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Ence D, Smith KE, Fan S, Gomide Neves L, Paul R, Wegrzyn J, Peter GF, Kirst M, Brawner J, Nelson CD, Davis JM. NLR diversity and candidate fusiform rust resistance genes in loblolly pine. G3 GENES|GENOMES|GENETICS 2022; 12:6460333. [PMID: 34897455 PMCID: PMC9210285 DOI: 10.1093/g3journal/jkab421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently, single nucleotide polymorphism (SNP) markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for a nucleotide-binding site leucine-rich repeat (NLR) protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified 10 SNPs and 2 quantitative trait loci associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.
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Affiliation(s)
- Daniel Ence
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Katherine E Smith
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
- USDA Forest Service, Southern Research, Southern Institute of Forest Genetics, Saucier, MS 39574, USA
| | - Shenghua Fan
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546, USA
- Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
| | | | - Robin Paul
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Gary F Peter
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - C Dana Nelson
- USDA Forest Service, Southern Research, Southern Institute of Forest Genetics, Saucier, MS 39574, USA
- USDA Forest Service, Southern Research Station, Forest Health Research and Education Center, Lexington, KY 40546, USA
| | - John M Davis
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
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Moricca S, Ginetti B. Saprophytic growth of the alder rust fungus Melampsoridium hiratsukanum on artificial media. Fungal Biol 2015; 119:568-79. [PMID: 26058533 DOI: 10.1016/j.funbio.2015.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 02/12/2015] [Accepted: 03/03/2015] [Indexed: 11/25/2022]
Abstract
The first axenic culture of a free living saprophytic stage of the exotic rust fungus Melampsoridium hiratsukanum is reported. Colonies were obtained from one-celled, dikaryotic urediniospores on eight nutrient media out of twelve. Modified Harvey and Grasham (HG) and Schenk and Hildebrandt (HS) media HG1 and SH1 and their bovine serum albumin (BSA)-enriched derivatives gave abundant mycelial growth, but modified Murashige and Skoog (MS) QMS media and their BSA-enriched modifications performed poorly, colony growth being low on QMS-1 and QMS1+BSA, and nil on QMS-5 and QMS-6, with or without BSA. Colonies initially grew poorly when subcultured for one month in purity, but much better after re-transfer to fresh media later: presumably because only the most exploitative genotypes survived, best able to cope with an uncongenial medium. Stabilised cultures survived, and remained vegetative, but only few reproductive colonies produced spore-like bodies. Though the agarised medium remains an inhospitable environment for this biotrophic parasite, it is shown that non-living media can nevertheless sustain the growth and sporulation of this fungus outside its natural hosts and habitat. Axenic culture promises important advances in basic and applied research on this rust, leading to a better understanding of its nutrition, metabolism, diversity and pathogenicity.
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Affiliation(s)
- Salvatore Moricca
- DISPAA, Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università di Firenze, Piazzale delle Cascine 28, I 50144 Firenze, Italy.
| | - Beatrice Ginetti
- DISPAA, Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università di Firenze, Piazzale delle Cascine 28, I 50144 Firenze, Italy
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Li H, Ghosh S, Amerson H, Li B. Major gene detection for fusiform rust resistance using Bayesian complex segregation analysis in loblolly pine. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:921-9. [PMID: 16896716 DOI: 10.1007/s00122-006-0351-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 06/21/2006] [Indexed: 05/11/2023]
Abstract
The presence of major genes affecting rust resistance of loblolly pine was investigated in a progeny population that was generated with a half-diallel mating of six parents. A Bayesian complex segregation analysis was used to make inference about a mixed inheritance model (MIM) that included polygenic effects and a single major gene effect. Marginalizations were achieved by using Gibbs sampler. A parent block sampling by which genotypes of a parent and its offspring were sampled jointly was implemented to improve mixing. The MIM was compared with a pure polygenic model (PM) using Bayes factor. Results showed that the MIM was a better model to explain the inheritance of rust resistance than the pure PM in the diallel population. A large major gene variance component estimate (> 50% of total variance), indicated the existence of major genes for rust resistance in the studied loblolly pine population. Based on estimations of parental genotypes, it appears that there may be two or more major genes affecting disease phenotypes in this diallel population.
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Affiliation(s)
- Hua Li
- Department of Forestry and Environmental Resources, North Carolina State University, Campus Box 8002, Raleigh, NC 27695, USA
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van Heerden SW, Amerson HV, Preisig O, Wingfield BD, Wingfield MJ. Relative Pathogenicity of Cryphonectria cubensis on Eucalyptus Clones Differing in Their Resistance to C. cubensis. PLANT DISEASE 2005; 89:659-662. [PMID: 30795393 DOI: 10.1094/pd-89-0659] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cryphonectria cubensis causes a destructive canker disease of Eucalyptus species. Management of this disease is primarily through breeding and selection of disease resistant trees. One means of selecting such trees is by artificial inoculation with the pathogen. In routine screening trials in South Africa, an isolate of C. cubensis, considered to be highly pathogenic, has been used for such inoculations. Although the most resistant clones under natural conditions are the same as those detected in inoculation trials, a question has arisen whether all clones respond similarly to different C. cubensis isolates. Thus, a trial consisting of five clones, known to differ in susceptibility to infection by C. cubensis, was established. These trees were inoculated with nine South African C. cubensis isolates previously shown to differ in pathogenicity. Inoculations showed a significant isolate × clone interaction as well as an "apparent immunity" for one clone × isolate interaction, providing evidence highly suggestive of a vertical resistance component in the pathosystem. Disease screening in this pathosystem has traditionally relied on a single pathogen isolate; however, considering data presented here, future reliance on a single isolate may be inadequate.
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Affiliation(s)
- S W van Heerden
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - H V Amerson
- Department of Forestry, North Carolina State University, Raleigh
| | - O Preisig
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria
| | - B D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria
| | - M J Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria
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