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Roman MG, Gangitano D, Figueroa A, Solano J, Anabalón L, Houston R. Use of Eucalyptus DNA profiling in a case of illegal logging. Sci Justice 2020; 60:487-494. [PMID: 33077031 DOI: 10.1016/j.scijus.2020.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/07/2020] [Accepted: 09/20/2020] [Indexed: 10/23/2022]
Abstract
Eucalyptus is grown world-wide for paper pulp, solid wood, and other industries. Theft or illegal cutting of the trees causes hardship to owners of plantations and countries whose economies rely on the sale and export of eucalyptus products. Unfortunately, many of these crimes go unpunished due to lack of forensic evidence. Over 1200 short tandem repeat (STR) markers have been identified in the genomes of genus Eucalyptus and related species. However, their importance and utility in aiding forensic investigations of wood theft have not been explored. This study evaluated nine STRs for diversity and applied them to a case involving suspected wood theft. As expected, three dinucleotide STR markers showed greater variability but resulted in harder to interpret profiles. Four STR tetranucleotide markers evaluated in this study were found to contain additional repeat structures (dinucleotide or trinucleotide) that enhanced their variability but resulted in profiles with peaks at multiple stutter positions and heterozygote peak imbalance. The most promising STR markers were EGM37 and EMBRA 1374. Though less variable, they yielded robust and reproducible DNA profiles. All nine STR markers were applied to a case involving suspected wood theft. Samples were collected from seized wood and from remaining stumps in a plantation. No DNA match was found, thus eliminating the evidence samples as having originated from the forest. Dendrochronology analysis also resulted in an exclusion. This case study represents the first report using STR markers in any eucalyptus species to provide DNA evidence in a case of suspected wood theft.
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Affiliation(s)
- Madeline G Roman
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA.
| | - David Gangitano
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA.
| | - Alejandra Figueroa
- Laboratorio de Criminalística Regional Temuco, Policía de Investigaciones de Chile, Región de La Araucanía, Chile.
| | - Jaime Solano
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Chile.
| | - Leonardo Anabalón
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Chile.
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA.
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Costa J, Vaillancourt RE, Steane DA, Jones RC, Marques C. Microsatellite analysis of population structure in Eucalyptus globulus. Genome 2017; 60:770-777. [PMID: 28679070 DOI: 10.1139/gen-2016-0218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Eucalyptus globulus subsp. globulus Labill. (Tasmanian Blue Gum), native to southeast Australia, is a benchmark species for the pulp and paper industry. We genotyped 397 trees from 16 populations of E. globulus representing the native diversity in Australia using 24 microsatellite loci. Eight genetically distinct groups were detected, consistent with genetic groupings detected in previous quantitative and molecular studies. A sample of 29 Portuguese individuals was added to help clarify the origin of the Portuguese landrace. The results suggest a southern and eastern Tasmania origin for the Portuguese landrace. This genetic framework will enable researchers to investigate the provenance of individuals of unknown pedigree and assess the levels of representation of E. globulus natural variation in the Portuguese landrace.
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Affiliation(s)
- Joana Costa
- a RAIZ, Instituto de Investigação da Floresta e do Papel, Herdade de Espirra, 2985-270 Pegões-Gare, Portugal
| | - René E Vaillancourt
- b School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, 7001, Tasmania, Australia.,c ARC Training Centre for Forest Value, University of Tasmania, Private Bag 55, Hobart, 7001, Tasmania, Australia
| | - Dorothy A Steane
- b School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, 7001, Tasmania, Australia
| | - Rebecca C Jones
- b School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, 7001, Tasmania, Australia
| | - Cristina Marques
- a RAIZ, Instituto de Investigação da Floresta e do Papel, Herdade de Espirra, 2985-270 Pegões-Gare, Portugal
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Sumathi M, Yasodha R. Microsatellite resources of Eucalyptus: current status and future perspectives. BOTANICAL STUDIES 2014; 55:73. [PMID: 28510953 PMCID: PMC5430318 DOI: 10.1186/s40529-014-0073-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/30/2014] [Indexed: 06/07/2023]
Abstract
Eucalyptus is the premier paper pulp, short rotation plantation species grown all over the world. Genetic improvement programs integrating molecular marker tools are in progress in many parts of the globe to increase the productivity. Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. Further, highly informative SSRs were used for the clonal identity, genetic fidelity and in certification of breeder's rights. Eucalyptus genetic linkage maps generated with microsatellite loci were used successfully to identify quantitative trait loci (QTLs) for various economically important traits. Progressively more numbers of microsatellites are being linked to genes associated with adaptive and functional variations, therefore making their utility broader in genetic applications. Availability of common SSR markers across the species provides an opportunity to validate the expression of QTLs across variable genetic backgrounds and accurately compare the position of QTLs in other species. Recent evidences suggest that the presence of SSRs in micro RNAs of plant species play a role in the quantitative trait expression. Similar studies in eucalypts may provide new insights into the genetic architecture of transcript-level variations and post transcriptional gene regulation. This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection.
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Affiliation(s)
- Murugan Sumathi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, Coimbatore, 641 002 India
| | - Ramasamy Yasodha
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, Coimbatore, 641 002 India
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Abstract
Simple sequence repeats (SSRs) have proven to be extremely valuable DNA markers for genetic mapping and population genetic analyses. However, data collected across laboratories or even within laboratories are difficult to combine due to challenges in standardizing allele names, especially for nonmodel systems. Here we provide a new approach for standardizing SSR allele names that combines several previously recognized components for standardization, including reference samples/alleles, cumulative binsets, static between-allele spacing, and interval allele naming.
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Thumma BR, Southerton SG, Bell JC, Owen JV, Henery ML, Moran GF. Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens. TREE GENETICS & GENOMES 2010; 6:305-317. [PMID: 0 DOI: 10.1007/s11295-009-0250-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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6
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NEVILL PAULG, REED ALASTAIR, BOSSINGER GERD, VAILLANCOURT RENEE, LARCOMBE MATHEW, ADES PETERK. Cross-species amplification ofEucalyptusmicrosatellite loci. Mol Ecol Resour 2008; 8:1277-80. [DOI: 10.1111/j.1755-0998.2008.02362.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Poke FS, Vaillancourt RE, Potts BM, Reid JB. Genomic research in Eucalyptus. Genetica 2005; 125:79-101. [PMID: 16175457 DOI: 10.1007/s10709-005-5082-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 04/05/2005] [Indexed: 11/25/2022]
Abstract
Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.
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Affiliation(s)
- Fiona S Poke
- Cooperative Research Centre for Sustainable Production Forestry and School of Plant Science, University of Tasmania, Churchill Avenue, Private Bag 55, Hobart, Tasmania 7001, Australia.
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Andrew RL, Peakall R, Wallis IR, Wood JT, Knight EJ, Foley WJ. Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in eucalyptus. Genetics 2005; 171:1989-98. [PMID: 16143624 PMCID: PMC1456121 DOI: 10.1534/genetics.105.042952] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marker-based methods for estimating heritability and genetic correlation in the wild have attracted interest because traditional methods may be impractical or introduce bias via G x E effects, mating system variation, and sampling effects. However, they have not been widely used, especially in plants. A regression-based approach, which uses a continuous measure of genetic relatedness, promises to be particularly appropriate for use in plants with mixed-mating systems and overlapping generations. Using this method, we found significant narrow-sense heritability of foliar defense chemicals in a natural population of Eucalyptus melliodora. We also demonstrated a genetic basis for the phenotypic correlation underlying an ecological example of conditioned flavor aversion involving different biosynthetic pathways. Our results revealed that heritability estimates depend on the spatial scale of the analysis in a way that offers insight into the distribution of genetic and environmental variance. This study is the first to successfully use a marker-based method to measure quantitative genetic parameters in a tree. We suggest that this method will prove to be a useful tool in other studies and offer some recommendations for future applications of the method.
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Affiliation(s)
- R L Andrew
- School of Botany and Zoology, Australian National University, Daley Road, Canberra, ACT 0200, Australia.
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Ottewell KM, Donnellan SC, Moran GF, Paton DC. Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other eucalyptus species. ACTA ACUST UNITED AC 2005; 96:445-51. [PMID: 15843635 DOI: 10.1093/jhered/esi057] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eucalyptus leucoxylon is a widespread woodland tree species found in southeastern Australia that has suffered from, and continues to be, threatened by the impacts of habitat clearance and degradation. Populations now consist predominantly of scattered individuals, and their conservation status is of increasing concern. We report the development and characterization of a set of eight highly polymorphic microsatellite loci for E. leucoxylon. The loci can be amplified in three PCR multiplexes and electrophoresed in a single lane, allowing rapid throughput of large numbers of samples. A total of 111 alleles were detected in 68 individuals with an average of 12.3 alleles per locus, a mean expected heterozygosity of 0.83, and a mean observed heterozygosity of 0.72. The combined probabilities of identity and probabilities of paternity exclusion allow an extremely precise level of individual identification, indicating that these microsatellite markers will be ideal for population genetic and parentage-type studies in E. leucoxylon. The markers also exhibited an average of 76% conservation within the subgenus Symphyomyrtus, to which E. leucoxylon belongs, and 53% conservation across other subgenera of Eucalyptus, demonstrating the potential of these markers in ecological and breeding studies in a wide range of Eucalyptus species.
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Affiliation(s)
- K M Ottewell
- Department of Environmental Biology, Evolutionary Biology Unit and Centre for Evolutionary Biology and Biodiversity, University of Adelaide, North Terrace, Adelaide, South Australia
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Increased inbreeding and inter-species gene flow in remnant populations of the rare Eucalyptus benthamii. CONSERV GENET 2005. [DOI: 10.1007/s10592-004-7830-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Devey ME, Bell JC, Uren TL, Moran GF. A set of microsatellite markers for fingerprinting and breeding applications in Pinus radiata. Genome 2002; 45:984-9. [PMID: 12416633 DOI: 10.1139/g02-064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fifty microsatellite markers were developed and characterized in Pinus radiata, and from among these, a subset of 10 easily scored and highly polymorphic markers was selected for use in fingerprinting, quality control, and breeding applications. The markers were characterized based on reliable and reproducible amplification, observed and expected heterozygosities, number of alleles, a low frequency of null alleles, and a lack of close linkage with other selected markers. Allele numbers and frequencies were estimated using 24 first-generation breeding clones from Australia and New Zealand. Observed heterozygosities for the selected markers were all greater than 0.67, and there was an average of 10.5 alleles/locus. The occurrence of null alleles was checked with megagametophytes from mother trees for loci that appeared to be homozygous. The 10 markers are not closely linked (r < 0.20 and LOD > 3) to each other. The selected microsatellites fall into three discrete size classes, and with appropriate selection of fluorescent dyes for 5' end labeling, can be multiplexed with up to 6 markers/sample on an ABI PRISM 310 or similar instrument.
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Affiliation(s)
- M E Devey
- CSIRO Forestry and Forest Products, Kingston, ACT, Australia.
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