Working towards building a sustainable cotton industry for the future

Cotton Breeding Australia projects

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Cotton for the future

Cotton Breeding Australia (CBA) is a joint venture between CSIRO Plant Industry and Cotton Seed Distributors. It was created in 2007 to fund cotton breeding and research targeted to assist the breeding program deliver superior varieties. 

CBA’s achievements to date include new varieties with improved yield, pest and disease resistance and fibre quality.

CBA funds several projects from the CSIRO Cotton Breeding and Biotechnology teams based in Narrabri and Canberra. 

The achievements of the projects included in this collaboration to date have been:

Core breeding project

The core cotton breeding project has a large crossing and regional evaluation program – up to 16 sites are used across the industry’s geographical spread. The majority of experiments are located on growers’ farms and so receive commercial management. 

The breeding team has developed new varieties with improved yield, adaptation, disease resistance and fibre quality.

The varieties have been developed with the inclusion of a range of insect resistance and herbicide tolerance traits such as Bollgard II®, Roundup Ready Flex® or Liberty Link®.

A key focus of this program is breeding for pest and disease resistance. One recent highlight is the commencement of field testing of Bollgard III®/Roundup Ready Flex® material being developed to improve management of resistance to Bt in Helicoverpa.

Scientists are now making progress breeding varieties for resistance to Bacterial Blight, Verticillium Wilt and Fusarium Wilt. In collaboration with the biotechnology team, molecular markers are now being used to more rapidly develop Cotton Bunchy Top resistant varieties. Active scoping research is underway for breeding resistance to Black Root Rot and Alternaria.

CSIRO breeders cooperate with biotechnology research (new traits, screening, quality assurance), agronomy (farming systems), pathology (disease assessment for resistance) and post harvest processing (ginning and spinning new varieties). Results from these interactions ensure the best performance and adaptability of new varieties. 

The exceptional adoption by growers of varieties such as Sicot 71BRF and Sicot 74BRF reflect the excellent varietal performance.  Other specialist varieties such as Sicot 75BRF (Fusarium resistance), Siokra 24BRF (dryland systems) and Sicala 340BRF (premium quality) ensure the variety portfolio will match many circumstances.

Core biotechnology project

The biotech team has developed streamlined processes for screening transgenic breeding lines for commercial traits, which will help deliver key new transgenic varieties to the industry. Varieties such as Sicot71BRF are now contributing to the next varieties with BGIII and CBT resistance. The team also routinely contributes towards many of the other CBA projects through molecular analysis of both conventional and transgenic plants, production of mutagenised seeds and in assisting with the production of transgenic cotton plants containing a variety of experimental traits. 

This is an incubator project for new ideas and the team gather preliminary data to help in the formulation of new biotech projects within CBA.

Host plant resistance project

This project has discovered new sources of resistance to spider mites and silverleaf whitefly in a range of cotton genotypes and species. While the mechanisms of these resistance traits have not been completely determined, some biochemical traits (jasmonate, salicylate) and some morphological traits have been implicated. The first stage of introgressing mite resistance into a G. hirsutum background has commenced in the core breeding project, with the expected outcome of mite resistant material that can be used in the breeding program. Assuming this is successful, the long term benefit to industry will be cotton varieties with elevated levels of resistance to mites and whitefly, resulting in reduced reliance on pesticides. This will reduce growing costs, risks of pesticide resistance and environmental contamination, as well as providing a more robust approach to IPM.

Heat stress project

Research is identifying differences between cotton genotypes for tolerance to high temperature stress, to provide a framework for integration of stress tolerance into the CSIRO breeding program. 

Recent highlights include the improvement of approaches to undertake rapid screens for respiratory enzyme viability, chlorophyll fluorescence and leaf temperature on genotypes grown in the field.  

Scientists have identified significant variation in progeny of a ‘heat tolerant’ by ‘heat susceptible’ cross, and these results were generally consistent for three generations of evaluation in the glasshouse and field.  

Researchers are also evaluating the use of these screening approaches in the different climates of Narrabri, Moree, Mungindi and St George. Complementing the screening of advanced conventional CSIRO germplasm, studies are continuing to investigate the heat tolerance of genotypes from diverse origins. Following identification of genes responsive to high temperatures in the growth cabinet, we have collected samples using field material exposed to high temperatures to further evaluate gene expression. 

Improving Cotton Fibre (Cotton Fibre Development) project

Critical regulatory genes (transcription factors) in the initiation of fibre development on the cotton seed have been identified and are being manipulated to try to improve cotton fibre yield. Early results are promising with transgenic plants being produced that have more fibre initials at the start of fibre development. As it is difficult to measure yield components on individual plants, an OGTR application for a field trial of various combinations of the plants over-producing these transcription factors has been submitted,  which should allow field assessment of fibre yield and quality over the next two of years. 

Designer Fibres project 

A top Australian cell wall chemist has been recruited to research and develop analytical methods for studying cotton fibre cell wall composition. This will help our molecular biologists select gene targets for genetic modification. Already the scientists are measuring differences in composition of many of the minor polymer components of the cell walls, but more research is needed to relate these to differences in fibre properties. If the right genes can be identified, this approach could eventually make fibres with novel cell wall compositions that could give Australia a competitive advantage in the global fibre market.

Cell Wall Pectin project 

This project has identified differences in the pectin composition in the fibre cell walls of Pima and Upland cotton,. Transgenic cotton plants with more or less of the cell wall enzymes are being produced to measure changes to fibre quality. Early results are promising, and plants over-producing these pectin modifying enzymes had a more rapid early elongation. However, more analysis needs to be done to confirm whether this translates into fibres of better quality, and that the changes are caused by alterations in the structure of the pectin in fibre cell walls.

Cotton molecular marker project

The aim of this project is the identification of DNA markers that can be used as substitutes for field disease screening in early generation cotton breeding. This project is scoping modern high throughput marker technologies based on the cotton genome that should accelerate the pace of breeding in the future. Using markers identified from partially re-sequencing the genomes of many varieties varying in disease resistance, the group hopes to be able to develop screening DNA chips that will help the breeding program maintain and advance the tolerance of our cultivars to fungal diseases like fusarium and verticillium wilt but also eventually to other important agronomic traits. 

The team has identified a marker for Cotton Bunchy Top resistance, which is now being routinely used for screening breeding lines from the core breeding project in Narrabri.

RNA silencing project

This project’s main objective is to identify a role for natural plant gene silencing pathways in defence against fungal diseases and hence a potential strategy for engineering better disease tolerance in crops. These mechanisms of gene silencing were known to be important for conferring resistance to virus diseases in plants, but this was the first time that those pathways were shown to be important for defense against fungal diseases like fusarium wilt. While most of the work was done in a model plant, Arabidopsis, the same mechanisms will be tested in cotton and for application to the management of fusarium wilt. 

Cotton Mutant project

This project has developed several different mutant populations in cotton that are being screened for plants that will assist in our objectives to understand cotton fibre quality and other agronomic characteristics. The first short and immature fibre mutants have been found, and are being studied at the biochemical and molecular levels using techniques being developed in the Designer Fibres project.  Those populations are also being bulked up as a resource for future screening to find other novel mutants in fibre or other plant attributes.

References

Roundup Ready™ and Roundup Ready Flex™ are trade marks owned by the Monsanto Company.