Finalisation of project agreements with all parties occurred at the end of 2002, but the official project start date was retained at July 2002, as per the original project proposal. The commencement of most activity related to molecular marker activity, which was dependent on funding, was delayed until the start of 2003, but it is planned to catch up with these delays and no overall adverse effects on the project are expected.

The project is proceeding in five (linked) main activity areas, corresponding to each of the five objectives. Progress in these are summarised briefly below.

(i) To assess genetic diversity in germplasm collections and select a core set of clones for future breeding.
Work done on genetic characterisation of germplasm collected from China and other parts of the world has commenced. 497 wild (Saccharum. spontaneum and E. arundinaceus) clones collected from different provinces in China, have been selected for genetic characterisation. 96 S. spontaneum and 83 E. arundinaceus clones from the germplasm collection housed in BSES, Australia, have also been selected for marker analysis. 150 clones, and 100 clones, from Australia and China respectively, have also been selected to represent the genetic diversity sampled within core commercial breeding programs. The latter clones include key ancestors and cultivars in both programs. DNA has been extracted from most clones and marker analysis has commenced.

Arrangements have also commenced regarding collection of samples from wild (S. spontaneum and E. arundinaceus) clones from the ISSCT world collection in the USA and a collection in Brazil: representative clones from these collections are planned to be sampled by the end of 2003.

(ii) To develop improved clones derived from wild germplasm.
A range of crosses (78 in total) were made at both YSRI and GSIRI in December 2002 from germplasm derived from wild clones collected in China. The wild clones, or clones recently derived from the wild clones, were crossed with either S. officinarum or with commercial type varieties. Some seed has already been sown in China, and some seed has been reserved for later shipment to Australia. Families and individual clones derived from these crosses will be evaluated for cane yield and sugar content later in the project, and clones with good performance and capturing new sources of genetic variability (as per the genetic diversity studies) will be transferred to breeding programs for use as parent material.

(iii) To evaluate DNA marker assisted introgression of exotic germplasm in sugarcane improvement.
The aims of the research in this component are to examine several case study populations to assess and develop methods for marker assisted introgression in sugarcane. Populations suitable for research plans in this component have been produced and are currently being propagated in the field, in preparation for planting replicated yield evaluation trials during 2004 and 2005 as per project plans. DNA characterisation of these populations will commence in 2004.

(iv) To undertake GxE studies between China and Australia.
Twenty clones characterised extensively across a large number of environments in Australian sugarcane production regions were sent to YSRI after a 1 year closed quarantine period in Australia. These are currently being grown in closed quarantine in Kunming by YSRI. Several clones were damaged during transport and will be deleted from further work, but this is not expected to have a significant effect on research objectives.

(v) To develop capability in YSRI and GSIRI in application of molecular marker technology and sugarcane breeding.
An operational molecular marker laboratory at YSRI has been developed to a stage where AFLP markers are being assessed, and screening of germplasm for component 1 in the project will shortly commence. A molecular marker laboratory at GSIRI is presently in the process of being equipped, and is expected to be operational by the end of 2003. A trip to Australia by project staff in China was conducted in 2002. The aim of the trip was to demonstrate a range of methodologies and research associated with sugarcane improvement being done or being developed in Australia. The group of eight project staff from China visited a number of research centres from Cairns to Canberra with particular focus on field research associated with sugarcane, and biotechnology projects with relevance to plant improvement.

Year 2 (01/07/2003-30/06/2004)
Assess genetic diversity in germplasm collections and select a core set of clones for future breeding.
Work on genetic characterisation of germplasm collected from China and other parts of the world is well underway but not yet completed. This component was delayed during 2003-04 due to some technical problems with commissioning the marker laboratories in China. These problems have been addressed in the Yunnan Sugar Research Institute (YSRI) lab, with Amplified Fragment Length Polymorphism (AFLPs) now being run routinely in that laboratory. In YSRI, gel running has been completed for the Erianthus material, and is underway for the S. spontaneum material. Some technical problems are still being experienced in the Guangzhou Sugarcane Industry Research Institute (GSIRI) laboratory at the time of writing this report. One hundred clones representing material in the core breeding programs in China will soon be done in the GSIRI laboratory.
In Australia, commercial-type clones (ancestors, parents, cultivars) representing genetic diversity in Australian breeding programs have been scored for AFLP markers and these data analysed. S. spontanem and Erianthus arundinaceus clones from the Australian germplasm collection have also been characterised with AFLP markers but the data not yet analysed. DNA has been extracted from S. spontaneum and Erianthus clones collected from collections in the USA and Brazil. Characterisation of all the material from the overseas collections is being delayed until around August when a capillary sequencer machine will be available which will allow more efficient scoring.
Final analysis of this component of work is expected to be completed by the end of 2004. This will focus on understanding the relationships between clones in available germplasm collections, both within and between the different collections. A second focus will be on the identification of a core set of clones for future breeding efforts that sample a large portion of genetic diversity in these two species of interest to introgression breeding.
Develop improved clones derived from wild germplasm.
A further 62 crosses producing viable seed were produced at both YSRI and GSIRI in 2003-04 from basic germplasm or germplasm derived from wild clones collected in China. The wild clones, or clones recently derived from the wild clones, were crossed with either S. officinarum or with commercial type varieties. Some seed has already been sown in China, and seed has been brought to Australia. Generally for most crosses, about half the seed is kept in China and half taken to Australia. Quarantine protocols have been developed with AQIS for importing this material to Australia, as it is the first time true sugarcane seed (as opposed to vegetative cuttings) have been brought in. Currently seedlings from 71 crosses are being grown in quarantine in Australia. Families and individual clones derived from these crosses will be evaluated for cane yield and sugar content later in the project, and clones with good performance and capturing new sources of genetic variability (as per the genetic diversity studies) will be transferred to breeding programs for use as parent material.
Evaluate DNA marker assisted introgression of exotic germplasm in sugarcane improvement.
The aims of the research in this component are to examine several case study populations to assess and develop methods for marker assisted introgression in sugarcane. Populations suitable for research plans in this component have been produced and are currently being propagated in the field, at Kaiyuan in Yunnan, and Hainan, in preparation for planting replicated yield evaluation trials during 2004 and 2005.
Undertake GxE studies between China and Australia.
Twenty six clones needed for this component of the project are currently under propagation in Yunnan and Guangdong. These include 15 unselected clones and six cultivars extensively evaluated across many environments in Australia, and 3 other cultivars grown in China and available in Australia. As reported in the 2002-03 progress report, some damage of cane sent to China for this component occurred, and this limited available planting material, resulting in the need for an additional cycle of propagation. This will cause a one year delay in the original timeframe of trial establishment, but project objectives will still be achieved.
Develop capability in YSRI and GSIRI in application of molecular marker technology and sugarcane breeding.
An operational molecular marker laboratory at YSRI has been developed to a stage where AFLP markers are being assessed, and screening of germplasm for component 1 in the project will shortly commence. A molecular marker laboratory at GSIRI is presently in the process of being equipped, and is expected to be operational soon. A trip to Australia by project staff in China was conducted in 2002. The aim of the trip was to demonstrate a range of methodologies and research associated with sugarcane improvement being done or being developed in Australia. The group of eight project staff from China visited a number of research centres from Cairns to Canberra with particular focus on field research associated with sugarcane, and biotechnology projects with relevance to plant improvement.

The project is proceeding in five (linked) main activity areas, corresponding to each of the five objectives. Progress in these are summarised briefly below.

(i) To assess genetic diversity in germplasm collections and select a core set of clones for future breeding.

Work on genetic characterisation of germplasm collected from China and other parts of the world has been almost completed, with data analysis and manuscript writing underway. Characterisation of Erianthus arundinaceus from China has been completed. The results showed that the Chinese representatives of this species are genetically diverse compared with material in the Australian collection; the latter material being mostly sourced from Indonesia. Within China, there is a clear general difference between clones collected in eastern versus western regions.

Characterisation of all non-Chinese S. spontaneum clones (including clones from Australian, USA and Brazillian collections) has been finished. Characterisation of the Chinese S. spontaneum in the laboratory at YSRI has proved problematic and is still being completed. Final analysis of data for S. spontaneum has been awaiting final laboratory analysis at YSRI.

The above analysis will be used in helping target small core sets of clones from both species that represent most available genetic diversity available for use in Chinese and Australian collections. An agreement for exchange of basic germplasm clones between YSRI and CSIRO-BSES was made in 2004. Selection of clones for exchange will be finalised based on results from the diversity study.

Work in the remainder of 2005 will focus on reporting the results obtained in the scientific literature.

(ii) To develop improved clones derived from wild germplasm.

This component of the project has been successful, and completed, ahead of schedule.

A further 40 crosses were made at YSRI and GSIRI in 2003/04 from parents derived from wild clones collected in China. These involved crossing the clones derived from basic germplasm clones with either S. officinarum or with commercial type varieties. Some seed has been sown in China, while some seed has been brought to Australia. Generally for most crosses, about half the seed is kept in China and half taken to Australia. We have spent a lot of time liasing with AQIS in developing quarantine protocols for importing this material to Australia, since this is the first time true sugarcane seed (as opposed to vegetative cuttings) have been imported. Families and individual clones derived from these crosses are being evaluated in China and Australia, and families and clones with good performance and capturing new sources of genetic variability will be used for further breeding. It is important that future plans are discussed and carefully made for use of this material, in order to develop commercial benefits (via cultivars) from the outputs in this section of the project.

(iii) To evaluate DNA marker assisted introgression of exotic germplasm in sugarcane improvement.

The aims of the research in this component are to examine several case study populations to assess and develop methods for marker assisted introgression in sugarcane. Populations suitable for research plans in this component have been produced and were successfully established in replicated field trials in Yunnan, Guangzhou and Australia in 2004/2005. In Yunnan, two populations derived from a S. spontaneum clone are being grown. One of these populations is also being evaluated in Australia. In Guangzhou, two populations derived from an Erianthus arundinceus clone are being evaluated. Marker characterisation on these populations has commenced at YSRI and GSIRI.

(iv) To undertake GxE studies between China and Australia.

Twenty six clones needed for this component of the project are currently undergoing a second cycle of propagation in Yunnan, Guangdong and Australia, in preparation for planting field trials in 2005/06. These include 15 unselected clones and six cultivars extensively evaluated across many environments in Australia, and 3 other cultivars grown in China and available in Australia.

(v) To develop capability in YSRI and GSIRI in application of molecular marker technology and sugarcane breeding.

Molecular marker laboratories at both YSRI and GSIRI have been developed and both micro-satellite (SSR) and AFLP markers are being run. These markers are the main ones being applied in the current project, and are currently the most widely used in sugarcane generally. Some minor problems with gel clarity with AFLPs are still being found however. Several trips have been conducted by CSIRO staff to assist in addressing the problems with routine operations, and these trips have been successful in identifying and addressing problems.

The project is proceeding in five linked activity areas, corresponding to each of the five objectives. Progress in these are summarised briefly below.

(i) To assess genetic diversity in germplasm collections and select a core set of clones for future breeding.

Data collation needed to characterise genetic relationships among germplasm collected from China and other parts of the world has been completed, with reporting and manuscript writing progressing. A paper on characterisation of the diversity within S. spontaneum was presented at the ISSCT Sugarcane Breeding and Germplasm conference in Ecuador in May 2006. A manuscript for submission to a journal on these data is also being prepared. In summary, the results highlighted extremely high genetic diversity within S. spontaneum (in relation to S. officinarum and commercial sugarcane), and also showed two general groupings corresponding to clones collected in Southern India and Indonesia on the one hand, and northern India and China on the other.

A manuscript on characterisation of the genetic diversity within Erianthus arundinaceus is still in the early stages. As indicated in the previous annual report, the results from the Erianthus study showed that the Chinese representatives of this species are genetically diverse compared with material in the Australian collection; the latter material being mostly sourced from Indonesia. Within China, there is a clear general difference between clones collected in eastern versus western regions. A paper on the relationship of the Chinese species Erianthus rockii in relation to other species in the Saccharum was published.

Following an agreement for exchange of basic germplasm clones between China (YSRI) and Australia (BSES-CSIRO) made in 2004, a selection of clones for exchange has been made and these have been placed in quarantine.

(ii) To develop improved clones derived from wild germplasm.

As indicated in the previous annual report, this component of the project has been successful in producing a wide range of clones derived from wild germplasm, which are now being further evaluated and used within sugarcane breeding programs in China and Australia. This includes the first reports in the world of introgression of Erianthus spp. into sugarcane, which opens up new diversity to sugarcane breeding programs.

Field trials in China and Australia to evaluate progeny from S. officinarum/commercial sugarcane x S. spontaneum developed in this project were sampled and measured in 2006. These experiments have been successful, and the better clones from these trials will be evaluated further and used in further crosses with elite sugarcane parents. High correlations between families in the trials in Australia and China for stalk weight and sucrose content were observed. This result is important. Apart from being the first report of genetic x country interactions in sugarcane, it also indicates that selection trial results in either country will be useful for predicting performance in the other, and has important implications for planning further cooperation to maximise mutual benefits from joint exploitation of the germplasm resources generated in this project in future years.

The evaluation, further breeding, and commercial extension of progeny from component 2 in this project is required to realise commercial and social benefits from the success achieved in this area in the project. In both China and Australia but particularly the former, there is rapidly emerging interest in producing energy sources (especially ethanol) from sugarcane: this is emerging as a major national goal in China, for economic, environmental and national security reasons. Possible characteristics of some clones developed in this project (high dry matter yields, drought tolerance, strong ratooning ability, and other traits) means there may be significant opportunities arising from this project in this regard. Further discussions within the project team and with other parties will occur soon in relation to this, aiming to establish if any mutually beneficial R&D opportunities exist. It is worth noting that many poor regions in western China could benefit strongly from the emerging opportunities to produce ethanol from crops.

(iii) To evaluate DNA marker assisted introgression of exotic germplasm in sugarcane improvement.

This component aims to assess and develop methods for marker assisted introgression in sugarcane through several case study breeding populations. Populations have been produced in prior years and were successfully established in replicated field trials in Yunnan, Guangzhou and Australia in 2004/2005. In Yunnan, two populations derived from a S. spontaneum clone are being grown. One of these populations is also being evaluated in Australia. In Guangzhou, two populations derived from an Erianthus arundinceus clone are being evaluated.

These populations were sampled in November to December, 2005, in China, and in July 2006 in Australia. Analysis of variance of the results from China indicate that the data obtained is of good quality (high broad-sense heritabilities for key traits) and will provide a good basis for subsequent QTL analysis when collection of marker data is completed in 2007. Results from the Australian sampled trial are still being processed at the time of writing this report.Marker characterisation on these populations is well underway in YSRI and GSIRI, and will shortly commence in CSIRO.

(iv) To undertake GxE studies between China and Australia.

Following transfer through quarantine, and two cycles of propagation in previous years in the project, clones selected for this component of the project were successfully established in five field trials in China in early 2006. The same clones were previously evaluated extensively in Australia. Comparison of results (to be obtained next year) will provide information about the usefulness of data collected in both countries for predicting performance in the other.

(v) To develop capability in YSRI and GSIRI in application of molecular marker technology and sugarcane breeding.

As indicated in prior annual reports, molecular marker laboratories at both YSRI and GSIRI have been developed with assistance from Australian staff in this project, with both micro-satellite (SSR) and AFLP markers being run. Training of staff in China on in-situ hybridisation methodology also occurred in 2006.