DNA ‘chips’ herald new era in plant breeding

Revolutionary new DNA marker tools that function almost like biological computer chips have opened the way to an unprecedented capability to exploit the vast genetic variation of the wheat gene pool.

New varieties the tip of a technology iceberg

To develop more productive and resilient crop varieties, breeders are attempting to deliver cultivars with the most complex type and mix of genetic traits ever attempted. 

Advanced screening for phenotype (observable characteristics such as water use efficiency) and software tools that help breeders set up the most productive crosses for particular agro-climates are part of the solution for dealing with this complexity. 

But the GRDC also invests in biotechnology, in particular tools that can simplify trait discovery, selection and subsequent transfer into cultivated varieties. While the technology can take many forms, there is one area where important gains have been achieved only recently. 

This involves the development of molecular markers that can ‘see’, compare and select differences in the genetic make-up of Australian bread wheat varieties and other material considered important by researchers and breeders.

These recently developed markers – called SNPs – form the centrepiece of a technology platform that is accelerating research in trait characterisation and gene discovery.

Image of Dr Matt Hayden

Dr Matthew Hayden: co-developer of a simple, cost-effective genotyping technology expected to significantly boost plant breeding capability.

PHOTO: Paul Jones

Key points

  • New molecular markers that make it easy to ‘interrogate’ the genetic differences between bread wheat genomes have been developed to accelerate trait discovery and uptake by plant breeders
  • The technology takes the form of thousands of markers assembled into DNA sets that can perform like computer chips to process genetic information

A powerful class of molecular markers called SNPs (pronounced “snips”) are on the verge of revolutionising plant breeders’ ability to more fully exploit the vast genetic diversity that makes up the wheat genome.

This expected step-change in plant breeders’ capacity to keep delivering high-performance wheat varieties that can cope with changing growing conditions comes from the development of SNP ‘chips’. These are the assembly of two sets of SNP markers – one set of 9000 markers (dubbed 9K) and another that includes 90,000 markers (90K).

Unlike in the past, when SNP markers had to be developed individually for each trait of interest, the 9K or 90K sets can be deployed collectively across all wheat trait developments. Then, much like a computer chip facilitates intensive data scanning, these SNP ‘chips’ can scan all DNA from a wheat variety and analyse the miniscule (but potentially important) amount of genetic variation.

Normally a SNP marker detects ‘single nucleotide polymorphisms’, meaning each marker detects a subtle difference in DNA sequence between wheat lines. As such, SNPs have already been used to more easily compare the genetic make-up of breeding material through the process known as ‘genotyping’.

Now this can be done on a vastly increased scale. Also, of particular relevance to Australian grain growers, the two SNP sets have been assembled to comprise specific Australia-relevant markers.

A man checking plants in a hot house

Dr Colin Cavanagh in a CSIRO glasshouse in Canberra.

PHOTO: Carl Davies, CSIRO

The SNP marker sets are the result of a GRDC-supported research collaboration between Dr Matthew Hayden of the Victorian Department of Environment and Primary Industries and Dr Colin Cavanagh of CSIRO Plant Industry.

The significance of their achievement is that genes make up just a small proportion of all the DNA in the wheat genome. They are hard to see and harder still to find when working back from a paddock-based trait, such as early vigour or drought tolerance at flowering time.

So when deployed collectively, the 9K and 90K sets of SNP markers can be used to scan all DNA from a wheat variety, but in this case the DNA ‘chips’ process genetic variation.

“This provides a simple, cost-effective genotyping technology that has important applications along the length of the breeding pipeline,” Dr Hayden says.

“It provides stepping stones to markers that can directly select for the trait variant of interest and also to finding the genes that underlie the trait. Breeders can then use these markers to select for the desired form of the trait in their breeding programs.”

Accelerator technology

To maximise the value of this technology for bread and durum wheat breeding, Dr Hayden and Dr Cavanagh have devised further innovations.

To ensure their markers process the most relevant genetic variation, they developed the SNPs by sequencing only the expressed portion of the genome – the genes that are active at specific stages of development such as germination and grain filling. They also ensured that the SNP markers could distinguish between similar genes present on bread wheat’s A, B and D subgenomes.

The 90K SNP chip also contains two additional sets of markers. The first is a set of about 4500 SNPs discovered from the diploid ancestor of bread wheat’s D-genome, Aegilops tauschii.

“These SNPs are particularly useful when working with synthetic wheats (durum crosses) because the D genome is an important conduit for bringing in genetic biodiversity from the gene pool of wheat’s wild relatives,” Dr Hayden says.

“The other thing we added to the 90K chip was about 9000 markers to interrogate genetic diversity in durum. That means the 90K chip can be used to type DNA differences between varieties for both bread wheat and durum wheat.”

The two scientists then mapped the site in the genome recognised by each bread wheat SNP marker. This map was integrated with information from other genomic resources, including the database produced by the International Wheat Genome Sequencing Consortium and the quantitative trait loci (QTL) maps (see Ground Cover issue 109, pages 18-19).

“So the 9K and 90K SNP chips can resolve the genetic origin of important plant traits and then select for those traits,” Dr Hayden says. “That makes the SNP markers a tool of universal relevance across the wheat breeding pipeline.”

Local application, global resources

The potential drawback to SNP technology is that it is expensive and time-consuming to develop and requires specialist molecular expertise and equipment to use.

“So rather than expect individual Australian pre-breeding laboratories to establish their own SNP technology, the GRDC has invested in centralising SNP development and application on behalf of all Australian pre-breeders and breeders,” Dr Hayden says.

“That means we now have scientists to help breeders use this technology. This includes using the 90K chip to map a trait genetically – something which previously could only be tracked phenotypically.”

Dr Hayden also took steps to ensure that SNP chips – which are manufactured by the specialist biotechnology firm Illumina – remain affordable beyond the life of the GRDC project.

This has required developing economies of scale: an achievement made possible through an alliance with Associate Professor Eduard Akhunov of the Kansas State University Department of Plant Pathology in the US who was working on a similar SNP tool kit for US-relevant germplasm.

Together, the Australian and US researchers have established the International Wheat SNP Consortium to allow SNP chip production runs of 10,000 units – the scale needed to ensure researchers can afford the chips (now down to about $60).

Aside from the vastly improved breeding capacity, the SNP project shows there is a commercial market for advanced molecular diagnostic tools for agricultural crop species. All 50,000 units of the 90K SNP chip were sold out at the chip’s launch. That has made the wheat SNP chip Illumina’s biggest agricultural product.

Since the research project’s completion, the GRDC is continuing to provide SNP services and is supporting expansion of the development to include durum and barley.

More information:

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GRDC Project Code DAV00103

Region Overseas, South