PhD Scholarship: Disease genomics of two New Zealand finfish species

We are seeking a highly motivated PhD student to be part of a group to
investigate the disease genomics of the New Zealand snapper (Chrysophrys
auratus) and trevally (Pseudocaranx georgianus).

Dr. Maren Wellenreuther, Plant and Food Research (PFR), Nelson, New Zealand
Dr. Steve Bird, Waikato University, New Zealand

Aquaculture is the fastest growing food-production sector and
New Zealand has the potential to develop a range of locally grown
finfish species to meet this increasing demand. New genomics-based
selective breeding programs are needed to help develop recently
domesticated fish species into premium products. Plant and Food Research
( is known worldwide for its innovative
breeding and genomics research, and it is leading the development of
New Zealand seafood genomics.

This PhD project will involve working alongside a group of experienced
researchers to study the genomes of the New Zealand snapper and trevally
to identify and characterize immune genes, screen for genome-wide
disease markers using a pedigree from domesticated populations,
evaluate the bacterial disease metacommunities and conduct gene
expression analyses using transcriptomics and qPCR. This will involve
using high-throughput sequencing approaches, coupled with automated and
error-reduced phenotyping. The overall goal is to characterize the immune
systems of both fish species to better understand disease resistance in
domesticated populations, facilitating a rapid and efficient selective
breeding programme.

PhD Project Aims
1. Use whole genome assemblies and transcriptomes to identify immune
genes and pathways,
2. Use genomic information to improve detection of novel disease QTLs,
3. Assess stress and disease resistance of hatchery individuals, and
understand their bacterial disease communities.

This PhD project will provide an excellent opportunity to learn the latest
interdisciplinary technologies and apply them to fish genomics. The
PhD student will gain experience working in academic, government and
private sector institutions. They will be a member of a highly active and
collaborative group of researchers, and help develop new technological
approaches and applied-genomic tools.

The successful candidate will be a highly motivated researcher,
with a strong background and interest in genomics and molecular
biology. Experience with a coding and/or scripting languages
is a bonus. This position will be based primarily in Nelson
( and comes with a three-year scholarship that
provides a stipend and university (domestic-level) fees. This project
is supported by the MBIE grant ‘Enhancing production of New Zealand’s
seafood sector using accelerated breeding techniques’.

Applicants should send a CV, a statement of their research
interests and a cover letter to Maren Wellenreuther
( and Steve Bird
( Candidate selection will begin mid-December
but applications will be considered until the position is
filled. The ideal starting date is 1 April 2017. International
students with strong credentials are welcome and encouraged to
apply. For more information about studying at Waikato University
and the entry requirements for the PhD program please see…/postgraduate-stu…/higher-degrees/.

Maren Wellenreuther
Senior Scientist


T: +64 3 989 7658
F: +64 3 546 7049
The New Zealand Institute for Plant & Food Research Limited

Postal Address: Plant & Food Research
Box 5114, Port Nelson, Nelson, 7043, New Zealand
Physical Address: Plant & Food Research
Seafood Research Unit, 293 Akersten St, Port Nelson, Nelson, 7010, New Zealand