RADseq approaches and applications for forest tree genetics

TL Parchman, JP Jahner, KA Uckele… - Tree Genetics & …, 2018 - Springer
As tree species vary extensively in genome size, complexity, and resource development,
reduced representation methods have been increasingly employed for the generation of …

High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra

A Konar, O Choudhury, R Bullis, L Fiedler, JM Kruser… - BMC genomics, 2017 - Springer
Background Restriction site associated DNA sequencing (RADseq) has the potential to be a
broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest …

Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

MJ Karam, F Lefèvre… - Molecular Ecology …, 2015 - Wiley Online Library
We combined restriction site associated DNA sequencing (RADseq) using a
hypomethylation‐sensitive enzyme and messenger RNA sequencing (mRNA seq) to …

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

NC Rochette, AG Rivera‐Colón… - Molecular ecology, 2019 - Wiley Online Library
For half a century population genetics studies have put type II restriction endonucleases to
work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD …

Deriving genotypes from RAD-seq short-read data using Stacks

NC Rochette, JM Catchen - Nature protocols, 2017 - nature.com
Restriction site-associated DNA sequencing (RAD-seq) allows for the genome-wide
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …

RNA-seq analysis in forest tree species: bioinformatic problems and solutions

U Lopez de Heredia, JL Vázquez-Poletti - Tree Genetics & Genomes, 2016 - Springer
Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has
allowed a growing number of gene expression studies focused on forest trees in the last 5 …

Harnessing the power of RADseq for ecological and evolutionary genomics

KR Andrews, JM Good, MR Miller, G Luikart… - Nature Reviews …, 2016 - nature.com
High-throughput techniques based on restriction site-associated DNA sequencing (RADseq)
are enabling the low-cost discovery and genotyping of thousands of genetic markers for any …

Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference

ABA Shafer, CR Peart, S Tusso… - Methods in Ecology …, 2017 - Wiley Online Library
Restriction site‐associated DNA sequencing (RAD‐seq) provides high‐resolution
population genomic data at low cost, and has become an important component in ecological …

Selecting RAD-Seq data analysis parameters for population genetics: the more the better?

N Díaz-Arce, N Rodríguez-Ezpeleta - Frontiers in genetics, 2019 - frontiersin.org
Restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely
used tool in molecular ecology studies as it allows to cost-effectively recover thousands of …

RADSeq: next-generation population genetics

JW Davey, ML Blaxter - Briefings in functional genomics, 2010 - academic.oup.com
Next-generation sequencing technologies are making a substantial impact on many areas of
biology, including the analysis of genetic diversity in populations. However, genome-scale …