A set of 156 SNP markers for teak (Tectona grandis Linn. f.)

Dunker, Bianca; Dormontt, Eleanor E.; Dijk, Kor‐jent van; Dixon, R. R. M.; Jardine, Duncan I.; Kireta, Dona; Nurtjahjaningsih, I. L. G.; Win, Thwe Thwe; Rimbawanto, A.; Lowe, A. J.

doi:10.1007/s12686-019-01099-7

Cited by 6 publications

(4 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To facilitate the long-term uptake of genetic data into population monitoring and management, TSI is also trialing the use of low-density SNP arrays, where reduced subsets of informative SNP loci identified through the above WGS and population genomic approaches are selected and optimized for high-throughput automated genotyping. SNP arrays can be flexibly designed to contain loci targeted to specific conservation applications: for example, to ascertain population structure and monitor neutral and adaptive genetic diversity ( 58 – 60 ), assess parentage and kinship ( 61 , 62 ), and monitor introgression/hybridization ( 63 ). Besides the initial investment in SNP discovery and multiplex primer design, downstream genotyping costs are highly affordable (e.g., MassARRAY iPlex system ∼AUD$11 per sample per 50-plex) with minimal requirements for data analysis, making the routine genetic analysis of populations accessible to a wider array of end-users.…”

Section: Threatened Species Initiativementioning

confidence: 99%

Threatened Species Initiative: Empowering conservation action using genomic resources

Hogg

Ottewell²,

Latch

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.

show abstract

Section: Threatened Species Initiativementioning

confidence: 99%

Threatened Species Initiative: Empowering conservation action using genomic resources

Hogg

Ottewell²,

Latch

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…To achieve these aims, a set of 132 neutral SNP loci (Dunker et al 2020) were applied to over 1,000 tree samples taken from across the natural range of teak in Myanmar, Thailand and Lao PDR, and samples from naturalized populations and plantations in Indonesia, Lao PDR and PNG (Dormontt et al 2019). Population genetic structure across the natural range of teak in Myanmar produced self-assignments that were 69% accurate to the fine-scale collection site level.…”

Section: Box 13 Document Legality In Teak Supply Chainsmentioning

confidence: 99%

Asia-Pacific roadmap for innovative technologies in the forest sector

J.M.,

N.,

2021

View full text Add to dashboard Cite

“…This lack of knowledge generates a challenge for researchers [11]. Over time, the genetic diversity of teak has been investigated in several studies with different techniques, such as using isoenzymes as molecular markers [20] and random amplified polymorphic DNA (RAPD) [21,22], amplified fragment length polymorphisms (AFLPs) [23][24][25][26], microsatellite markers [27][28][29], and single nucleotide polymorphisms (SNPs) [13,30,31].…”

Section: Introductionmentioning

confidence: 99%

Reassessing the genetic variability of Tectona grandis through high-throughput genotyping: Insights on its narrow genetic base

dos Anjos,

Gilio,

Amorim

et al. 2023

PLoS ONE

View full text Add to dashboard Cite

Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its first sources of diversity and little is known about the genetic origin and genetic variability. Thus, this study aimed to investigate the genetic diversity and genetic population structure existing in a representative teak germplasm bank collection. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 3 giga bases per sample, the sequences are aligned using the genome, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four populations with considerable genetic variability between and within them. While the genetic variability in teak is generally known to be narrow, this study confirmed the presence of genetic variability scale in teak, which is contrary to what was initially expected.

show abstract

A set of 156 SNP markers for teak (Tectona grandis Linn. f.)

Cited by 6 publications

References 12 publications

Threatened Species Initiative: Empowering conservation action using genomic resources

Threatened Species Initiative: Empowering conservation action using genomic resources

Asia-Pacific roadmap for innovative technologies in the forest sector

Reassessing the genetic variability of Tectona grandis through high-throughput genotyping: Insights on its narrow genetic base

Contact Info

Product

Resources

About