plant biotechnology

International consortia tackle the global challenge to increase wheat yields at the APPF

Field of ripe wheat

Two international consortia of scientists from the United States, Great Britain, Mexico and Australia are currently carrying out research projects of global importance at the Australian Plant Phenomics Facility’s (APPF) Adelaide node for the International Wheat Yield Partnership (IWYP).

The first research project, Improving Yield by Optimising Energy Use Efficiency, is phenotyping an Excalibur x Kukri RIL population to determine genetics controlling energy use efficiency (EUE) in wheat. The aim is to identify genetic loci and markers to enable breeding of high-yielding germplasm with:

  • low rates of leaf respiratory CO2 released per unit growth,
  • optimised levels of sugars, organic and amino acids for growth, and
  • increased biomass at anthesis.

More than 85-90% of the energy captured by plants is used in high-cost cellular processes, such as transport of nutrients and respiration, meaning about only 10-15% is allocated to yield. Thus, any small gain in energy redistribution and use for a costly process can have a marked positive impact on biomass accumulation and yield.

Improvements in EUE can be achieved at the cell, tissue and whole-plant level, with respiration being a prime target.

“Our initial screening of 138 Australian commercial cultivars revealed a two-fold variation in rates of leaf respiration, three-fold variation in the ratio of respiration to growth rate during early development, and significant heritability of 35%. This demonstrates there is untapped genetic variation in EUE amenable to fine-tuning and optimisation of biomass accumulation in the lead-up to anthesis, with concomitant positive knock-on effects on yield”, said Australian National University’s Barry Pogson, Project Lead and Director of the ARC Centre of Excellence in Plant Energy Biology (AUS).

The project has partners at University of Western Australia (AUS), CIMMYT (MEX) and  the University of Adelaide (AUS).

The second research project, AVP1, PSTOL1 and NAS – Three High-Value Genes for Higher Wheat Yield, aims to enhance wheat yield by exploiting and building synergy of three high value genes (AVP1, PSTOL1 and NAS) and enabling molecular breeding by:

  • developing two-gene and three-gene pyramiding combinations of AVP1, PSTOL1 and NAS using available transgenic wheat lines and quantifying the additive effects on yield in multi-location field and greenhouse trials (as a proof of concept),
  • identifying wheat orthologs and allelic variants of TaAVP1, TaPSTOL1 and TaNAS, and designing molecular markers to the best alleles for marker-assisted breeding,
  • providing basic understanding of the physiological and molecular mechanisms behind improved yield and selecting wheat lines with the best allelic combination and field performance, and
  • assessing the necessity for using genome editing technologies to optimise gene function and enhance positive effect on wheat yield by modifying expression of the wheat alleles.

The genes Vacuolar Proton Pyrophosphatase 1 (AVP1), Phosphorus Starvation Tolerance 1 (PSTOL1) and Nicotianamine Synthase (NAS) have been shown to improve plant biomass production and grain yield. Over-expression of these genes results in improved biomass production and grain yield in a range of plant species, including cereals (rice, barley, wheat), in optimal growing conditions. The enhanced yield of the plants is believed to be due to improved sugar transport from source to sinks (AVP1), enhanced root growth and nutrient uptake (AVP1, PSTOL1) and increase in shoot biomass and tiller number (AVP1, PSTOL1, NAS2).

“Identifying and pyramiding the wheat orthologues of these high-value genes provides a real opportunity to produce wheat with significantly improved field performance and higher grain yield,” said Project Lead, Stuart Roy, from the University of Adelaide (AUS).

The project has partners at University of Melbourne (AUS), Arizona State University (USA), Cornell University (USA), University of California, Riverside (USA) and Rothamsted Research (GBR).

These extensive projects will continue throughout 2017 and into 2018.

 

Why is this research so important?

Wheat is the most widely grown of any crop globally, providing 20% of daily calories and protein. By 2050 wheat demand is expected to increase by 60%. To meet this demand, annual potential wheat yield increases must effectively double – an exceptional challenge.

In November 2012, funding agencies and organisations from the G20 countries agreed to work together and formed the global Wheat Initiative to develop a strategic approach to supporting research that would lead to dramatically increasing the genetic yield potential of wheat.

An essential pillar of this strategy is the International Wheat Yield Partnership (IWYP), a novel collaborative approach, enabling the best scientific teams from across the globe to work together in an integrated program to address the challenge of raising the genetic yield potential of wheat by up to 50% in the next two decades all over the world. IWYP builds on the initial research concepts of the Wheat Yield Consortium established by CIMMYT.

To deliver increased wheat yield, a combination of fundamental bioscience and applied research will be needed. IWYP will deliver this through a focused program of research to develop new knowledge, models and wheat lines suited to multiple environments ensuring global gains in wheat yields are achieved.

IWYP will target six key research scope areas:

  • uncovering genetic variation that creates the differences in carbon fixation and partitioning between wheat lines,
  • harnessing genes from wheat and other species through genetic modification to boost carbon capture and fixation to increase biomass production,
  • optimising wheat development and growth to improve grain yields and harvest index,
  • developing elite wheat lines for use in other breeding programs,
  • building on discoveries in wheat relatives and other species, and
  • fostering breakthrough technology development that can transform wheat breeding.

The “IWYP Science Program” provides a unique plan to generate new discoveries and provides for their rapid incorporation into wheat crops grown throughout the world. IWYP’s overarching aims are to stimulate new research, amplify the output from existing programs and make scientific discoveries available to farmers in developing and developed nations.

 

The Australian Plant Phenomics Facility

The APPF provides state-of-the-art phenotyping tools and expertise to help academic and commercial plant scientists from Australia and around the world understand and relate the performance of plants to their genetic make-up. Research facilitated at the APPF is leading to the development of new and improved crops, more sustainable agricultural practices, improved maintenance and regeneration of biodiversity in the face of declining arable land area and the challenges of climate change. Our services.

Do you need access to plant phenotyping capabilities? The PIEPS scheme can help!

Do you have an exceptional plant science research project destined to deliver high impact outcomes for agriculture? The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme was announced in May and is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.

The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.

Don’t miss this an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.

Applications close:  30 September 2017

For more information and to applyAPPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS).

To find out how the APPF can support your research, contact us.

Learn more about projects at the Australian Plant Phenomics Facility and keep in touch.

 

 

Growing rice faster – uncovering the triggers behind early canopy closure

By combining high-resolution image-based phenotyping with functional mapping and genome prediction, a new study has provided insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics in rice.

The more rapidly leaves of a plant emerge and create canopy closure, the more successful the plant, in establishment, resource acquisition and ultimately yield. An early vigor trait is particularly important in aerobic rice environments, which are highly susceptible to water deficits. The timing of developmental ‘triggers’ or switches that initiate tiller formation and rapid exponential growth are a critical component of this trait, however, searching for the switch that initiates this growth has proven challenging due to the complex genetic basis and large genotype-by-environment effect, and the difficulty in accurately measuring shoot growth for large populations.

“The availability of large, automated phenotyping platforms, such as those at Australian Plant Phenomics Facility (APPF), allow plants to be non-destructively phenotyped throughout the lifecycle in a controlled environment, and provide high resolution temporal data that can be used to examine these important developmental switches,” said PhD student, Malachy Campbell.

Malachy and team, including Bettina Berger and Chris Brien from the APPF, phenotyped a panel of ~360 diverse rice accessions throughout the vegetative stage (11-44 day old plants) at The Plant Accelerator® at APPF. A mathematical equation was used to describe temporal growth trajectories of each accession. Regions of the genome that may regulate early vigor were inferred using genome-wide association (GWA) mapping. However, many loci with small effects on shoot growth trajectories were identified, indicating that many genes contribute to this trait. GWA, together with RNA sequencing identified a gibberellic acid (GA) catabolic gene, OsGA2ox7, which could be influencing GA levels to regulate vigor in the early tillering stage.

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Dr Malachy Campell in The Plant Accelerator® at the Australian Plant Phenomics Facility’s Adelaide node

For some traits where genetic variation is controlled by a small number of loci, breeders can use MAS to identify individuals carrying the favourable locus/loci for the given trait, and select them for the next generation. For complex traits that are regulated by many loci, it becomes very difficult to detect loci that are associated with the trait. However, an alternative approach, genomic selection (GS), considers the total genetic contribution of all loci to the given trait. With this approach, loci across the genome can be used to predict the performance of individuals that have not yet been phenotyped (i.e. those in future generations). Since many loci were found to be contributing to early vigor, the team explored the possibility of using GS for improving this trait. Shoot growth trajectories could be predicted with reasonable accuracy, with greater accuracies being achieved when a higher number of markers were used. These results suggest that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage in rice. The approach of combining high-resolution image-based phenotyping, functional mapping and genome prediction could be widely applicable for complex traits across numerous crop species.

Read the full paper, published in The Plant Genome, here. (doi:10.3835/plantgenome2016.07.0064).

Decadal Plan for Australian Agricultural Sciences 2017-2026 released

Grow. Make. Prosper. The Decadal Plan for Australian Agricultural Sciences was published in June 2017 and presents the strategic vision for Australian Agricultural Sciences in the next decade.

The plan outlines strategies to improve the strength and efficiency of agricultural research in Australia in ways that will increase the ability of governments and producers to maintain productivity and efficiency in the face of evolving natural challenges. Successfully identifying, developing and deploying the next generation of game-changing scientific advances remains an active and ongoing challenge. The plan also outlines strategies to capitalise on emerging technologies that will affect the agricultural sciences.

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Agriculture is vitally important to Australia’s economy and social fabric, and contributes to global health and wellbeing. It faces a range of challenges across biophysical, economic and social arenas. Opportunities for technological and production improvements are continuously being identified from scientific research. However, to attain step change improvements in profitability, productivity and sustainability into the future will require integrated multidisciplinary research underpinned by a well-resourced science research pipeline.

The Australian Plant Phenomics Facility plays a key role in supporting the next generation of agricultural research designed to answer some of these challenges. This month we will meet with colleagues from fellow NCRIS facilities TERN, BPA, ALA, NeCTAR and NCI to explore opportunities for collaboration, determine where overlaps or synergies occur and discuss bigger picture ideas to ensure NCRIS funding is used most effectively.

Read the full Decadal Plan for Australian Agricultural Sciences (2017-2026) here.

Find out more about the APPF here.

National National Collaborative Research Infrastructure Strategy (NCRIS)

Terrestrial Ecosystem Research Network (TERN)

Bioplatforms Australia (BPA)

Australian Atlas of Living (ALA)

National eResearch Collaboration Tools and Resources (NeCTAR)

National Computational Infrastructure (NCI)

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A step closer to salt tolerant chickpea crops

A recent study has collected phenotypic data of chickpea (Cicer arietinum L.) which can now be linked with the genotypic data of these lines. This will enable genome-wide association mapping with the aim of identifying loci that underlie salinity tolerance – an important step in developing salt tolerant chickpeas.

In this study, Judith Atieno and co-authors utilised image-based phenotyping at the Australian Plant Phenomics Facility to study genetic variation in chickpea for salinity tolerance in 245 diverse accessions (a diversity collection, known as the Chickpea Reference Set).

Chickpea is an important legume crop, used as a highly nutritious food source and grown in rotation with cereal crops to fix nitrogen in the soil or to act as a disease break. However, despite its sensitivity to salt, chickpea is generally grown in semi-arid regions which can be prone to soil salinity. This results in an estimated global annual chickpea yield loss of between 8–10%.

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Salinity tolerance phenotyping in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node at the Waite Research Precinct – Plants were imaged at 28 DAS for 3 consecutive days prior to 40 mM NaCl application in two increments over 2 days. Plants were daily imaged until 56 DAS. Right pane shows 6-week-old chickpeas on conveyor belts leaving the imaging hall proceeding to an automatic weighing and watering station.

 

The study found, on average, salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the diversity panel with seed number being the major determinant for salinity tolerance measured as yield. The study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.

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Genotypic variation for salinity tolerance in the Chickpea Reference Set. Varying levels of salinity tolerance exhibited by different chickpea genotypes. Exposure of sensitive genotypes to 40 mM NaCl caused severe stunted growth, leaf damage, and led to less number of reproductive sites (flowers and pods) compared to moderately tolerant and tolerant genotypes.

 

The rapid development of new, high-resolution and high-throughput phenotyping technologies in plant science has provided the opportunity to more deeply explore genetic variation for salinity tolerance in crop species and identify traits that are potentially novel and relevant to yield improvement. The Australian Plant Phenomics Facility provides state-of-the-art phenotyping and analytical tools and expertise in controlled environments and in the field to help academic and commercial plant scientists understand and relate the performance of plants to their genetic make-up. A dedicated cross-disciplinary team of experts provides consultation on project design and high quality support.

To read the full paper in Scientific Reports, “Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping” (doi:10.1038/s41598-017-01211-7), click here.

To find out more about the Australian Plant Phenomics Facility and how we can support your research click here.

 

 

 

Last chance to secure an internship – apps close tomorrow!

This is your chance to investigate your plant science questions with the support of the highly skilled Australian Plant Phenomics Facility (APPF) team and the incredible technology and infrastructure we have available.

Internships are offered at the APPF in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate students are strongly encouraged to apply!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

 

Why apply for an internship with the APPF?

Well, aside from the fact we are a pretty nice bunch…

PhD student Rohan Riley, from Western Sydney University, undertook his research at APPF’s Adelaide node (The Plant Accelerator®) after being awarded a Postgraduate Student Internship Grant with us in 2015.

His research attempted to explain the unpredictability of plant growth responses in terms of resource limitation by introducing fungal communities to plants which are isolated from soils containing high or low levels of salinity and analysing the effects on plant stress at the phenotypic level.

This is what he had to say about his experience:

”Using daily phenotyping following the application of salt stress and controlled watering-to-weight in The Plant Accelerator® allowed for an unprecedented resolution and range of plant genetic changes in response to combinations of nutrient level, salinity and two different fungal communities that would not otherwise be achievable in a regular greenhouse,” said Rohan.

rohan_brachy

”As a PhD student with limited experience in greenhouse experiments, the highly controlled growth conditions, large-scale automation, digital imaging and software technology (high-throughput phenotyping) at The Plant Accelerator® provided me with the work-space, expertise and technical support to make a complicated experiment possible.”

“It has been an amazing experience to conduct this experiment at The Plant Accelerator®. I am walking away from the facility with a big smile on my face, an incredible dataset for my PhD research and invaluable experience in greenhouse based plant research.”

To find out more about Rohan’s research:  https://www.researchgate.net/profile/Rohan_Riley

It’s a date! 5th International Plant Phenotyping Symposium, 2-5 October 2018

The Australian Plant Phenomics Facility is thrilled to announce the dates for the 5th International Plant Phenotyping Symposium (IPPS) will be 2-5 October 2018!

We look forward to welcoming the international plant phenotyping community to the host city, Adelaide, South Australia, where you will get the full Australian experience all in one state. From cage diving to fine dining, there’s a wine barrel full of reasons why South Australia was named as one of Lonely Planet’s best regions to visit in 2017! Find out more about this vibrant city before you arrive here.

We will post more details about the symposium as they come to hand – make sure you have elected to follow our blog! – and on the Australian Plant Phenomics Facility‘s website.

Adelaide

2018 Host City, Adelaide, South Australia   (Image source: South Australian Tourism Commission)

 

2017 Calendar of Global Plant Science Events

A Calendar of Global Plant Science Events for 2017 and beyond has now been established on the Australian Plant Phenomics Facility’s website.

Quickly find out what is happening each month around the world in plant science and where, then be sure to check back in regularly for updates (why not bookmark the page as a ‘favourite’).

If you don’t already follow our blog, be sure to subscribe to receive the latest APPF updates and research news.