New Zealand Next Generation Sequencing Conference - Innovative ...

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GBS method described by Elshire et al., 2011 (PLoS
ONE 6:e19379), however, through the addition of
specific nucleotides within and following the
restriction enzyme cut site to the PCR primer we are
able to reduce the complexity of the genome in a
controlled manner. Varying the number of samples
and the ‘size’ of the reduced genome per lane on an
Illumina HiSeq2000 allows for differing magnitudes
of SNPs to be genotyped and interrogated. The
method for reducing the complexity of the genome,
sequencing and bioinformatics pipeline for GBS in
sheep will be presented.
Using Next Generation Sequencing techniques to identify Single Nucleotide
Polymorphisms in Chinook Salmon
Hayley Baird
AgResearch, Invermay
Biography
Hayley Baird graduated from Otago University with
a BSc(Hons) in microbiology. She is now a
research associate for AgResearch Animal
Genomics at Invermay. The majority of her time
over the last few years has involved working with
the Illumina iSCAN in particular the sheep 50 and
5k chips, however the area of her research
thatsheI’ll be talking about is the Aquaculture
industry and the process of creating a SNP chip for
Chinook salmon.
Abstract
Understanding and improving feed conversion
efficiency (FCE) in farmed New Zealand Chinook
salmon is a high priority for the industry. A
research programme has been established with
two main goals: 1) tank-based performance and
genetic evaluation of 160 families focussing on
growth, feed intake, body fat and FCE and 2) the
development of a new panel of single nucleotide
polymorphism (SNP) markers that will be used to
search for markers linked to QTL. Since there is no
salmon genome assembly available we had to
come up with a strategy that did not require a
reference genome. We utilised three different nextgeneration
sequencing platforms (454, SOLiD and
Illumina HiSeq) to take us straight to SNPs. After
stringent filtering we arrived at 95,000 SNPs.
Comparative genomics indicated that these SNPs
were evenly distributed across the salmon genome.
An Illumina 6K SNP chip has been developed and
4 large families genotyped for mapping and
eventual QTL analysis.
Session 6
Tailoring high-throughput sequencing approaches to next-generation plant virology in
south-west Australia
Steve Wylie
Murdoch University, Australia
Biography
Steve Wylie attended Otago University in the
1980s and completed an honours degree in the
botany department before moving to Western
Australia to study plant viruses of pasture legumes
for his PhD. The chance discovery of viruses in
Abstract
Given the great age of the Australian continent,
high endemism amongst its plant flora, and the
varied ecosystems present, we hypothesised that
its indigenous viral flora would be much richer than
that currently described. Many exotic plants and
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