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Fan S, Georgi LL, Hebard FV, Zhebentyayeva T, Yu J, Sisco PH, Fitzsimmons SF, Staton ME, Abbott AG, Nelson CD. Mapping QTLs for blight resistance and morpho-phenological traits in inter-species hybrid families of chestnut ( Castanea spp.). FRONTIERS IN PLANT SCIENCE 2024; 15:1365951. [PMID: 38650705 PMCID: PMC11033410 DOI: 10.3389/fpls.2024.1365951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Chestnut blight (caused by Cryphonectria parasitica), together with Phytophthora root rot (caused by Phytophthora cinnamomi), has nearly extirpated American chestnut (Castanea dentata) from its native range. In contrast to the susceptibility of American chestnut, many Chinese chestnut (C. mollissima) genotypes are resistant to blight. In this research, we performed a series of genome-wide association studies for blight resistance originating from three unrelated Chinese chestnut trees (Mahogany, Nanking and M16) and a Quantitative Trait Locus (QTL) study on a Mahogany-derived inter-species F2 family. We evaluated trees for resistance to blight after artificial inoculation with two fungal strains and scored nine morpho-phenological traits that are the hallmarks of species differentiation between American and Chinese chestnuts. Results support a moderately complex genetic architecture for blight resistance, as 31 QTLs were found on 12 chromosomes across all studies. Additionally, although most morpho-phenological trait QTLs overlap or are adjacent to blight resistance QTLs, they tend to aggregate in a few genomic regions. Finally, comparison between QTL intervals for blight resistance and those previously published for Phytophthora root rot resistance, revealed five common disease resistance regions on chromosomes 1, 5, and 11. Our results suggest that it will be difficult, but still possible to eliminate Chinese chestnut alleles for the morpho-phenological traits while achieving relatively high blight resistance in a backcross hybrid tree. We see potential for a breeding scheme that utilizes marker-assisted selection early for relatively large effect QTLs followed by genome selection in later generations for smaller effect genomic regions.
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Affiliation(s)
- Shenghua Fan
- Forest Health Research and Education Center, Department of Horticulture, University of Kentucky, Lexington, KY, United States
| | - Laura L. Georgi
- Forest Health Research and Education Center, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Lexington, KY, United States
- Virginia Chapter, The American Chestnut Foundation, Meadowview, VA, United States
| | - Frederick V. Hebard
- Virginia Chapter, The American Chestnut Foundation, Meadowview, VA, United States
| | - Tetyana Zhebentyayeva
- Forest Health Research and Education Center, Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, United States
| | - Jiali Yu
- Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Paul H. Sisco
- Carolinas Chapter, The American Chestnut Foundation, Asheville, NC, United States
| | - Sara F. Fitzsimmons
- North Central Office, The American Chestnut Foundation, University Park, PA, United States
| | - Margaret E. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Albert G. Abbott
- Forest Health Research and Education Center, Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, United States
| | - C. Dana Nelson
- Forest Health Research and Education Center, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Lexington, KY, United States
- Southern Institute of Forest Genetics, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Saucier, MS, United States
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Islam-Faridi N, Hodnett GL, Zhebentyayeva T, Georgi LL, Sisco PH, Hebard FV, Nelson CD. Cyto-molecular characterization of rDNA and chromatin composition in the NOR-associated satellite in Chestnut (Castanea spp.). Sci Rep 2024; 14:980. [PMID: 38225361 PMCID: PMC10789788 DOI: 10.1038/s41598-023-45879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 10/25/2023] [Indexed: 01/17/2024] Open
Abstract
The American chestnut (Castanea dentata, 2n = 2x = 24), once known as the "King of the Appalachian Forest", was decimated by chestnut blight during the first half of the twentieth century by an invasive fungus (Cryphonectria parasitica). The Chinese chestnut (C. mollissima, 2n = 2x = 24), in contrast to American chestnut, is resistant to this blight. Efforts are being made to transfer this resistance to American chestnut through backcross breeding and genetic engineering. Both chestnut genomes have been genetically mapped and recently sequenced to facilitate gene discovery efforts aimed at assisting molecular breeding and genetic engineering. To complement and extend this genomic work, we analyzed the distribution and organization of their ribosomal DNAs (35S and 5S rDNA), and the chromatin composition of the nucleolus organizing region (NOR)-associated satellites. Using fluorescent in situ hybridization (FISH), we have identified two 35S (one major and one minor) and one 5S rDNA sites. The major 35S rDNA sites are terminal and sub-terminal in American and Chinese chestnuts, respectively, originating at the end of the short arm of the chromosome, extending through the secondary constriction and into the satellites. An additional 5S locus was identified in certain Chinese chestnut accessions, and it was linked distally to the major 35S site. The NOR-associated satellite in Chinese chestnut was found to comprise a proximal region packed with 35S rDNA and a distinct distal heterochromatic region. In contrast, the American chestnut satellite was relatively small and devoid of the distal heterochromatic region.
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Affiliation(s)
- Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, Southern Institute of Forest Genetics, USDA Forest Service, Southern Research Station, Texas A&M University, College Station, TX, 77843, USA.
| | - George L Hodnett
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, 40546, USA
| | - Laura L Georgi
- Meadowview Research Farms, The American Chestnut Foundation, 29010 Hawthorne Drive, Meadowview, VA, 24361, USA
| | - Paul H Sisco
- The American Chestnut Foundation, 50 North Merrimon Ave., Suite 115, Asheville, NC, 28804, USA
| | - Frederick V Hebard
- Meadowview Research Farms, The American Chestnut Foundation, 29010 Hawthorne Drive, Meadowview, VA, 24361, USA
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Forest Health Research and Education Center, Lexington, KY, 40546, USA
- USDA Forest Service, Southern Institute of Forest Genetics, Harrison Experimental Forest, 23332 Success Road, Saucier, MS, 39574, USA
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Fernandes P, Colavolpe MB, Serrazina S, Costa RL. European and American chestnuts: An overview of the main threats and control efforts. FRONTIERS IN PLANT SCIENCE 2022; 13:951844. [PMID: 36092400 PMCID: PMC9449730 DOI: 10.3389/fpls.2022.951844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Chestnuts are multipurpose trees significant for the economy and wildlife. These trees are currently found around the globe, demonstrating their genetic adaptation to different environmental conditions. Several biotic and abiotic stresses have challenged these species, contributing to the decline of European chestnut production and the functional extinction of the American chestnut. Several efforts started over the last century to understand the cellular, molecular, and genetic interactions behind all chestnut biotic and abiotic interactions. Most efforts have been toward breeding for the primary diseases, chestnut blight and ink disease caused by the pathogens, Cryphonectria parasitica and Phytophthora cinnamomi, respectively. In Europe and North America, researchers have been using the Asian chestnut species, which co-evolved with the pathogens, to introgress resistance genes into the susceptible species. Breeding woody trees has several limitations which can be mostly related to the long life cycles of these species and the big genome landscapes. Consequently, it takes decades to improve traits of interest, such as resistance to pathogens. Currently, the availability of genome sequences and next-generation sequencing techniques may provide new tools to help overcome most of the problems tree breeding is still facing. This review summarizes European and American chestnut's main biotic stresses and discusses breeding and biotechnological efforts developed over the last decades, having ink disease and chestnut blight as the main focus. Climate change is a rising concern, and in this context, the adaptation of chestnuts to adverse environmental conditions is of extreme importance for chestnut production. Therefore, we also discuss the abiotic challenges on European chestnuts, where the response to abiotic stress at the genetic and molecular level has been explored.
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Affiliation(s)
- Patrícia Fernandes
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
- Green-It Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | | | - Susana Serrazina
- BioISI – Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Rita Lourenço Costa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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Pavese V, Moglia A, Gonthier P, Torello Marinoni D, Cavalet-Giorsa E, Botta R. Identification of Susceptibility Genes in Castanea sativa and Their Transcription Dynamics following Pathogen Infection. PLANTS 2021; 10:plants10050913. [PMID: 34063239 PMCID: PMC8147476 DOI: 10.3390/plants10050913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
Castanea sativa is one of the main multipurpose tree species valued for its timber and nuts. This species is susceptible to two major diseases, ink disease and chestnut blight, caused by Phytophthora spp. and Cryphonectria parasitica, respectively. The loss-of-function mutations of genes required for the onset of pathogenesis, referred to as plant susceptibility (S) genes, are one mechanism of plant resistance against pathogens. On the basis of sequence homology, functional domain identification, and phylogenetic analyses, we report for the first time on the identification of S-genes (mlo1, dmr6, dnd1, and pmr4) in the Castanea genus. The expression dynamics of S-genes were assessed in C. sativa and C. crenata plants inoculated with P. cinnamomi and C. parasitica. Our results highlighted the upregulation of pmr4 and dmr6 in response to pathogen infection. Pmr4 was strongly expressed at early infection phases of both pathogens in C. sativa, whereas in C. crenata, no significant upregulation was observed. The infection of P. cinnamomi led to a higher increase in the transcript level of dmr6 in C. sativa compared to C. crenata-infected samples. For a better understanding of plant responses, the transcript levels of defense genes gluB and chi3 were also analyzed.
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Torello Marinoni D, Nishio S, Valentini N, Shirasawa K, Acquadro A, Portis E, Alma A, Akkak A, Pavese V, Cavalet-Giorsa E, Botta R. Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp. PLANTS 2020; 9:plants9081048. [PMID: 32824716 PMCID: PMC7465717 DOI: 10.3390/plants9081048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/29/2022]
Abstract
Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
- Correspondence:
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan;
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan;
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Alberto Alma
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Aziz Akkak
- Dipartimento di Scienze Agrarie, degli Alimenti e dell’Ambiente, Università degli Studi di Foggia, Via Napoli 25, 71121 Foggia, Italy;
| | - Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Emile Cavalet-Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
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Westbrook JW, Zhang Q, Mandal MK, Jenkins EV, Barth LE, Jenkins JW, Grimwood J, Schmutz J, Holliday JA. Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade-off with American chestnut ancestry implies resistance is polygenic. Evol Appl 2020; 13:31-47. [PMID: 31892942 PMCID: PMC6935594 DOI: 10.1111/eva.12886] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 01/04/2023] Open
Abstract
American chestnut was once a foundation species of eastern North American forests, but was rendered functionally extinct in the early 20th century by an exotic fungal blight (Cryphonectria parasitica). Over the past 30 years, the American Chestnut Foundation (TACF) has pursued backcross breeding to generate hybrids that combine the timber-type form of American chestnut with the blight resistance of Chinese chestnut based on a hypothesis of major gene resistance. To accelerate selection within two backcross populations that descended from two Chinese chestnuts, we developed genomic prediction models for five presence/absence blight phenotypes of 1,230 BC3F2 selection candidates and average canker severity of their BC3F3 progeny. We also genotyped pure Chinese and American chestnut reference panels to estimate the proportion of BC3F2 genomes inherited from parent species. We found that genomic prediction from a method that assumes an infinitesimal model of inheritance (HBLUP) has similar accuracy to a method that tends to perform well for traits controlled by major genes (Bayes C). Furthermore, the proportion of BC3F2 trees' genomes inherited from American chestnut was negatively correlated with the blight resistance of these trees and their progeny. On average, selected BC3F2 trees inherited 83% of their genome from American chestnut and have blight resistance that is intermediate between F1 hybrids and American chestnut. Results suggest polygenic inheritance of blight resistance. The blight resistance of restoration populations will be enhanced through recurrent selection, by advancing additional sources of resistance through fewer backcross generations, and by potentially by breeding with transgenic blight-tolerant trees.
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Affiliation(s)
| | - Qian Zhang
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVAUSA
| | | | | | | | | | - Jane Grimwood
- HudsonAlpha Institute for BiotechnologyHuntsvilleALUSA
| | | | - Jason A. Holliday
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVAUSA
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Zhebentyayeva TN, Sisco PH, Georgi LL, Jeffers SN, Perkins MT, James JB, Hebard FV, Saski C, Nelson CD, Abbott AG. Dissecting Resistance to Phytophthora cinnamomi in Interspecific Hybrid Chestnut Crosses Using Sequence-Based Genotyping and QTL Mapping. PHYTOPATHOLOGY 2019; 109:1594-1604. [PMID: 31287366 DOI: 10.1094/phyto-11-18-0425-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The soilborne oomycete Phytophthora cinnamomi-which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development. Introduction of resistant genotypes is the most practical solution for disease management in forests because treatment with fungicides and eradication of the pathogen are neither practical nor economically feasible in natural ecosystems. Using backcross families derived from crosses of American chestnuts with two resistant Chinese chestnut cultivars Mahogany and Nanking, we constructed linkage maps and identified quantitative trait loci (QTLs) for resistance to P. cinnamomi that had been introgressed from these Chinese chestnut cultivars. In total, 957 plants representing five cohorts of three hybrid crosses were genotyped by sequencing and phenotyped by standardized inoculation and visual examination over a 6-year period from 2011 to 2016. Eight parental linkage maps comprising 7,715 markers were constructed, and 17 QTLs were identified on four linkage groups (LGs): LG_A, LG_C, LG_E, and LG_K. The most consistent QTLs were detected on LG_E in seedlings from crosses with both 'Mahogany' and 'Nanking' and LG_K in seedlings from 'Mahogany' crosses. Two consistent large and medium effect QTLs located ∼10 cM apart were present in the middle and at the lower end of LG_E; other QTLs were considered to have small effects. These results imply that the genetic architecture of resistance to P. cinnamomi in Chinese chestnut × American chestnut hybrid progeny may resemble the P. sojae-soybean pathosystem, with a few dominant QTLs along with quantitatively inherited partial resistance conferred by multiple small-effect QTLs.
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Affiliation(s)
- Tetyana N Zhebentyayeva
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802
- Clemson University Genomics and Computational Biology Laboratory, Clemson, SC 29634
| | - Paul H Sisco
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Laura L Georgi
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - M Taylor Perkins
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | | | - Frederick V Hebard
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - C Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, U.S. Department of Agriculture Forest Service, Saucier, MS 39574
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
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Powell WA, Newhouse AE, Coffey V. Developing Blight-Tolerant American Chestnut Trees. Cold Spring Harb Perspect Biol 2019; 11:a034587. [PMID: 31110131 PMCID: PMC6601460 DOI: 10.1101/cshperspect.a034587] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An invasive fungal pathogen has reduced the American chestnut (Castanea dentata), once a keystone tree species within its natural range in the eastern United States and Canada, to functional extinction. To help restore this important canopy tree, blight-tolerant American chestnut trees have been developed using an oxalate oxidase-encoding gene from wheat. This enzyme breaks down oxalate, which is produced by the pathogen and forms killing cankers. Expressing oxalate oxidase results in blight tolerance, where the tree and the fungus can coexist, which is a more evolutionarily stable relationship than direct pathogen resistance. Genetic engineering (GE) typically makes a very small change in the tree's genome, potentially avoiding incompatible gene interactions that have been detected in some chestnut hybrids. The GE American chestnut also retains all the wild American chestnut's alleles for habitat adaptation, which are important for a forest ecosystem restoration program.
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Affiliation(s)
- William A Powell
- American Chestnut Research and Restoration Project, College of Environmental Science and Forestry, Syracuse, New York 13210, USA
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, USA
| | - Andrew E Newhouse
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, USA
| | - Vernon Coffey
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, USA
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Westbrook JW, James JB, Sisco PH, Frampton J, Lucas S, Jeffers SN. Resistance to Phytophthora cinnamomi in American Chestnut ( Castanea dentata) Backcross Populations that Descended from Two Chinese Chestnut ( Castanea mollissima) Sources of Resistance. PLANT DISEASE 2019; 103:1631-1641. [PMID: 31033400 DOI: 10.1094/pdis-11-18-1976-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Restoration of American chestnut (Castanea dentata) depends on combining resistance to both the chestnut blight fungus (Cryphonectria parasitica) and Phytophthora cinnamomi, which causes Phytophthora root rot, in a diverse population of C. dentata. Over a 14-year period (2004 to 2017), survival and root health of American chestnut backcross seedlings after inoculation with P. cinnamomi were compared among 28 BC3, 66 BC4, and 389 BC3F3 families that descended from two BC1 trees (Clapper and Graves) with different Chinese chestnut grandparents. The 5% most resistant Graves BC3F3 families survived P. cinnamomi infection at rates of 75 to 100% but had mean root health scores that were intermediate between resistant Chinese chestnut and susceptible American chestnut families. Within Graves BC3F3 families, seedling survival was greater than survival of Graves BC3 and BC4 families and was not genetically correlated with chestnut blight canker severity. Only low to intermediate resistance to P. cinnamomi was detected among backcross descendants from the Clapper tree. Results suggest that major-effect resistance alleles were inherited by descendants from the Graves tree, that intercrossing backcross trees enhances progeny resistance to P. cinnamomi, and that alleles for resistance to P. cinnamomi and C. parasitica are not linked. To combine resistance to both C. parasitica and P. cinnamomi, a diverse Graves backcross population will be screened for resistance to P. cinnamomi, survivors bred with trees selected for resistance to C. parasitica, and progeny selected for resistance to both pathogens will be intercrossed.
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Affiliation(s)
| | - Joseph B James
- 2 The American Chestnut Foundation and Chestnut Return Farms, Seneca, SC 29672
| | - Paul H Sisco
- 1 The American Chestnut Foundation, Asheville, NC 28804
| | - John Frampton
- 3 Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Sunny Lucas
- 4 United States Department of Agriculture Forest Service Resistance Screening Center, Asheville, NC 28806
| | - Steven N Jeffers
- 5 Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
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Abstract
American chestnut (Castanea dentata Borkh.) was a dominant tree species in its native range in eastern North America until the accidentally introduced fungus Cryphonectria parasitica (Murr.) Barr, that causes chestnut blight, led to a collapse of the species. Different approaches (e.g., genetic engineering or conventional breeding) are being used to fight against chestnut blight and to reintroduce the species with resistant planting stock. Because of large climatic differences within the distribution area of American chestnut, successful reintroduction of the species requires knowledge and consideration of local adaptation to the prevailing environmental conditions. Previous studies revealed clear patterns of genetic diversity along the northeast-southwest axis of the Appalachian Mountains, but less is known about the distribution of potentially adaptive genetic variation within the distribution area of this species. In this study, we investigated neutral and potentially adaptive genetic variation in nine American chestnut populations collected from sites with different environmental conditions. In total, 272 individuals were genotyped with 24 microsatellite (i.e., simple sequence repeat (SSR)) markers (seven genomic SSRs and 17 EST-SSRs). An FST-outlier analysis revealed five outlier loci. The same loci, as well as five additional ones, were significantly associated with environmental variables of the population sites in an environmental association analysis. Four of these loci are of particular interest, since they were significant in both methods, and they were associated with environmental variation, but not with geographic variation. Hence, these loci might be involved in (temperature-related) adaptive processes in American chestnut. This work aims to help understanding the genetic basis of adaptation in C. dentata, and therefore the selection of suitable provenances for further breeding efforts.
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Ji F, Wei W, Liu Y, Wang G, Zhang Q, Xing Y, Zhang S, Liu Z, Cao Q, Qin L. Construction of a SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of Nut Traits in Chinese Chestnut ( Castanea mollissima Blume). FRONTIERS IN PLANT SCIENCE 2018; 9:816. [PMID: 29963069 PMCID: PMC6011034 DOI: 10.3389/fpls.2018.00816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 05/28/2018] [Indexed: 05/09/2023]
Abstract
Chinese chestnut is a wildly distributed nut species with importantly economic value. The nut size and ripening period are mainly desired breeding objectives in Chinese chestnut. However, high-density linkage maps and quantitative trait loci (QTL) analyses related to nut traits are less than satisfactory, which hinders progress in the breeding of Chinese chestnut. Here, a single nucleotide polymorphism (SNP)-based high-density linkage map was constructed through genotyping-by-sequencing (GBS) of an F1 cross between the two widely grown Chinese chestnut cultivars 'Yanshanzaofeng' and 'Guanting No. 10'. The genetic linkage map consists of 2,620 SNP markers with a total length of 1078.06 cM in 12 linkage groups (LGs) and an average marker distance of 0.41 cM. 17 QTLs were identified for five nut traits, specifically single-nut weight (SNW), nut width (NW), nut thickness (NT), nut height (NH), and ripening period (RP), based on phenotypic data from two successive years. Of the 17 QTLs, two major QTLs, i.e., qNT-I-1 and qRP-B-1 related to the NT and RP traits, respectively, were exploited. Moreover, the data revealed one pleiotropic QTL at 23.97 cM on LG I, which might simultaneously control SNW, NT, and NW. This study provides useful benchmark information concerning high-density genetic mapping and QTLs identification related to nut size and ripening period, and will accelerate genetic improvements for nuts in the marker-assisted selection (MAS) breeding of Chinese chestnut.
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Affiliation(s)
- Feiyang Ji
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Wei Wei
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yang Liu
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Guangpeng Wang
- Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Sciences, Changli, China
| | - Qing Zhang
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yu Xing
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Shuhang Zhang
- Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Sciences, Changli, China
| | - Zhihao Liu
- Novogene Bioinformatics Technology Co., Ltd., Tianjin, China
| | - Qingqin Cao
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
- Department of Biological Science and Engineering, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
| | - Ling Qin
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
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12
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Rigling D, Prospero S. Cryphonectria parasitica, the causal agent of chestnut blight: invasion history, population biology and disease control. MOLECULAR PLANT PATHOLOGY 2018; 19:7-20. [PMID: 28142223 PMCID: PMC6638123 DOI: 10.1111/mpp.12542] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 05/25/2023]
Abstract
Chestnut blight, caused by Cryphonectria parasitica, is a devastating disease infecting American and European chestnut trees. The pathogen is native to East Asia and was spread to other continents via infected chestnut plants. This review summarizes the current state of research on this pathogen with a special emphasis on its interaction with a hyperparasitic mycovirus that acts as a biological control agent of chestnut blight. TAXONOMY Cryphonectria parasitica (Murr.) Barr. is a Sordariomycete (ascomycete) fungus in the family Cryphonectriaceae (Order Diaporthales). Closely related species that can also be found on chestnut include Cryphonectria radicalis, Cryphonectria naterciae and Cryphonectria japonica. HOST RANGE Major hosts are species in the genus Castanea (Family Fagaceae), particularly the American chestnut (C. dentata), the European chestnut (C. sativa), the Chinese chestnut (C. mollissima) and the Japanese chestnut (C. crenata). Minor incidental hosts include oaks (Quercus spp.), maples (Acer spp.), European hornbeam (Carpinus betulus) and American chinkapin (Castanea pumila). DISEASE SYMPTOMS Cryphonectria parasitica causes perennial necrotic lesions (so-called cankers) on the bark of stems and branches of susceptible host trees, eventually leading to wilting of the plant part distal to the infection. Chestnut blight cankers are characterized by the presence of mycelial fans and fruiting bodies of the pathogen. Below the canker the tree may react by producing epicormic shoots. Non-lethal, superficial or callusing cankers on susceptible host trees are usually associated with mycovirus-induced hypovirulence. DISEASE CONTROL After the introduction of C. parasitica into a new area, eradication efforts by cutting and burning the infected plants/trees have mostly failed. In Europe, the mycovirus Cryphonectria hypovirus 1 (CHV-1) acts as a successful biological control agent of chestnut blight by causing so-called hypovirulence. CHV-1 infects C. parasitica and reduces its parasitic growth and sporulation capacity. Individual cankers can be therapeutically treated with hypovirus-infected C. parasitica strains. The hypovirus may subsequently spread to untreated cankers and become established in the C. parasitica population. Hypovirulence is present in many chestnut-growing regions of Europe, either resulting naturally or after biological control treatments. In North America, disease management of chestnut blight is mainly focused on breeding with the goal to backcross the Chinese chestnut's blight resistance into the American chestnut genome.
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Affiliation(s)
- Daniel Rigling
- Swiss Federal Institute for ForestSnow and Landscape Research (WSL)Birmensdorf8903Switzerland
| | - Simone Prospero
- Swiss Federal Institute for ForestSnow and Landscape Research (WSL)Birmensdorf8903Switzerland
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13
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Santos C, Nelson CD, Zhebentyayeva T, Machado H, Gomes-Laranjo J, Costa RL. First interspecific genetic linkage map for Castanea sativa x Castanea crenata revealed QTLs for resistance to Phytophthora cinnamomi. PLoS One 2017; 12:e0184381. [PMID: 28880954 PMCID: PMC5589223 DOI: 10.1371/journal.pone.0184381] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/22/2017] [Indexed: 11/18/2022] Open
Abstract
The Japanese chestnut (Castanea crenata) carries resistance to Phytophthora cinnamomi, the destructive and widespread oomycete causing ink disease. The European chestnut (Castanea sativa), carrying little to no disease resistance, is currently threatened by the presence of the oomycete pathogen in forests, orchards and nurseries. Determining the genetic basis of P. cinnamomi resistance, for further selection of molecular markers and candidate genes, is a prominent issue for implementation of marker assisted selection in the breeding programs for resistance. In this study, the first interspecific genetic linkage map of C. sativa x C. crenata allowed the detection of QTLs for P. cinnamomi resistance. The genetic map was constructed using two independent, control-cross mapping populations. Chestnut populations were genotyped using 452 microsatellite and single nucleotide polymorphism molecular markers derived from the available chestnut transcriptomes. The consensus genetic map spans 498,9 cM and contains 217 markers mapped with an average interval of 2.3 cM. For QTL analyses, the progression rate of P. cinnamomi lesions in excised shoots inoculated was used as the phenotypic metric. Using non-parametric and composite interval mapping approaches, two QTLs were identified for ink disease resistance, distributed in two linkage groups: E and K. The presence of QTLs located in linkage group E regarding P. cinnamomi resistance is consistent with a previous preliminary study developed in American x Chinese chestnut populations, suggesting the presence of common P. cinnamomi defense mechanisms across species. Results presented here extend the genomic resources of Castanea genus providing potential tools to assist the ongoing and future chestnut breeding programs.
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Affiliation(s)
- Carmen Santos
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação Agrária e Veterinária, I.P., Avenida da República, Oeiras, Portugal
| | - Charles Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, USDA Forest Service, Saucier, Mississippi, United States of America
- Forest Health Research and Education Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Tetyana Zhebentyayeva
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Genomics & Computational Biology Laboratory, Clemson University, Clemson, South Carolina, United States of America
| | - Helena Machado
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação Agrária e Veterinária, I.P., Avenida da República, Oeiras, Portugal
| | - José Gomes-Laranjo
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas, Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Rita Lourenço Costa
- Laboratório de Biologia Molecular, Instituto Nacional de Investigação Agrária e Veterinária, I.P., Avenida da República, Oeiras, Portugal
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa - Tapada da Ajuda, Lisboa, Portugal
- * E-mail:
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14
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Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, Abbott AG. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics 2015; 16:744. [PMID: 26438416 PMCID: PMC4595192 DOI: 10.1186/s12864-015-1942-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 09/19/2015] [Indexed: 01/03/2023] Open
Abstract
Background Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. Results The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. Conclusions On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1942-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA.
| | | | - Bode Olukolu
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA.
| | | | - Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, U.S. Forest Service, Saucier, MS, USA.
| | - John E Carlson
- The School of Forest Resources and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Albert G Abbott
- Department of Forestry, Forest Health Research and Education Center, Lexington, KY, USA.
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15
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Multilocus PCR Assays Elucidate Vegetative Incompatibility Gene Profiles of Cryphonectria parasitica in the United States. Appl Environ Microbiol 2015; 81:5736-42. [PMID: 26070681 DOI: 10.1128/aem.00926-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/08/2015] [Indexed: 11/20/2022] Open
Abstract
Chestnut blight is a devastating disease of Castanea spp. Mycoviruses that reduce virulence (hypovirulence) of the causative agent, Cryphonectria parasitica, can be used to manage chestnut blight. However, vegetative incompatibility (vic) barriers that restrict anastomosis-mediated virus transmission hamper hypovirulence efficacy. In order to effectively determine the vegetative incompatibility genetic structure of C. parasitica field populations, we have designed PCR primer sets that selectively amplify and distinguish alleles for each of the six known diallelic C. parasitica vic genetic loci. PCR assay results were validated using a panel of 64 European tester strains with genetically determined vic genotypes. Analysis of 116 C. parasitica isolates collected from five locations in the eastern United States revealed 39 unique vic genotypes and generally good agreement between PCR and tester strain coculturing assays in terms of vic diversity and genotyping. However, incongruences were observed for isolates from multiple locations and suggested that the coculturing assay can overestimate diversity at the six known vic loci. The availability of molecular tools for rapid and precise vic genotyping significantly improves the ability to predict and evaluate the efficacy of hypovirulence and related management strategies.
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16
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Newhouse AE, Polin-McGuigan LD, Baier KA, Valletta KER, Rottmann WH, Tschaplinski TJ, Maynard CA, Powell WA. Transgenic American chestnuts show enhanced blight resistance and transmit the trait to T1 progeny. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:88-97. [PMID: 25438789 DOI: 10.1016/j.plantsci.2014.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 04/01/2014] [Accepted: 04/03/2014] [Indexed: 05/24/2023]
Abstract
American chestnut (Castanea dentata) is a classic example of a native keystone species that was nearly eradicated by an introduced fungal pathogen. This report describes progress made toward producing a fully American chestnut tree with enhanced resistance to the blight fungus (Cryphonectria parasitica). The transgenic American chestnut 'Darling4,' produced through an Agrobacterium co-transformation procedure to express a wheat oxalate oxidase gene driven by the VspB vascular promoter, shows enhanced blight resistance at a level intermediate between susceptible American chestnut and resistant Chinese chestnut (Castanea mollissima). Enhanced resistance was identified first with a leaf-inoculation assay using young chestnuts grown indoors, and confirmed with traditional stem inoculations on 3- and 4-year-old field-grown trees. Pollen from 'Darling4' and other events was used to produce transgenic T1 seedlings, which also expressed the enhanced resistance trait in leaf assays. Outcrossed transgenic seedlings have several advantages over tissue-cultured plantlets, including increased genetic diversity and faster initial growth. This represents a major step toward the restoration of the majestic American chestnut.
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Affiliation(s)
- Andrew E Newhouse
- State University of New York College of Environmental Science & Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Linda D Polin-McGuigan
- State University of New York College of Environmental Science & Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Kathleen A Baier
- State University of New York College of Environmental Science & Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Kristia E R Valletta
- State University of New York College of Environmental Science & Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | | | | | - Charles A Maynard
- State University of New York College of Environmental Science & Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - William A Powell
- State University of New York College of Environmental Science & Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA.
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17
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Jacobs DF, Dalgleish HJ, Nelson CD. A conceptual framework for restoration of threatened plants: the effective model of American chestnut (Castanea dentata) reintroduction. THE NEW PHYTOLOGIST 2013; 197:378-393. [PMID: 23163342 DOI: 10.1111/nph.12020] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/17/2012] [Indexed: 05/22/2023]
Abstract
We propose a conceptual framework for restoration of threatened plant species that encourages integration of technological, ecological, and social spheres. A sphere encompasses ideas relevant to restoration and the people working within similar areas of influence or expertise. Increased capacity within a sphere and a higher degree of coalescing among spheres predict a greater probability of successful restoration. We illustrate this with Castanea dentata, a foundation forest tree in North America that was annihilated by an introduced pathogen; the species is a model that effectively merges biotechnology, reintroduction biology, and restoration ecology. Because of C. dentata's ecological and social importance, scientists have aggressively pursued blight resistance through various approaches. We summarize recent advancements in tree breeding and biotechnology that have emerged from C. dentata research, and describe their potential to bring new tools to bear on socio-ecological restoration problems. Successful reintroduction of C. dentata will also depend upon an enhanced understanding of its ecology within contemporary forests. We identify a critical need for a deeper understanding of societal influences that may affect setting and achieving realistic restoration goals. Castanea dentata may serve as an important model to inform reintroduction of threatened plant species in general and foundation forest trees in particular.
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Affiliation(s)
- Douglass F Jacobs
- Department of Forestry and Natural Resources, Hardwood Tree Improvement and Regeneration Center, Purdue University, West Lafayette, Indiana, USA
| | - Harmony J Dalgleish
- Department of Forestry and Natural Resources, Hardwood Tree Improvement and Regeneration Center, Purdue University, West Lafayette, Indiana, USA
- Department of Biology, College of William and Mary, Williamsburg, Virginia, USA
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, Saucier, Mississippi, USA
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18
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Bodénès C, Chancerel E, Gailing O, Vendramin GG, Bagnoli F, Durand J, Goicoechea PG, Soliani C, Villani F, Mattioni C, Koelewijn HP, Murat F, Salse J, Roussel G, Boury C, Alberto F, Kremer A, Plomion C. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC PLANT BIOLOGY 2012; 12:153. [PMID: 22931513 PMCID: PMC3493355 DOI: 10.1186/1471-2229-12-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/22/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany
- New address: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Jerome Durand
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Pablo G Goicoechea
- NEIKER-Tecnalia, Dpto Biotecnologia, PO Box 46, Vitoria-Gasteiz, 01080, Spain
| | - Carolina Soliani
- Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, Bariloche, CC277 8400, Argentina
| | - Fiorella Villani
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | - Claudia Mattioni
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | | | - Florent Murat
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Jerome Salse
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Guy Roussel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Florian Alberto
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
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19
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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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20
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Andrade GM, Nairn CJ, Le HT, Merkle SA. Sexually mature transgenic American chestnut trees via embryogenic suspension-based transformation. PLANT CELL REPORTS 2009; 28:1385-97. [PMID: 19578855 DOI: 10.1007/s00299-009-0738-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/16/2009] [Accepted: 06/18/2009] [Indexed: 05/07/2023]
Abstract
The availability of a system for direct transfer of anti-fungal candidate genes into American chestnut (Castanea dentata), devastated by a fungal blight in the last century, would offer an alternative or supplemental approach to conventional breeding for production of chestnut trees resistant to the blight fungus and other pathogens. By taking advantage of the strong ability of embryogenic American chestnut cultures to proliferate in suspension, a high-throughput Agrobacterium tumefaciens-mediated transformation protocol for stable integration of foreign genes into the tree was established. Proembryogenic masses (PEMs) were co-cultivated with A. tumefaciens strain AGL1 harboring the plasmid pCAMBIA 2301, followed by stringent selection with 50 or 100 mg/l Geneticin. A protocol employing size-fractionation to enrich for small PEMs to use as target material and selection in suspension culture was applied to rapidly produce transgenic events with an average efficiency of four independent transformation events per 50 mg of target tissue and minimal escapes. Mature somatic embryos, representing 18 transgenic events and derived from multiple American chestnut target genotypes, were germinated and over 100 transgenic somatic seedlings were produced and acclimatized to greenhouse conditions. Multiple vigorous transgenic somatic seedlings produced functional staminate flowers within 3 years following regeneration.
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Affiliation(s)
- Gisele M Andrade
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
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21
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Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC PLANT BIOLOGY 2009; 9:51. [PMID: 19426529 PMCID: PMC2688492 DOI: 10.1186/1471-2229-9-51] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 05/09/2009] [Indexed: 05/07/2023]
Abstract
UNLABELLED BACKGROUND1471-2229-9-51: American chestnut (Castanea dentata) was devastated by an exotic pathogen in the beginning of the twentieth century. This chestnut blight is caused by Cryphonectria parasitica, a fungus that infects stem tissues and kills the trees by girdling them. Because of the great economic and ecological value of this species, significant efforts have been made over the century to combat this disease, but it wasn't until recently that a focused genomics approach was initiated. Prior to the Genomic Tool Development for the Fagaceae project, genomic resources available in public databases for this species were limited to a few hundred ESTs. To identify genes involved in resistance to C. parasitica, we have sequenced the transcriptome from fungal infected and healthy stem tissues collected from blight-sensitive American chestnut and blight-resistant Chinese chestnut (Castanea mollissima) trees using ultra high throughput pyrosequencing. RESULTS We produced over a million 454 reads, totaling over 250 million bp, from which we generated 40,039 and 28,890 unigenes in total from C. mollissima and C. dentata respectively. The functions of the unigenes, from GO annotation, cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. In silico expression analyses showed that many of the stress response unigenes were expressed more in canker tissues versus healthy stem tissues in both American and Chinese chestnut. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either American or Chinese chestnut canker tissues. CONCLUSION Our study resulted in the identification of a large set of cDNA unigenes from American chestnut and Chinese chestnut. The ESTs and unigenes from this study constitute an important resource to the scientific community interested in the discovery of genes involved in various biological processes in Chestnut and other species. The identification of many defense-related genes differentially expressed in canker vs. healthy stem in chestnuts provides many new candidate genes for developing resistance to the chestnut blight and for studying pathways involved in responses of trees to necrotrophic pathogens. We also identified several candidate genes that may underline the difference in resistance to Cryphonectria parasitica between American chestnut and Chinese chestnut.
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Affiliation(s)
- Abdelali Barakat
- The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USA
| | - Denis S DiLoreto
- The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USA
| | - Yi Zhang
- The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USA
| | - Chris Smith
- Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Kathleen Baier
- Department of Environmental Science and Forestry, State University of New York, Syracuse, NY, USA
| | - William A Powell
- Department of Environmental Science and Forestry, State University of New York, Syracuse, NY, USA
| | - Nicholas Wheeler
- Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Ron Sederoff
- Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - John E Carlson
- The School of Forest Resources, Department of Horticulture, The Huck Institutes of the Life Sciences, The Pennsylvania State University, 323 Forest Resources Building, University Park, PA 16802, USA
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Freeman JS, Potts BM, Vaillancourt RE. Few Mendelian genes underlie the quantitative response of a forest tree, Eucalyptus globulus, to a natural fungal epidemic. Genetics 2008; 178:563-71. [PMID: 18202395 PMCID: PMC2206102 DOI: 10.1534/genetics.107.081414] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Accepted: 11/07/2007] [Indexed: 11/18/2022] Open
Abstract
Foliar fungal pathogens from the genus Mycosphaerella affect eucalyptus in natural forests and plantations worldwide. QTL analysis was conducted to dissect the genetic control of resistance in Eucalyptus globulus to a natural infection by Mycosphaerella leaf disease, using a clonally replicated outbred F2 family (112 genotypes) planted in a field trial. Two major QTL, with high LOD support (20.2 and 10.9) and high genomewide significance, explained a large proportion (52%) of the phenotypic variance in the severity of damage by Mycosphaerella cryptica, which may be indicative of oligogenic control. Both QTL were validated in a second F2 family and one was validated in a third F2 family. The mean values of different genotype classes at both major QTL argue for Mendelian inheritance with resistance dominant over susceptibility. There were strong correlations between the levels of Mycosphaerella damage in related genetic material planted in three widely separated locations in Tasmania. These findings together provide evidence that the genes controlling resistance to Mycosphaerella damage are stable in different genetic backgrounds and across different environments.
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Affiliation(s)
- Jules S Freeman
- School of Plant Science and Cooperative Research Centre for Forestry, University of Tasmania, Hobart, Tasmania 7001, Australia.
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Kirst M, Myburg A, Sederoff R. Genetic mapping in forest trees: markers, linkage analysis and genomics. GENETIC ENGINEERING 2004; 26:105-41. [PMID: 15387295 DOI: 10.1007/978-0-306-48573-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Matias Kirst
- Forest Biotechnology Group, North Carolina State University, Campus Box 7247, Raleigh, NC 27695, USA
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Hayashi E, Kondo T, Terada K, Kuramoto N, Kawasaki S. Identification of AFLP markers linked to a resistance gene against pine needle gall midge in Japanese black pine. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1177-81. [PMID: 15067405 DOI: 10.1007/s00122-003-1537-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2003] [Accepted: 11/10/2003] [Indexed: 05/21/2023]
Abstract
Bulked segregant and AFLP analyses of two mapping populations (R17 x S6 and R17 x S1) were used to identify markers linked to Rpgm, the only known gene responsible for resistance to pine needle gall midge in Pinus thunbergii Parl. Rpgm was found to be bracketed by ACCC/CCTTT(190) on one side at a distance of 6.6 cM and ACGT/CCCGC(250) at 15.3 cM on the other side. The segregation of these markers was analyzed in two other families in order to determine their phase and transferability. One of the two additional resistant parents carried ACCC/CCTTT(190) in the homozygous state while the marker was in coupling (plus marker allele linked with an R allele) in a resistant parent, R17. The marker ACGT/CCCGC(250) was in a repulsion phase in R17 and was not detected in the other two resistant pine trees. Out of four AFLP markers identified, only ACGT/CCAAT(290) was transferable in all resistant trees tested, although its phase was opposite for different trees. These results indicate that in applying those markers to select resistant trees, the phase state of the markers in each resistant tree with respect to Rpgm needs to be considered.
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Affiliation(s)
- E Hayashi
- Forest Tree Breeding Center, Ishi, Juo, Taga, 319-1301, Ibaraki, Japan.
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Scalfi M, Troggio M, Piovani P, Leonardi S, Magnaschi G, Vendramin GG, Menozzi P. A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:433-41. [PMID: 14574454 DOI: 10.1007/s00122-003-1461-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2003] [Accepted: 08/13/2003] [Indexed: 05/17/2023]
Abstract
The genetic linkage map of European beech ( Fagus sylvatica L.) that we report here is the first to our knowledge. Based on a total of 312 markers (28 RAPDs, 274 AFLPs, 10 SSRs) scored in 143 individuals from a F(1) full-sib family. Two maps (one for each parent) were constructed according to a "two-way pseudo-testcross" mapping strategy. In the male map 119 markers could be clustered in 11 major groups (971 cM), while in the female map 132 markers were distributed in 12 major linkage groups (844 cM). In addition, four and one minor linkage groups (doublets and triplets) were obtained for the male and female map respectively. The two maps cover about 82% and 78% of the genome. Based on the position of 15 AFLP and 2 SSR loci segregating in both parents, seven homologous linkage groups could be identified. In the same pedigree we investigated the association with genetic markers of several quantitative traits: leaf area, leaf number and shape in 2 different years, specific leaf area, leaf carbon-isotope discrimination and tree height. A composite interval-mapping approach was used to estimate the number of QTLs, the amount of variation explained by each of them, and their position on the genetic linkage maps. Eight QTLs associated with leaf traits were found that explained between 15% and 35% of the trait variation, five on the female map and three on the male map.
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Affiliation(s)
- M Scalfi
- Dipartimento di Scienze Ambientali, Università di Parma, Parco Area delle Scienze 11/A, 43100, Parma, Italy
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Fritz RS, Moulia C, Newcombe G. Resistance of Hybrid Plants and Animals to Herbivores, Pathogens, and Parasites. ACTA ACUST UNITED AC 1999. [DOI: 10.1146/annurev.ecolsys.30.1.565] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
▪ Abstract Interspecific hybridization can disrupt normal resistance of plant and animal species to their parasites. Resistance to parasites is affected by hybridization in the following ways: no difference between hybrids and parentals, additivity, hybrid susceptibility, and dominance to susceptibility. Similar patterns were seen across host taxa. Responses of different parasite species vary widely to the same hybrid host, which indicates diverse genetic effects of interspecific hybridization on resistance. Differences between field and common garden or laboratory studies suggest that environmental factors in hybrid zones influence the patterns seen in the field. Based on recent studies of hybrid-parasite interactions, three avenues of future research will provide a more complete understanding of the roles of hybrids and the roles of parasites in host evolution. First, the relationship between inheritance of putative resistance mechanisms of hosts and responses of parasites needs study using analyses of recombinant progenies. Second, the interaction among environmental variation in hybrid zones, resistance mechanisms, responses of parasites, and the impact of parasites on host fitness needs experimental analysis using reciprocal transplant experiments in hybrid zones. Finally, the role of hybrids in the community structure and interactions of parasites needs study.
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Affiliation(s)
- Robert S. Fritz
- Department of Biology, Vassar College, Poughkeepsie, New York 12604-0133
| | - Catherine Moulia
- Laboratoire Genome, Populations, Interactions; UPR 9060 CNRS, CC105, UM II Place Eugene Bataillon, Montpellier Cedex O5, France
| | - George Newcombe
- Puyallup Research & Extension Center, Washington State University, Puyallup, Washington 98371-4998 USA
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