Abstract Detail

Recent Topics Posters

Sinn, Brandon [1], Simon, Sandra [2], Fama, Nicole [2], DiFazio, Stephen [2], Barrett, Craig [2].

Flexible, economical methods for genome-scale variant discovery using ISSR sequencing.

The capability to generate densely sampled single nucleotide polymorphism (SNP) data is essential in diverse subdisciplines of plant biology, including crop breeding, pathology, forensics, forestry, ecology, evolution, and conservation genomics. However, access to the expensive equipment, reagents, and bioinformatics infrastructure required for genome-scale sequencing and SNP variant detection is still a limiting factor in the developing world and for institutions with limited resources. Here we present ‘ISSRseq,’ a PCR-based method using inter-simple sequence repeats (ISSR) in single-primer reactions and compare different variants of ISSR-based approaches to SNP generation. Briefly, with ISSRseq we amplify ISSR regions individually or in multiplex, pool them if individually amplified, and conduct library preps with or without fragmentation using a low-cost, efficient commercial kit, and sequence entire ISSR regions on an Illumina MiSeq. We test our method on diverse focal taxa at the population level, including a vulnerable North American orchid, Corallorhiza bentleyi (non-model), and Populus deltoides (model), the latter of which has chromosome-level genome annotations. We further present a bioinformatic pipeline that assembles, conservatively filters, and formats data using freely available software and user-friendly UNIX shell scripts. Based on 20 individual ISSR primers in the IUCN red-listed, genetically depauperate Corallorhiza bentleyi, we generate >5,000 SNP loci among 40 individuals, of which >100 loci are significant outliers putatively under selection. Our approach has is: 1) flexible, 2) repeatable, 3) amenable to small amounts of DNA from scarce material, and 4) easy to conduct for undergraduate students or researchers with less experience in genomics.

1 - Otterbein University, Biology, Westerville, OH, USA
2 - West Virginia University, Biology, 53 Campus Drive, Morgantown, WV, 26506, US

Keywords:
SNP
microsatellite
outlier
Population genomics
non-model
adaptation.

Presentation Type:
Session: P, Recent Topics Posters
Location: Arizona Ballroom/Starr Pass
Date: Monday, July 29th, 2019
Time: 5:30 PM
Number: PRT022
Abstract ID:1399
Candidate for Awards:None