plant growth

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).

This is your chance! An invaluable opportunity to access phenotyping capabilities to further your plant science research

Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?

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 apply:  APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)

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

Fertiliser start-up gets a boost at APPF

Plant Technologist

Resource Recovery Australia together with CSIRO, Cape York Partnership, Balkanu and Kalan Enterprises are developing new income streams for Cape York’s Aboriginal communities by producing organic soil-conditioners from an unlikely source, feral pigs, which cause vast environmental damage to native ecosystems.

A pilot project at the Australian Plant Phenomics Facility’s (APPF) Adelaide node, tested the effect of the ‘Feraliser’ at different concentrations on tomato growth.

“The data collected using the high-throughput phenotyping Smarthouse at the APPF provided valuable insights into the effectiveness of our product. We now know Feraliser performs just as well as the leading organic soil-conditioners currently on the market,” said Emmaline Froggatt from Resource Recovery Australia.

“Feraliser is very much at the start-up phase of development so costs are a big issue for us. The Australian Plant Phenomics Facility provided the information we needed without the expense of a full field trial.”

Find out more about Resource Recovery Australia.

To find out how the Australian Plant Phenomics Facility can support your research, go to our website or contact us.

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.

 

 

 

Taking the kinks out of curves

In a recent paper, researchers have developed a methodology suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

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An example of curve registration.  a The salinity sensitivity (SS) curves of the 16 functions from an arbitrary family, b SS curves after the curve registration, and c the corresponding time-warping functions. The salinity sensitivity on the y-axis of a and b refers to the derivative of the relative decrease in plant biomass

 

Advanced high-throughput technologies and equipment allow the collection of large and reliable data sets related to plant growth. These data sets allow us to explore salt tolerance in plants with sophisticated statistical tools.

As agricultural soils become more saline, analysis of salinity tolerance in plants is necessary for our understanding of plant growth and crop productivity under saline conditions. Generally, high salinity has a negative effect on plant growth, causing decreases in productivity.  The response of plants to soil salinity is dynamic, therefore requiring the analysis of growth over time to identify lines with beneficial traits.

In this paper the researchers, led by KAUST and including Dr Bettina Berger and Dr Chris Brien from the Australian Plant Phenomics Facility (APPF), use a functional data analysis approach to study the effects of salinity on growth patterns of barley grown in the high-throughput phenotyping platform at the APPF. The method presented is suitable to reduce the noise in large-scale data sets and thereby increases the precision with which salinity tolerance can be measured.

Read the full paper, “Growth curve registration for evaluating salinity tolerance in barley” (DOI: 10.1186/s13007-017-0165-7) here.

Find out how the Australian Plant Phenomics Facility can support your plant science research here.

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High-throughput phenotyping in the Smarthouse™ at the Adelaide node of the APPF

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Barley plants growing in the Smarthouse™