SNP DISCOVERY: NEXT GENERATION SEQUENCING Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

By Paul A Hohenlohe, S. Amish, Julian Catchen, F. Allendorf, Gordon Luikart. 2011

378 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/95fe37ac5006193709f5dfc44510bd1a8d9ee2b5

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Citations in the corpus

Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences (2011, methodology): “In a recent study of trout populations, Stacks ﬂ agged loci that differed from Hardy-Weinberg expectations, thereby successfully removing the effects of the recent (25 – 100 million years ago) salmonid genome duplication (Hohenlohe et al. 2011).”
Genetic, morphological, and chemical patterns of plant hybridization (2014, background): “NGS is considered an emerging technique which is thought to improve our knowledge about hybridization and introgression because no prior knowledge of the sequence of the target organisms is required (Hohenlohe et al. 2011).”
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species (2012, unknown): “Subsequently, studies extended RADseq to species that lack a reference genome sequence, but have restricted variant discovery to only those regions that contained at most one or two polymorphic sites [10– 12].”
Genotyping‐by‐Sequencing for Plant Breeding and Genetics (2012, background): “…et al., 2008; Gore et al., 2009a, 2009b; Huang et al., 2009; Deschamps et al., 2010; Hyten et al., 2010; You et al., 2011; Nelson et al., 2011; Hohenlohe et al., 2011; Byers et al., 2012). h ese studies have focused on assaying a few key genotypes with a reducedrepresentation approach (Baird…”
Stacks: an analysis tool set for population genomics (2013, background): “…inferring population genomics statistics, short-read sequencing adds new levels of sampling variation during all aspects of the library preparation and sequencing process, notably at the very beginning of population genomic analyses (Hohenlohe et al. 2011; Davey et al. 2012; Gautier et al. 2012).”
Special features of RAD Sequencing data: implications for genotyping (2012, background): “2011); for population studies, repetitive regions and duplicates can be screened by filtering by read coverage or by testing patterns of heterozygosity (Hohenlohe et al. 2011).”