Aims to:

Identify new sources of resistance to a range of sugarcane and sorghum diseases by:

• Identifying candidate genes for pest and disease resistance in sugarcane and sorghum
• Constructing an EST library from sugarcane, and identifying putative defence-related ESTs
• Producing resistance gene analogues from sorghum and sugarcane, using primers to conserved regions of different classes of resistance genes, and by screening sugarcane EST libraries
• Determining the genetic linkage map location of ESTs and RGAs, and identifying genes that map to known resistance gene loci
• Investigating the use of candidate genes as perfect markers for marker assisted selection in sugarcane and sorghum
• Providing ESTs or RGAs for further characterisation using in vitro and in vivo techniques, and for use as transgenes for crop improvement (Sub-Project: "Sugarcane resistance gene function")

 Where we're at:

CRC for Tropical Plant Protection funding for this project ceased at 30 June 2002. Research outcomes from this project have been transferred to the BSES sugarcane and the DPIQ sorghum breeding programs. Genes for resistance to major pathogens identified in sugarcane have been transferred to Sub-Project: "Sugarcane resistance gene function"

• Approximately 400 clones were generated from sugarcane stem, root and leaf tissue RNA using primers designed in Sub-Project 2.4b to conserved RGA motifs, and sequenced, revealing approximately 160 putative RGAs. In addition, the CSIRO/SRDC sugarcane EST collection was also searched for RGA sequences, and 15 additional RGA sequences were identified. Cluster analysis using the nucleotide sequence of all of these RGAs identified 55 unique RGA contigs.
• RGAs from the EST collection, and sugarcane stem, leaf and root tissue RNA were mapped in sorghum and sugarcane. Representatives of 44 of the 55 RGA contigs were screened over the eight parents of the three sorghum and one sugarcane mapping populations:
  • At least one polymorphic probe-enzyme combination was identified for 35 of the 44 RGAs between the parents of the sugarcane mapping population. Of these, 31 gave scorable results over the entire population, generating 77 markers, and this information has been incorporated into our sugarcane map.
  • Thirty-one (31) RGAs were mapped in our major reference sorghum population, generating 37 markers. Results have been incorporated into the sorghum map.
  • There are 23 RGAs in common between the two maps.
• Sorghum mapping populations were scored for rust, leaf blight and sorghum midge resistance. Two RGAs co-locate to QTL for rust resistance. One of the RGAs is homologous to the maize rust resistance gene Rp1-D, and it maps to the major rust resistance QTL in sorghum. Primers were designed to the Rp1-D homologue and used to amplify this region from resistant and susceptible sorghum progeny. Five different sequences were isolated with three sequence classes only found in resistant progeny, and two sequence classes only found in susceptible progeny.In collaboration with Sub-Project: "Sugarcane resistance gene function", a full-length clone of one of the rust resistance homologues has been isolated and sequenced.
• These sequences were compared with the maize rust resistance gene and recently published sorghum homologues from the same chromosomal region in a different sorghum variety:
  • the maize gene clustered with one of the resistance progeny sequence classes
  • the other two resistance progeny sequence classes clustered together
  • the three published sorghum homologues clustered with the two susceptible progeny sequence classes.
  These results suggest that the published sorghum homologues are derived from a less resistant version of this major sorghum rust resistance QTL.
• The sugarcane mapping population was scored for common rust and Pachymetra resistance. Seven of the RGAs showed significant association with common rust resistance in sugarcane, with three of the seven associated over two years of data. One sugarcane RGA has a strong homology to a known rust resistance gene in maize, Rp1-D.

Scientific Highlights:

• Identification of twelve unique RGAs from the CSIRO sugarcane stem EST collection of 5500 unique clones.
• Fifty-five (55) putative RGAs revealed from approximately 400 clones generated and sequenced from sugarcane stem, leaf and root tissue RNA.
• Map locations have been determined for:
  • 31 RGAs in sugarcane, generating 77 markers
  • 31 RGAs in sorghum, generating 37 markers
  • 23 RGAs are common to sugarcane and sorghum
• Seven RGAs significantly associated with rust and Pachymetra resistance have been found with one year’s data, including one RGA with strong homology to a known maize rust resistance gene (Rp1-D). Using two years phenotypic data:
  • no RGAs were significantly associated with Pachymetra resistance over both years;
  • only 3 of the 7 RGAs were significantly associated with rust resistance.
• Our sorghum mapping populations have been scored for rust, leaf blight and sorghum midge resistance. Two RGAs co-locate to quantitative trait loci (QTL) for rust. One RGA co-locates to a major rust resistance QTL in sorghum. This RGA has strong homology to a know rust resistance gene in maize, Rp1-D.
  • Partial homologues of the RGA were isolated from pools of resistant and susceptible sorghum from a sorghum mapping population.
  • Three sequence classes were isolated from the resistant progeny, and two different sequence classes were isolated from the susceptible progeny; there were no sequences in common between the two progeny pools.
  • All five sequence classes were shown to map to the same location as the RGA.
  • Sequence comparison of these five sequence classes with recently published sorghum sequences and the maize rust resistance gene homologue clusters the maize rust resistance gene with one of the resistant progeny sequence classes. The other published sorghum sequences cluster with the susceptible progeny sequence classes.

Industry Outcomes:

• Perfect markers for rust resistance in sugarcane and sorghum are available to the BSES sugarcane and the DPIQ sorghum breeding programs.
• Genes for resistance to major pathogens identified in sugarcane may be used in genetic engineering of elite varieties.
• RC-based markers have been developed for efficient identification of rust resistance QTLs in sorghum.

For more information contact:

Dr Lynne McIntyre
CSIRO
Phone: +61 (0)7 3214 2321
Email: Lynne.McIntyre@csiro.au