Cotton Breeding Australia

Above: David Thodey AO, CSIRO Chair and James Kahl, CSD Chair and the announcement of the extension of the CBA partnership to 2029.

CSD and CSIRO have been working together since 1971, with over 100 cotton varieties released to the Australian market.

This partnership was formalised in 2007, through the formation of the Cotton Breeding Australia (CBA) joint venture - a targeted research fund set up to facilitate the research and development of future cotton varieties for Australian growers.

Since 2007, the CBA collaboration has invested over $100 million towards this research; and in 2018, the partnership was formally extended to June 2029. Click here to read more about this announcement.

CBA research is focussed on the future issues and challenges for cotton production in Australia, and both CSD and CSIRO consider the CBA partnership critical in ensuring that cotton remains at the forefront of Australian innovation, well into the future.

CBA research activities are overseen by a Management Committee with both CSD and CSIRO members; and through a Scientific Committee with CSD, CSIRO, Cotton Research & Development Corporation and Cotton Australia members.

Please take some time to learn more about some of the highlights of CBA breeding and biotechnology research.

Principal Investigators: Warwick Stiller, Shiming Liu, Heidi Clements, Greg Constable, Peter Reid, Danny Llewelyn (QA)


This project has delivered significant industry outcomes in the form of new varieties and trait packages that have completely displaced previous varieties and traits.

Five new varieties containing Bollgard 3/RRF have been released, with Sicot 714B3F, Sicot 746B3F and Sicot 748B3F having particular commercial success. While not widely grown, Sicot 754B3F has proved itself with a premium fibre package that has enabled some growers and merchants to achieve significant price premiums. Sicot 707B3F was the first variety to be released directly for the southern growing regions, specifically to address low micronaire concerns.

Two new varieties containing Roundup Ready Flex were released - Sicot 711RRF which replaced Sicot 71RRF and Sicot 812RRF which has better staple specifically for the dryland industry.

Two new conventional lines were also delivered to CSD - CSX5432 and CSX8308. These are high performing lines that address the concerns of some growers that we are not providing choice and locking them in to having to grow varieties with GM traits.

Detailed Research Results

Bollgard 3/RRF (B3F)

Up to 2017/18, CSIRO has developed more than 50 breeding families with the B3F trait combination to provide a range of options into the future.

This B3F breeding material is derived from new elite conventional lines and aims to offer improvements in yield, regional or system adaptation, fibre quality and disease resistance. This material will form the basis of new introgression for B3XF families.

XtendFlex development

Since 2012, CSIRO has been working to develop elite germplasm that contains Monsanto’s XtendFlex trait. This trait provides tolerance to Dicamba and glufosinate and is paired with the existing RRF trait, with or without Bollgard 3.

Fifteen families are now at various stages of development, with the first set of lines in replicated trials in 2016/17. It is expected that this initial family will produce a ‘concept’ product (which is not intended to be a commercial product) to be used to further evaluate and refine the herbicide system in Australia.

Due to the loss of disease screening Nurseries because of hail &/or low expression of disease over the last two seasons, screening will continue over the coming years to refine selections prior to commercialisation. These lines were in CSD nursery production in 2017/18.

Development is also underway for lines containing XtendFlex alone. Because the XtendFlex donor also contained Bollgard II, it has taken considerable work to remove those traits from these families.

Elite conventional

Good progress is being made in the development of a wide suite of conventional germplasm to address CSIRO breeding targets. In particular CSIRO are conscious of having options for future production systems, as well as platforms for future transgenic traits. In 2013/14, the breeding program moved to having an Advanced Line Trial which contains the best lines from each of the breeding programs in the one experiment at all sites. This has reduced duplication of control varieties in experiments and enables better evaluation of the most advanced lines.

Improved combination of fibre traits

CSIRO are also studying the association between yield and fibre quality to (a) understand reasons for the negative association and (b) to design a breeding approach to identify high quality lines with better yield. Good progress is being made in both objectives. For cotton to remain competitive amongst synthetic fibres, cotton fibre quality must be improved, but not at the expense of yield reductions.

The current targets CSIRO are aiming for are >1.24 inch length; >32 g/tex strength; <180 ug/m fineness; and target yield within 5% of Sicot 71.

Fusarium nurseries

Fusarium nurseries are a critical component of the CSIRO breeding process and CSIRO continually strive to improve resistance to this.

In excess of 8,000 plots were grown in two separate Fusarium nurseries on the Downs to measure resistance to Fusarium in cotton breeding material. The Cowan site was completely wiped out by hail just after Christmas 2017 and due to the hot, dry season, the disease pressure at the Anchor field site was significantly lower than normal. No fusarium data has been able to be collected from the 2017/18 season. This, combined with losing the Cowan site to a severe hail storm in 2015/16 has significantly impacted our ability to screen for and hence improve fusarium resistance. However, screening will continue over the coming years to refine selections prior to commercialisation.

Principal Researcher: Dr Danny Llewellyn (100%)

Executive Summary

The Core Biotechnology and Core Breeding projects are very closely integrated with common goals.

The Core Biotech project provides all the molecular screening (DNA-based, ELISA-based and biochemical screening) needed to follow Genetically Modified (GM), and increasingly non-GM, traits through the crossing and selection programs to produce new varieties and also provides any additional support for the QA service project in the quality control over all steps leading to the production of seed to be handed on to CSD for commercial seed increase.

It also increasingly applies the molecular markers developed in the separate Disease Marker Genotyping project (CBA04) as the breeding team begin to integrate those largely disease traits into their mainstream programs (eg., for Cotton Bunchy Top (CBT) resistance, bacterial blight resistance, nematode resistance and Okra leaf).

The Core Biotech team also contributes to the Genomic Selection project that is assessing potential new breeding technologies for their application to cotton.

Principal Researcher: Dr Iain Wilson, Dr Qian-Hao Zhu and Dr Danny Llewellyn

Executive Summary

Working in close cooperation with the Cotton breeders, the disease marker group has had a successful year that moves us closer to developing more disease resistant germplasm.

Molecular markers have been developed and validated for CBT, bacterial blight and okra leaf. These are now routinely used in the Cotton Breeding process. This technology will greatly enhance the ability of the breeders to make significant gains in the future.

Disease markers for diseases such as Black Root Rot, Verticillium Wilt and Fusarium Wilt are currently being identified and validated and should be able to accelerate the development of new cultivars carrying resistance.

Markers have been found that are diagnostic for the recessive fuzzless seed trait and a paper on the genetics of the recessive fuzzless seed trait has been published.

Principal Investigators: Carlos Trapero

Executive Summary

Significant progress has been made regarding the Verticillium Wilt (VW) resistance component of the project.

In the first instance, fields suitable to evaluate material for resistance to VW have been identified. They have allowed screening of a range of Gossypium germplasm and a few genotypes within them have been targeted for introgression of VW resistance into elite material.

Furthermore, lines developed to validate molecular markers associated with VW resistance have been phenotyped and the most resistant lines selected to develop additional VW resistant lines.

Finally, the level of VW resistance of a number of advanced and pre-commercial lines from the core breeding program have been assessed and will be used as an additional trait for the final selection of these lines.

Regarding host plant resistance to Silver Leaf Whitefly (SLW), one Okra-Glabrous B3F breeding line has been tested in large field plots and proven to harbour a lower population of SLW compared to a commercial cultivar in these conditions, suggesting that whole fields planted with a variety having Okra and Glabrous traits will still maintain their high level of resistance to this pest and therefore could be an alternative option if the SLW threat became even more serious a problem. Backcross breeding lines selected for resistance to Two Spotted Spider Mites have also been validated in the field.

The development of molecular markers appears very positive as well, with plant material being developed to use for the marker validation experiments next year and preliminary results showing that two markers are needed in order to have a high level of resistance in glasshouse conditions. Field experiments will show the feasibility of using these markers as a routine screening tool to speed up the selection process in the breeding program.

Principal Researcher: Dr Filomena Pettolino

Executive Summary

This project is undertaking fundamental research into cotton fibres. It is making significant discoveries in regards to the chemical composition of fibre cell walls.

The results of this research may identify novel ways that the cotton fibre can be manipulated to compete against synthetic fibres.

Key highlights of the research have been:

  • Comprehensive analysis of fibre composition at maturity and through development has identified cell wall components involved in fibre quality traits
  • Sophisticated analysis of mature fibre from G. hirsutum, G. barbadense and G. arboreum revealed differences in cellulose microfibril structure
  • Five cotton-related papers were published during the course of this project
  • Funding to pursue the Novel Fibres part of the original project proposal was successfully attained through the CSIRO Synthetic Biology Future Science Platform and is progressing as a separate project

Principal Researchers: Philippe Moncuquet, Washy Gapare, Qian-Hao Zhu, Iain Wilson, Shiming Liu, Warren Conaty and Warwick Stiller

Executive Summary

This is a long term project that aims to develop and evaluate in cotton a new molecular based breeding approach called Genomic Selection (GS) that is now being widely used in livestock breeding and increasingly in crop breeding.

The objective is to be able to predict the phenotypic potential (for example, yield, fibre quality or other agronomic properties) of breeding selections or populations based on the combinations of large numbers of single nucleotide polymorphisms (SNPs) markers present in individual plants.

GS, if validated, will eventually be used by our breeders as an aid to help select parents in crossing, to identify progenies in segregating populations with the best genetic make-up, and will reduce the amount of field based screening required to generate elite cultivars.

Procedures have been established to enable breeding lines to be sampled each year for genotyping and the collection of phenotype data for the GS statistical model development. Weather stations have been established at breeding sites to enable long term integration of environmental data with genetic data to improve the GS models. Using the 63K Cotton SNP Chip genotyping platform and models developed specifically for cotton breeding, a training population consisting of  all historical varieties for which seeds (and hence DNA) are available, year 2014 and year 2015 breeding lines (a total of 922 lines) was used to predict year 2016/2017 phenotypes (validation population) (a total of 347 breeding lines). Prediction accuracies for fibre length averaged 0.37 and for fibre strength averaged 0.28. It is hoped that with the addition of further field data these predictions will increase and become of value for selection.

To enable GS to be applied to cotton breeding once predictions becomes informative, genotyping needs to become cheaper and preferably applied to seeds. A pilot genotyping experiment with DArT has indicated they have the potential to deliver a genotyping system capable of being applied to cotton breeding. Experiments are currently under way to determine whether it possible for this system to be applied to seed genotyping.

Principal Investigators: Warren Conaty and Susan Jaconis

Executive Summary

The aim of this project is to develop a better physiological understanding of the complexities of cotton crop performance under heat and water stress, and to use that knowledge to develop capacity within the breeding program to reliably rank germplasm for heat and water stress tolerance in order to accelerate the production of varieties better adapted for future warmer and drier production environments.

To date this project has developed an understanding of the physiological interactions between heat and water stress. This has enabled a focus on pollen viability and germination, as well as crop water use as targets for germplasm screening. The project has developed and delivered a dryland germplasm screening protocol, enabling more reliable detection of superior rainfed cultivars. Over the final months of the project, assessments of the utility of pollen viability and canopy temperature as targets for physiological abiotic stress resistance screening will be finalised.

Principal Investigators: Shiming Liu

Executive Summary

Much of Australian cotton is grown on sodic soils with very high clay content and high pH. Excessive Na+ in the soils has a detrimental impact on cotton nutrient uptake and use, and can cause nutrient related stresses and reduce nutrient use efficiency, particularly for K and P.

The effects of Na might limit further increases in yield, so breeding cotton with reduced Na uptake is important to increase cotton sodicity tolerance, to maximise yield and its stability as well as to increase K and P use efficiency.

This is a new PhD training project due to commence in 2019 and aims to gain a better understanding of the Na exclusion mechanism and to identify molecular markers for the trait to facilitate more rapid introgression in the breeding program.

The key outcomes from this joint project on cotton genetics and nutrient use efficiency between CSIRO [via CBA] and Western Sydney University (WSU) are threefold:

  • new rapid screening tools for identifying sodicity tolerant cotton breeding lines;
  • new scientific evidence on mechanisms of cotton sodicity tolerance;
  • new research capacity of applying advanced plant physiology tools in cotton abiotic stress research.