Genome Analysis

Genomics is the study of an organism's entire genome, from genetic mapping to entire genomic DNA sequencing. It generates genetic material and large datasets which are used for discovering new genes and for elucidating global mechanisms of gene organization and regulation.

Sequencing of crop genomes is the ultimate goal of current plant genomic projects. However the sequencing of giant and repetitive genomes such as wheat and barley is a challenge which requires world-wide coordinated efforts.

Our goal in the ACPFG is first to create and provide genetic material for genomics studies in cereals. We develop mutant populations, segregating populations for genetic mapping, and Bacterial Artificial Chromosome (BAC) libraries for map-based cloning and genome sequencing. For example, the construction of fine genetic maps and the screening of BAC libraries were essential steps in the discovery of new genes such as HvBot1, a key barley gene conferring tolerance to toxic levels of soil boron (Sutton et al., 2007).

Our second goal is to study the structure and behavior of wheat and barley genomes. The 17 Gb of wheat are organized in 3 homoeologous genomes, A, B and D, sharing a high level of similarity. The construction of physical map is based on BAC libraries specific for a chromosome (Dolezel et al., 2007) or for a diploid ancestral parent (Feuillet et al., 2008).

The barley diploid genome is about the same size as each of the three separate wheat genomes but it has a higher density genetic map, making it a good model. By linking the physical map to the fine genetic map, we also investigate the intensity and distribution of recombination events along wheat chromosomes for understanding the inheritance of genes during breeding.

Resources

Mutant populations

A barley cv Golden Promise transposon tagged population has been created by using transgenesis to incorporate the maize Ac and Ds elements into barley. Some 450 lines carrying one or more unique genomic insertions are available for screening.

Further insertional mutations can be generated through activation of Ds transposition by the Ac element. We additionally have available a small subset of lines in which the Ds element has been backcrossed in to the adapted cultivar Flagship.

An EMS-generated mutant TILLING population comprising around 5,000 families of barley cv Flagship has been generated. The TILLING methodology enables high-throughput genotyping to identify an allelic series of point mutations in a target gene. This is a powerful tool in the analysis of gene function.

In wheat we have generated three mutant populations:

  1. gamma-Halberd
  2. EMS_Halberd
  3. gamma-Bobwhite.

Segregated populations

Our work with segregated populations provides high resolution genetic maps:

  • Triticum durum wheat population with Matthew Reynolds at CIMMYT (Mexico)F4:6 lines of PI94628//SOOTY_9/RASCON_37
  • Triticum aestivum wheat population
    • Kukri x RAC875 (300 doubled haploid lines plus 3,000 RIL lines)
    • Kukri x Excalibur (300 doubled haploid lines plus 3,000 RIL lines)
    • Gladius x Drysdale (5,000 RIL lines)
  • Barley Hordeum vulgare with Chengdao Li at DAFWA (Perth), and Vlamingh x Buloke 327 doubled haploid lines

BAC libraries

Four BAC libraries were made at the ACPFG covering:

  • Phalaris coerulescens: 92,000 clones; average insert size 108 kb
  • Rye Secale cereale cv Blanco: 373,632 clones; Av insert size 131 Kb
  • Barley Hordeum vulgare
    • Clipper x Sahara 3771 DH134: 221,184 clones; Av insert size 120 kb
    • cv Morex: Hind III library of 268,800 clones, Av insert size 115 kb; BamHI library

Techniques

  • Genomic and BAC DNA extraction
  • Southern blots
  • Molecular markers
  • Genetic mapping
  • BAC library screening
  • Glasshouse work
  • Robotic platform: QPix2 and Biomek 3000
  • Genomics software: MapManager, Qgene, FPC

Funded projects

GRDC project no UMU00037 - International Wheat Genome Sequencing Consortium assembly of chromosome 7A, coll. Rudi Appels (Murdoch University, WA).

People

Prof Peter Langridge Dr Delphine Fleury Dr Bujun Shi Dr Bao-Lam Huynh Margaret Pallotta Anzu Okada Zahra Shoaei Patricia Warner Hui Zhou

External collaboration

INRA Clermont-Ferrand (France), SCRI Dundee (Scotland), IPK Gatersleben (Germany), Insitute of Botanics Olomouc (Czech Republic), UC Davis (USA), CIMMYT (Mexico)

Honours and PhD projects

Please contact delphine.fleury@acpfg.com.au

Publications

Dolezel, J., Kubalakova, M., Paux, E., Bartos, J., and Feuillet, C. (2007). Chromosome-based genomics in the cereals. Chromosome Res 15, 51-66.

Feuillet, C., Langridge, P., and Waugh, R. (2008). Cereal breeding takes a walk on the wild side. Trends Genet 24, 24-32.

Sutton, T., Baumann, U., Hayes, J., Collins, N., Shi, B., Schnurbusch, T., Hay, A., Mayo, G., Pallotta, M., Tester, M., and Langridge, P. (2007). Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318, 1446-1449.

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