Cows

Aim

To establish “haplotagging” at UQ, a new low-cost (approx. $30/human sample) linked-read sequencing technique that produces phased haplotypes. Through a collaborative effort across three study organisms – cattle, mango and an Australian wildflower, we will develop an end-to-end pipeline which includes 1) high molecular weight DNA extraction, 2) haplotagging of these long DNA molecules and 3) a bioinformatics pipeline to reconstruct haplotypes after short-read sequencing.

Brief project outline

1. Generate high molecular weight DNA for cattle (Bos indicus), mango (Mangifera indica) and an Australian wildflower (Senecio lautus) at a competitive cost for high-throughput studies routinely using hundreds of samples.

2. Establish and optimise the haplotagging method of barcoding and reconstructing haplotypes in a diverse set of taxa – B. indicus, M. indica and S. lautus. We will build haplotagging Illumina libraries that will be sequenced using short-read Illumina sequencing technologies, thus producing the novel tagged short-reads for genomic phase deduction.  

3. Develop a bioinformatics pipeline for extracting haplotypes from tagged Illumina short-reads. The pipeline will include de- multiplexing pooled samples based on both individual and DNA molecule barcodes and reconstruction of haplotypes.

Genomics-based innovative aspect of proposal

Directly observing haplotypes is an important step for many genomics approaches. Long read sequencing can be used to directly determine haplotypes but is cost prohibitive for large numbers of samples. Here we will provide an end-to-end solution to the problem of identifying haplotypes by deploying a-ready-to implement molecular and bioinformatics method that is optimised across both plants and animals. Haplotagging both lowers the cost and increases the usability of genomics data, making large scale genomics studies cheaper and statistically more powerful.

Broad applicability of the technique

Retaining phased haplotypes in large populations at a low cost has a wide appeal throughout the genetics community. This is due to the significant advantage of having haplotypes in a diverse set of genetic analyses, including genome-wide association studies (GWAS), genomic prediction, genetic risk score calculations and population structure analyses.

 

Project members

Research collaborators

Dr Melanie Wilkinson

Dr Melanie Wilkinson

Postdoctoral Research Fellow
School of Biological Sciences, Faculty of Science
Daniel Ortiz-Barrientos

Associate Professor Daniel Ortiz-Barrientos

ARC Future Fellow
School of Biological Sciences, Faculty of Science
Associate Professor Craig Hardner

Associate Professor Craig Hardner

Principal Research Fellow
Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation
Dr Elizabeth Ross

Dr Elizabeth Ross

Research Fellow
Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation
Yingguang Frank Chan

Dr. Frank Chan

Max Planck Research Group Leader
Friedrich Miescher Laboratory of the Max Planck Society
Maddie James

Maddie James

Research Officer
School of Biological Sciences, Faculty of Science
Dr Hyungtaek Jung

Dr Hyungtaek Jung

School of Biological Sciences, Faculty of Science
Research Fellow
Dr Bradley Campbell

Dr Bradley Campbell

Research Fellow
Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation

Genome Innovation Hub

Valentine Murigneux

Valentine Murigneux

Senior research assistant
Genome Innovation Hub
Bioinformatician
QCIF Facility for Advanced Bioinformatics
Dr Sohye Yoon

Dr Sohye Yoon

Research Assistant
Genome innovation Hub
Stacey Andersen

Stacey Andersen

Senior Research Assistant
Genome Innovation Hub
Senior Research Assistant
IMB Sequencing Facility
Dr Subash Rai

Dr Subash Rai

Research Assistant
Genome Innovation Hub
Dr Jun Ma

Dr Jun Ma

Research Assistant
Genome Innovation Hub