmeå, Sweden
| | - Philippe Tanguay
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, Québec, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry CentreQuébec, Québec, Canada
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Roe AD, MacQuarrie CJK, Gros-Louis MC, Simpson JD, Lamarche J, Beardmore T, Thompson SL, Tanguay P, Isabel N. Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle. Ecol Evol 2014; 4:1876-89. [PMID: 24963382 PMCID: PMC4063481 DOI: 10.1002/ece3.1028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/20/2013] [Accepted: 12/31/2013] [Indexed: 01/11/2023] Open
Abstract
Trees bearing novel or exotic gene components are poised to contribute to the bioeconomy for a variety of purposes such as bioenergy production, phytoremediation, and carbon sequestration within the forestry sector, but sustainable release of trees with novel traits in large-scale plantations requires the quantification of risks posed to native tree populations. Over the last century, exotic hybrid poplars produced through artificial crosses were planted throughout eastern Canada as ornamentals or windbreaks and these exotics provide a proxy by which to examine the fitness of exotic poplar traits within the natural environment to assess risk of exotic gene escape, establishment, and spread into native gene pools. We assessed postzygotic fitness traits of native and exotic poplars within a naturally regenerated stand in eastern Canada (Quebec City, QC). Pure natives (P. balsamifera and P. deltoides spp. deltoides), native hybrids (P. deltoides × P. balsamifera), and exotic hybrids (trees bearing Populus nigra and P. maximowiczii genetic components) were screened for reproductive biomass, yield, seed germination, and fungal disease susceptibility. Exotic hybrids expressed fitness traits intermediate to pure species and were not significantly different from native hybrids. They formed fully viable seed and backcrossed predominantly with P. balsamifera. These data show that exotic hybrids were not unfit and were capable of establishing and competing within the native stand. Future research will seek to examine the impact of exotic gene regions on associated biotic communities to fully quantify the risk exotic poplars pose to native poplar forests.
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Affiliation(s)
- Amanda D Roe
- Natural Resources Canada, Canadian Forest ServiceQuébec, Québec, Canada
- Natural Resources Canada, Canadian Forest ServiceSault Ste. Marie, Ontario, Canada
| | - Chris JK MacQuarrie
- Natural Resources Canada, Canadian Forest ServiceSault Ste. Marie, Ontario, Canada
| | | | - J Dale Simpson
- Natural Resources Canada, Canadian Forest ServiceFredericton, New-Brunswick, Canada
| | - Josyanne Lamarche
- Natural Resources Canada, Canadian Forest ServiceSault Ste. Marie, Ontario, Canada
| | - Tannis Beardmore
- Natural Resources Canada, Canadian Forest ServiceFredericton, New-Brunswick, Canada
| | - Stacey L Thompson
- Natural Resources Canada, Canadian Forest ServiceQuébec, Québec, Canada
- Umeå University, Department of Ecology and Environmental Science, Umeå Plant Science CentreUmeå, Sweden
| | - Philippe Tanguay
- Natural Resources Canada, Canadian Forest ServiceQuébec, Québec, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest ServiceQuébec, Québec, Canada
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