By Genomics Aotearoa 26/02/2020


Dr David Chagné

New Zealand is involved in a US$12.8 million USDA grant to improve the quality of blueberry and cranberry.

The four-year project, led by North Carolina State University, is part of the USDA’s National Institute of Food and Agriculture Specialty Crop Research Initiative, which funds multi-year, multi-institutional collaborative projects.

Genomics Aotearoa and Plant and Food Research Ltd have just become part of this project, and we’re very excited about what that offers – for blueberry producers here, for the New Zealand economy, the consumer and for other genomics researchers.

But what does this actually mean for us?

As with all genome research, the solution is not in the sequencing itself, but in the opportunities it provides to use the genetic information for good.

And for us, it’s not just the research results but also the potential to leverage and collaborate internationally.  It’s important New Zealand keeps pace with global genomics.

The project involves researchers from seven US academic institutions, three USDA research centres and three international research partners; I see this as a great opportunity for Genomics Aotearoa to collaborate with some top plant geneticists in the US and to grow international linkages.

Global partnerships help us to be aware of new approaches of importance to the country, and to benchmark our research, to ensure we maintain a world-class standard in genomics and in bioinformatics, and are agile in the rapidly changing international research landscape.

Being involved in the VacciniumCAP project, as it is known, has the potential to open doors and create relationships, something that is really important for a small country like New Zealand. We are expecting the strong academic and industry partner support and new links from this new initiative will help to transfer genomics tools to expand the research behind fruit quality.

So what will it mean for producers?

The primary focus areas for blueberry and cranberry crop characteristic improvements are taste, quality and appearance including fruit disease resistance; and enhanced phytonutrient content.

The aim of the VacciniumCAP project is to study which fruit characteristics contribute to improve fruit quality and the genetic factors controlling these characteristics.

From this understanding, we hope new genetic and genomic resources can be created to support the selective breeding of blueberry cultivars with improved fruit quality attributes.

The focus is on genomic outcomes, but there are still many genomics tools to develop for blueberry and polyploid species.  Ultimately, the work we are doing will lead to developing DNA tests that can help select new cultivars with improved fruit quality attributes.

In the longer term, those areas of berry improvement will aim to improve production efficiency, handling and processing, productivity and profitability.

Genome analysis in polyploid species – species with multiple copies of genes such as tetraploid blueberry – is complex.

Genomics Aotearoa’s contribution to the project will be to develop a pan-genome for blueberry, including for tetraploid Northern Highbush varieties, as part of its High Quality Genome programme.

In collaboration with the VacciniumCAP partners, Genomics Aotearoa is evaluating new sequencing and bioinformatics techniques for assembling a high standard, chromosome-level, biologically accurate, near gapless and haplotyped whole genome assembly of blueberry.

Our focus is on improving best practice methods for whole genome haplotyping in polyploid species, which will greatly contribute to associating DNA and trait variation, and to ultimately improve the breeding of new types of blueberry.

And what are the implications for other researchers?

The blueberry is one of Genomics Aotearoa’s research exemplar projects.

The Genomics Aotearoa High Quality Genomes project is looking at improving long read sequencing across several challenging species, including:

  • Small samples: wasps, flies, ants, weevils.
  • Polyploids: blueberry, ryegrass, epichloe.
  • Large genomes: stick insect, rewarewa.

As part of the process, new software for base calling and assembly of long reads data must be evaluated and benchmarked.

Identifying and developing best practice alongside the practical community-relevant outcomes in blueberry provides Genomics Aotearoa with a model for bioinformatics methods, which can potentially be implemented for other polyploid species.

In other words, what we learn from the research and from our collaborators can be adapted for other genomic research to benefit New Zealand, linking health, conservation and environment, and primary production institutions and communities silos.

That, therefore, makes it very exciting to be part of the USDA VacciniumCAP project.

By Dr David Chagné, Genomics Aotearoa and Plant and Food Research Science Group Leader.