Cotton Biotechnology: Core Project IV

24 November, 2020

Project Leader: Danny Llewellyn
Brief Summary of Project Objectives: The aim of this project is to provide the molecular support needed for the core cotton breeding project to deliver new varieties to the industry, to support other CBA projects needing similar molecular or transformation expertise and to serve as an incubator for new ideas and projects.

Executive Summary

This project supports a senior scientist and a team of skilled technical staff who provide the core molecular capabilities needed for the successful development and deployment of new commercial cultivars containing GM traits by the Core Breeding project. The Core Biotech and Core Breeding projects are very closely integrated with common goals and regular interactions. 
The Core Biotech project provides all the molecular screening (DNA-based, ELISA-based and biochemical screening) needed to follow GM (and increasingly non-GM) traits through crossing and selection to produce new varieties and also provides any additional support for the CBA QA service project in the quality control over all steps in breeding leading to the production of seed to be handed on to CSD for commercial seed increase. This includes molecular screening of all plants used as parents in the crossing program.
The team also increasingly applies the molecular markers developed in the Disease Marker project (CBA04) as the breeding team begin integrating those largely disease and HPR traits into their mainstream programs. The Disease Marker project finds and validates the markers and the Core Biotech project applies them alongside our other molecular screening for the breeders. More screening markers will come into the Core Biotech project as that project identifies and validates Verticillium and Fusarium wilt resistance associated markers and markers for spider mite and whitefly resistance. The Core Biotech team also regularly contributes to the Genomic Selection I project that is assessing potential new breeding technologies for their applications to cotton.
Significant Achievements for the project over the last year include

  • The team performed many tens of thousands of ELISA assays for the insecticidal traits on seed and leaf samples, extracted tens of thousands of DNA samples from freeze-dried leaves from the glasshouse and field, and performed hundreds of thousands of PCR genotyping assays to provide the breeding program with presence/absence or zygosity information on the multiple GM traits needed to advance specific selections from many different breeding populations and to confirm the identity of all plants used in their crossing program. Screening for presence and zygosity of the XtendFlex (DGT)and the Lygus trait are also now routine
  • Screening for non-GM traits coming out of other CBA projects has continued especially for Cotton Bunchy Top resistance, but also some mutant herbicide tolerance traits, okra leaf, nematode resistance and bacterial blight resistance joining the suite of traits that have associated molecular markers that can be used as substitutes for phenotypic selection. The Core Biotech team has also started screening for commercial GM traits in less advanced experimental breeding material such as the HPR germplasm for mite and whitefly resistance, as it is becoming difficult to field test these without the lines also containing the commercial insect and especially herbicide resistance traits from Bayer.
  • The large volume of assays required for molecular breeding represent a significant HSE risk to staff and we have continued to explore new equipment to reduce those risks, utilising CBA and CSIRO capex funds. This has been very successful so far and staff report much fewer instances of injury or discomfort and there has also been an increase in the efficiency of all the screening that has been critical for getting through the coronavirus pandemic when staff numbers in the lab were severely restricted.
  • The Core Biotech team, in between activities for the breeding program, have contributed their expertise and time towards many of the other CBA and CSIRO funded cotton projects on an ad hoc basis through molecular analysis of both conventional and transgenic plants (collecting samples, making DNA or RNA and running molecular tests), helping quarantine staff process cotton material coming through quarantine for the breeding team (at least before all the Canberra glasshouses were destroyed by hail), making gene constructs and vectors for use by this and other projects, generating cotton tissue or fibre samples for molecular assays, assisting with the production of transgenic cotton plants containing different experimental traits being evaluated by other projects and in gaining the necessary regulatory approvals for any field testing of those GM cottons, as well as overseeing reporting back to the Regulator and contributing to submissions for reviews of the regulatory system.