Tag Archives: Australian Centre for Plant Functional Genomics

ARC Linkage round successes

The Waite Campus will be home to two new projects funded by the ARC Linkage Projects scheme.

In all, the University of Adelaide won $5.4 million for industry-linked research, 58% of the funding awarded to SA.

A team led by Prof Geoff Fincher from the ARC Centre of Excellence in Plant Cell Walls and A. Prof Jason Eglinton from the School of Agriculture, Food and Wine was awarded $675,000 a to study the physiology and genetics of barley grain germination in the malting and brewing industries. This project was highlighted in the recent edition of The Stock Journal and the Plant Cell Walls blog.

The other successful linkage project, led by Dr Trevor Garnett and Dr Sigrid Heuer from the Australian Centre for Plant Functional Genomics ($524,718 over 3 years) aims to improve the nitrogen use efficiency of cereal plants. The project will identify and investigate nitrogen uptake pathways to find what is limiting plants’ nitrogen uptake. Improving the nitrogen uptake process in plants will increase the plant’s ability to use nitrogen more efficiently, leading to reduced and more sustainable nitrogen fertiliser usage. This project has been highlighted on the ACPFG blog.

WRI Director Prof Mike Wilkinson is also an investigator on two projects based at the Australian Centre for Ancient DNA.

Recent research: Improved genetic markers for grain yield and quality

The genetic control of grain yield is very complex and involves many genes controlling processes such as growth and reproduction. Although introducing specific important agronomic traits has led to large advances in grain yield in the water-limited bread wheat production environment of southern Australia, recent yield improvements have been made through incremental genetic advances often without wheat breeders and researchers knowing the underlying physiological mechanisms. If the genetic/physiological basis was better understood, targeted breeding efforts could more rapidly improve traits driving grain yield in target environments. This study investigated the trait and genetic basis of grain yield and quality in a locally adapted wheat population.

The researchers used a doubled haploid population made from a cross between a relatively drought-tolerant breeders’ line and Kukri, a locally adapted variety less tolerant of drought. Experiments were performed in 16 environments over four seasons in southern Australia which fell into three distinctive rainfall patterns. Kernels per square metre was a large driver of grain yield and was further explained by kernels per spikelet, a measure of fertility, indicating these are key traits for improving yield in the target environment. The researchers found nine genetic loci for grain yield across the growing areas, individually accounting for between 3 and 18% of genetic variance within their respective growing areas. The gene variant (allele) from the relatively drought-tolerant breeders’ line increased grain yield, kernels per square metre and kernels per spikelet at most loci detected, particularly in the more heat stressed environments.

This work has provided a better understanding of the occurrences of these important loci in the local wheat breeding pool, helping wheat breeders maintain or improve these traits when designing cross-breeding programs. Three new loci associated with grain yield have potential for use in marker-assisted selection in breeding programs targeting improving grain yield in southern Australia and other similar climates.

Corresponding author: Dion Bennett
Organisations: Australian Centre for Plant Functional Genomics, Australian Grain Technologies
International Maize and Wheat Improvement Centre (CIMMYT)
Publication: Bennet, D., Izanloo, A., Reynolds, M., Kuchel, H., Langridge, P. And Schnurbusch, T. (2012) Genetic dissection of grain yield and physical grain quality in bread wheat (Triticum aestivum L.) under water-limited environments. Theoretical and applied genetics, 125:255-271.
Link: doi: 10.1007/s00122-012-1831-9

“Recent research” is a series of short, regular posts highlighting recent research papers from the Waite Campus.

New future for an old crop: barley enters the genomic age

Story orginally posted in News from the University of Adelaide, Thursday 18/10/12

Barley research at the University of Adelaide’s Waite Campus. Photo by Randy Larcombe

Higher yields, improved pest and disease resistance and enhanced nutritional value are among the potential benefits of an international research effort that has resulted in the mapping of the barley genome.

The work – conducted by the International Barley Sequencing Consortium (IBSC), which includes Australian researchers based at the University of Adelaide’s Waite Campus – is described in a paper published today in the prestigious journal Nature.

Barley is the world’s fourth most important cereal crop, and the second most important crop in Australian agriculture. Australia produces around seven million tonnes of barley a year, 65% of which is exported at a value of $1.3 billion annually. Australia also accounts for one third of the world’s malting barley trade.

The Australian research team was led by scientists at the Australian Centre for Plant Functional Genomics (ACPFG) and the University of Adelaide, who worked with colleagues at the ARC Centre of Excellence in Plant Cell Walls.

“This new analysis of all the genes in the barley genome is a major step forward for agricultural science and industry,” says Australian research leader and a senior author of the Nature paper, Professor Peter Langridge, Chief Executive Officer of the ACPFG.

“This will greatly accelerate the work in Australia and elsewhere to improve the quality of barley, enhance its disease and pest resistance and, most importantly, support efforts to improve the tolerance of barley to environmental stresses such as heat and drought.”

First cultivated more than 15,000 years ago, barley belongs to the same family as wheat and rye. Together, they provide about 30% of all calories consumed worldwide.

“Because barley is very closely related to wheat, these results from barley will have a major impact on wheat research,” Professor Langridge says. “Wheat is Australia’s most important crop, and improvements in wheat production globally will be a key to ensuring global food security.”

The barley genome is almost twice the size of that of humans. Determining the sequence of its DNA has presented a major challenge for the research team. This is mainly because its genome contains a large proportion of closely related sequences, which are difficult to piece together.

The team’s Nature paper provides a detailed overview of the functional portions of the barley genome, revealing the order and structure of most of its 32,000 genes. It also includes a detailed analysis of where and when genes are switched on in different tissues and at different stages of development.

The team has described regions of the genome carrying genes that are important to providing resistance to diseases, offering scientists the best possible understanding of the crop’s immune system.

The Australian component of this research has been funded by the Australian Research Council (ARC), the Grains Research and Development Corporation (GRDC) and the South Australian Government.

For more background on this story, please refer to the original here

Ancient genes and modern science deliver salt tolerant wheat

This post was first published on the Scientific American Guest Blog on the 18th of April, 2012. To go to the original article click here.

By Heather Bray and Matthew Gilliham

Ten thousand years ago, somewhere in the ‘fertile crescent’ near modern day Turkey, several small but amazing events kick-started the spread of farming, the birth of civilisation and ultimately changed the world.

Although we are still learning about the precise nature of these events, we know that at this time people began to collect seeds from local wild grasses to grow them for food, selecting the best seeds to grow in subsequent seasons. During this process of selection and cultivation the wild grasses cross-bred, or hybridised, leading to domesticated forms of ancient wheat such as einkorn and emmer. Selection and cultivation continued, giving rise to both modern bread wheat and durum wheat, used for making pasta and couscous. Wheat is now the most cultivated crop in the world and forms the staple food for 35% of the world’s population. However, thousands of years of repeated selection and crossing to obtain the best yields and quality has significantly narrowed wheat’s gene pool.

For a team of Australian researchers looking at the problem of salinity tolerance in durum wheat, the solution was clear: look at the ancestors and wild relatives of modern wheats for tolerance to salt and re-introduce these genes into modern wheat lines.

“It was some pretty big thinking about 15 years ago by our collaborators at CSIRO that started this work,” says Dr Matthew Gilliham of the University of Adelaide and the ARC Centre for Plant Energy Biology. Matthew is senior author on a paper recently published in Nature Biotechnology announcing the development of a line of durum wheat which is salt tolerant under commercial farming conditions.

A field of salt tolerant durum wheat grown in northern New South Wales, Australia, as part of a CSIRO field trial. (Richard James, CSIRO)

Salinity affects over 20% of the world’s agricultural land and is a major issue in Australia’s prime wheat-growing areas, with nearly 70% of this land susceptible to salinity. “Through the years, wheat has lost genetic diversity for things such as tolerance to harsh environmental conditions. That’s why we need to go back in time, get some genes from wild relatives and ancestors that grow in these harsh conditions and cross them back in.”

To find genes for salt tolerance, researchers from Australia’s CSIRO looked at Triticum monococcum, also known as einkorn. It is not a direct ancestor of bread wheat or durum, but it is closely related to the grasses that were, and it still grows in some parts of the world today. It can also grow in salty soil.

When the initial crosses between durum and the T. monococcum were made using traditional plant breeding methods, whole pieces of chromosomes containing thousands of genes were introduced. More years of crossing and selection were needed to reduce the number of genes from the T. monococcum in the durum lines and by 2009, researchers were trialling durum wheat lines with increased tolerance to salinity. But what where the genes and how did they work?

In salty soils, sodium ions from salt enter wheat plants via the roots. From there they enter the plant’s water-transport system from where they can be taken to the leaves. “The hypothesis we were working on is that salinity tolerance in cereal crops, especially wheat, is related to the ability to exclude sodium ions from the leaves. If you build up sodium levels in leaf cells you start to inhibit essential life processes like photosynthesis, so wheats that exclude salt from their leaves grow better in salty soils” explained Matthew.

“Our group, including researchers from the Australian Centre for Plant Functional Genomics, used a range of molecular and physiological tests to work out that the important gene in this story was the sodium transporter gene TmHKT1;5-A. We worked out where the gene was turned on, and what it did. This gene makes a protein that acts as a sodium selective transporter, which prevents the sodium from entering the shoots by filtering it out at the root level, it essentially turns the roots into a sodium selective sponge. Compared to the shoots, the build up of sodium in root cells does not inhibit cellular metabolism very much at all.”

Location of the gene encoding for the ancestral sodium transporter in cells (stained blue) surrounding the xylem of modern durum wheat roots. (A. Athman, University of Adelaide)

Although the understanding of the function of the sodium transporter involved transgenic (genetic modification) techniques, the introduction of the genes into the durum lines did not, meaning that the lines of wheat could be tested under commercial conditions without going through Australia’s strict regulatory framework for genetically modified organisms.

The durum line was trialled on a variety of field sites across Southern Australia including a commercial farm near Moree in northern New South Wales, These trials were led by CSIRO researchers Richard James and Rana Munns. Farmers in this area usually harvest about 2.5 tonnes per hectare, a typical and profitable yield for broad-acre, rain-fed (non-irrigated) cropping in semi-arid areas. However, like many farms in the grain producing areas of Australia, salinity is beginning to affect yields. On this farm, a commercial durum variety and the line with the introduced sodium transporter genes had the same performance on normal soil. But at the highest salinity level, the new line outperformed the commercial variety by approximately 25%. This means farmers can use varieties developed from the improved line across their farms, even in paddocks only partly affected by salinity with a significant yield advantage over the current varieties.

“Our research is the first to show that sodium exclusion genes increase grain yield in the field” said Matthew, which is why the group’s work is attracting a lot of attention, including publication in the prestigious Nature Biotechnology. But the team’s work is not over yet. They have already identified other genes from ancient relatives that may be useful in improving salinity tolerance further, highlighting the huge potential for improving modern wheat using the diversity already present in nature. “There are other aspects to the salt- tolerance story and more genes to identify and characterise” adds Matthew. “We haven’t solved the problem, we have just put one piece back in the puzzle.”

About the author: Dr Heather Bray is a science communicator with the Waite Research Institute and a research fellow in the School of History and Politics at the University of Adelaide. She is fascinated by both the science in agriculture and the social aspects of food production in contemporary Australia. Twitter handle: @heatherbray6

Dr Matthew Gilliham is a senior research fellow in the School of Agriculture, Food and Wine, supported by the ARC Centre for Plant Energy Biology. His research focuses on how plants use, transport and exclude nutrient elements and aims to develop more nutritious and productive plants tolerant to abiotic stresses. Twitter handle: @ionplants