The marker implementation and breeding program modification components of the project are progressing well after a slow start. As of July 2nd we still have not received the Indian germplasm in Australia which has delayed DArT analysis and crossing in Australia, although correspondence indicates that the materials could arrive any day. The Australian germplasm was sent to India last year and is being crossed with Indian parents to begin the germplasm development process. Key parental materials have been profiled with markers at PAU and DWR in India and at PBI in Australia. Populations segregating for markers were identified and screened using marker assisted selection for key genes in India. These materials were space planted in large populations and the lines positive for the target genes have been advanced for continued testing. Research Fellows have been identified and employed by DWR, although delays in finding the initial project payment delayed the appointment of the equivalent positions at PAU. Problems with money transfers to PAU have now been solved and future payments will arrive via courier.

While the molecular breeding work has progressed well following bureaucratic delays in the initial stages, the data management component of the initiative has failed to meet initial expectations. The International Crop Information System (ICIS) is the vehicle for data management and has been successfully installed at PBI although several IP security issues have impeded access (these have since been solved). The collaborators at NRCPB, the Indian mirror site for the project central database, have not installed ICIS since attending the ICIS developer's workshop in March. A visit by Graham McLaren planned in the later half of 2008 should kick-start this progress. The local breeders at PAU and DWR have compiled Excel spreadsheets of their parental and breeding materials related to the project and these will be uploaded into ICIS over the next month which will bring the breeding programs and local ICIS implementation back on schedule.

The marker implementation and breeding program modification components of the project are progressing well and marker assay numbers are steadily increasing with 8 - 10,000 assays performed on breeding program materials at both DWR and PAU in the past year. The Indian germplasm arrived in Australia late last year and DNA was extracted in quarantine and DArT analysis has been performed. Crosses have been made between Indian and Australian lines in quarantine at Cobbitty and F1 seed generated. Double haploids will be made on F2 plants positive for all target gene alleles. The Australian germplasm sent to India in the first year of the project has been crossed with Indian parents and progeny are under development. Key parental materials have been profiled with markers at PAU and DWR in India and at PBI in Australia. Populations segregating for markers were identified and screened using marker assisted selection for key genes in India. - this work continues as part of routine plant breeding at both Indian nodes. A full complement of Research Fellows has been employed on the project at DWR, PAU and NRCPB, although one has since moved to another position and will have to be replaced.
The molecular breeding work has progressed well and most milestones are no track after the delivery of the first shipment of Indian materials to Australian quarantine. The management of data using the International Crop Information System (ICIS) continues to lag behind scheduled milestones. However, significant ground has been made up in the past year. The ICIS central established at Cobbitty and the mirror site at NRCPB now contains project data. Local ICIS databases have been established at PAU and DWR and project materials have been entered. The breeding program at PAU is using ICIS as their primary pedigree management tool. DWR has entered most of their parental materials and will begin using ICIS to now generate nurseries and field books. Progress will be reviewed at an ICIS workshop of all project participants in June this year.

Molecular marker assays have continued to increase steadily over the past year. Initially, most assays were conducted on parental and to some extent, F1 materials. In the 2009/2010 season the vast majority of assays were conducted on segregating materials. The marker implementation labs at DWR and PAU produced approximately 15,000 assays in the 2009/2010 season which was less than the total number of assays planned. The capacity of both labs has been reached. Discussions are underway with ICAR to either increase the marker capacity through automated PCR at these locations or to provide cost-effective fee for service marker capacity. Recent progress in the development of SNPs has also complicated the decision as this marker system will be more efficient. However, there will be a significant lag in the development of an effective SNP platform and the costs of applying SNPs with remain high in the short to medium term.
The difficulty in moving DNA outside India has slowed the genotyping of new Indian materials using DArT. Discussions are underway with Triticarte and ICRISAT to provide this service in India. Once this service is in place it will be possible to genotype the full breadth of Indian wheat germplasm.
The Indo-Australian germplasm continues to be developed. Intermediate segregating generations have been harvested in India in the 2009/2010 season and fixed line progeny will be available by the end of the current project. Double haploids have been produced on the vanguard Indo-Australian crosses at Cobbitty and are being increased for distribution to India for planting in November. The gene profiles of F2 and BC1F2 progeny in the next wave of materials have been confirmed using markers and are under-going double haploid production at Cobbitty. It has been difficult to establish effective double haploid production in India. However, recent progress at PAU has resulted in the production of 300 haploid plants, many of which have been doubled over the past season.
The implementation of ICIS has progressed well at the local level since the last report. Local databases at DWR, PAU and PBI now contain germplasm lists, associated phenotypic data and molecular data. Data continues to be entered and incompatibility problems with up-dated versions of ICIS overcome. Nevertheless, the population of the central database at NRCPB has been slow. There is some data from each program (mainly parent lists, DArT profiles and marker data on parents) but little data on new materials. All three programs have made a commitment to use ICIS as their primary data management tool.

Molecular marker assays reached a plateau over the 2011/2012 season. The capacity of the local labs at both DWR and PAU to run marker assays is approximately 15,000 per year. However, the level of marker integration in the breeding programs at each node is reaching optimal levels and breeders at both Indian sites have become increasingly strategic in the use of markers; typical of maturing molecular breeding programs. Specific gene combinations are now being targeted with allele enrichment in the first segregating generations favourably skewing gene frequency. The development of SNP platforms has been rapid over the past year and ultimately the programs will move away from PCR and DArT to this more efficient marker system. In the short term this may be contracted on a fee for service basis and possible providers such as KBiosciences (UK) and an Australian/USA consortium have been approached. Implementation within the life of the current project will depend on cost per data point and agreement on the international transfer of DNA. The establishment of a DArT platform at ICRISAT raised in the last annual report has not been realized and this will not be an option for avoiding the international transfer of DNA.

The Indo-Australian germplasm continues to be developed in India and fixed lines are on target to be produced by the end of the project. A shipment of 1500 Indo-Australian SSD lines developed at Cobbitty has been prepared for shipment. New Indian import restrictions (the list of prohibited diseases has been increased and proof must be provided that the seed is disease free) have delayed the shipment. The seed is expected to arrive in India mid year and will be sown in the coming winter season. Approximately 1250 double haploid lines have been produced on the vanguard Indo-Australian crosses at Cobbitty. The top cross F2 plants selected for double haploid production were identified with molecular markers. It was decided to increase the seed once more before sending to India, thus providing sufficient seed to sow a plot at PBI, PAU and DWR in the coming winter seasons. While it has been difficult to establish effective double haploid production in India, the program at PAU has had some success and in 2010/11 double haploid lines were assessed in local yield trials in Punjab as were the initial outputs from the MAS program.

The ICIS database is now fully implemented at all nodes and used routinely to manage pedigrees and phenotypic data. While there is molecular data in the local ICIS databases the progress in entering these data has been slow due to the complexity of the GEMS/DMS interface. The process is now being modified by the software developers and we expect to move more molecular data into local ICIS databases in the near future. All local nodes have provided significant amounts of data to the central database at NRCPB. However, capacity problems have limited the upload into central (this is not related to hardware capacity as a new server has been dedicated to ICIS in New Delhi). The 32-bit MS Excel memory limit of 1GB of the algorithm written to speed up the loading of germplasm lists has been reach. Warren Constantino at IRRI is currently re-writing the algorithm and we expect to overcome the data backlog in June this year. Other projects with the wider Indo-Australian Molecular Breeding Program have provided trait data for upload into ICIS. Currently there is root and waterlogging trait data and associated pedigrees in ICIS with plans to expand the capture of these data across the Program in 2011/12.