A set of 204 SNP and INDEL markers for Bigleaf maple (Acer macrophyllum Pursch)

Jardine, Duncan I.; Dormontt, Eleanor E.; Dijk, Kor‐jent van; Dixon, R. R. M.; Dunker, Bianca; Lowe, Andrew J.

doi:10.1007/s12686-015-0486-7

Cited by 7 publications

(5 citation statements)

References 8 publications

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“…We used the method of Jardine et al . () which combines next generation sequencing technology with complexity reduction by AFLP (amplified fragment length polymorphism) (Vos et al . ; van Orsouw et al .…”

Section: Methodsmentioning

confidence: 99%

“…Twelve samples were randomly selected from each of the sampling sites for SNP screening. We used the method of Jardine et al (2015) which combines next generation sequencing technology with complexity reduction by AFLP (amplified fragment length polymorphism) (Vos et al 1995;van Orsouw et al 2007). Sequencing followed on the Ion Torrent Proton (Life Technologies) at the Australian Cancer Research Foundation (ACRF), Cancer Genomics Facility in Adelaide.…”

Section: Snp Screeningmentioning

confidence: 99%

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Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

et al. 2017

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Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo‐Australian Archipelago (IAA), the world's hotspot of marine biodiversity, seagrasses are a vital component but population genetic information is very limited. Here, we reconstructed the phylogeography of the seagrass Thalassia hemprichii in the IAA based on single nucleotide polymorphisms (SNPs) and then characterized the genetic structure based on a panel of 16 microsatellite markers. We further examined the relative importance of historical isolation and contemporary ocean currents in driving the patterns of genetic structure. Results from SNPs revealed three population groups: eastern Indonesia, western Indonesia (Sunda Shelf) and Indian Ocean; while the microsatellites supported five population groups (eastern Indonesia, Sunda Shelf, Lesser Sunda, Western Australia and Indian Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among population groups with a trend of southwestward migration from eastern Indonesia. Genetic diversity was generally higher in eastern Indonesia and decreased southwestward. The pattern of genetic structure and connectivity is attributed partly to the Pleistocene sea level fluctuations modified to a smaller level by contemporary ocean currents.

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Section: Methodsmentioning

confidence: 99%

Section: Snp Screeningmentioning

confidence: 99%

Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

et al. 2017

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“…One hundred and twenty-eight single nucleotid polymorphic (SNP) loci were designed to capture interindividual variation in bigleaf maple (Jardine et al 2015). Using these markers, a DNA reference database was developed consisting of 394 individuals from 43 sites across the range of the bigleaf maple.…”

Section: Box 12 Battling Illegal Logging Of Bigleaf Maplementioning

confidence: 99%

Asia-Pacific roadmap for innovative technologies in the forest sector

J.M.,

N.,

2021

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“…Of the 199 single nucleotide polymorphism (SNP) markers and five insertion/deletion (INDEL) markers from previously published work on A. macrophyllum [22], 183 were successfully re-multiplexed into five groups for the MassARRAY® iPLEX™ platform (Agena Bio-science™, San Diego, USA) using Assay Designer 4.0 (Agena Bio-science™, San Diego, USA). Amplification primers and extension primers were supplied by IDT (Integrated DNA Technologies, Coralville, USA), and contained the 5' 10mer tag (ACGTTGGATG) to remove them from the observed mass window and provide stability in a multiplex PCR.…”

Section: Genotypingmentioning

confidence: 99%

Forensic validation of a SNP and INDEL panel for individualisation of timber from bigleaf maple (Acer macrophyllum Pursch)

Dormontt

Jardine

Dijk

et al. 2020

Forensic Science International: Genetics

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Illegal logging is one of the largest illicit trades in the world, with high profits and generally low risks of detection and prosecution. Timber identification presents problems for law enforcement as traditionally used forensic methods such as wood anatomy and dendrochronology are often unable to confidently match wood evidence to the remains of illegally felled trees. Here we have developed and validated a set of genetic markers for individualisation in bigleaf maple (Acer macrophyllum), a high value timber species often felled illegally in the USA. Using 128 single nucleotide polymorphisms and three insertion/deletion markers developed through massively parallel sequencing, 394 individuals were genotyped on the MassARRAY® iPLEX™ platform (Agena Bio-science™, San Diego, USA) to produce a population reference database for the species. We demonstrate that the resulting DNA assay is reliable, species specific, effective at low DNA concentrations (< 1 ng/μL) and suitable for application to timber samples. The P ID for the most common profile, calculated using an overall dataset level F ST -correction factor, was 1.785 × 10 −25 and P ID-SIB across all individuals (treated as a single population) was 2.496 × 10 -22 . The further development of forensic identification assays for timber species has the potential to deliver robust tools for improved detection and prosecution of illegal logging crimes as well as for the verification of legality in reputable supply chains.

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A set of 204 SNP and INDEL markers for Bigleaf maple (Acer macrophyllum Pursch)

Cited by 7 publications

References 8 publications

Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

Asia-Pacific roadmap for innovative technologies in the forest sector

Forensic validation of a SNP and INDEL panel for individualisation of timber from bigleaf maple (Acer macrophyllum Pursch)

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