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Three Things not to Ignore from PAG Asia

by
Kahlil Lawless
| Mar 20, 2013

It has been an excellent three days at PAG Asia, with inspirational talks and stories comthreeing out from around the region. First I would like to thank the organisers, and second, all the people I met and who took the time to chat with me. It has been great to see new techniques, how innovation is being applied to the challenging biology of diverse species, and the dogged determination with which the complex biology behind unique traits has been pieced together over years of research.

Digesting the barrage of information is a challenge, but as I mull things over, a few themes have fomented in my cerebrum out of the morass of statistics and ball-of-yarn synteny diagrams. I think that if these three lessons were all I took home from PAG Asia 2013, it would make it worthwhile. My suggestions of three things not to ignore:

  1. Don’t ignore the biology
  2. Don’t ignore the history
  3. Don’t ignore the environment  

    Don’t ignore the basic biology. Different organisms can vary hugely in the way basic cell biology functions, and this presents unexpected challenges for applying genomic tools. In Graham Moore’s presentation on the mechanisms of correct chromosome pairing in polyploidy wheat illustrates the complexity of these processes and how this can make introgression of QTL regions from diversified subspecies difficult. Recombination frequencies in meiosis can also vary by region and species, as shown in Simon Southerton’s work in Eucalypt trees where recombination is so frequent that LD can frequently break down between functional traits and markers in as little as 100 bp in a single generation, making identification and application of markers of breeding value very hard.

      Don’t ignore species history – learn from it. The genetic history of a species has a strong effect on the applicability of certain technologies and can govern the limits of potential gains from genomic selection. The work in rice presented by Bin Han shows how the segregation of markers evident in existing populations that already have a long history of selective breeding reveals loci with underlying genes or DNA elements that govern desirable agronomic traits that may not be easily identifiable using classical GWAS. This technique becomes especially useful in species where the variant frequency has been significantly reduced by extensive inbreeding.

        Don’t ignore the environment. Phenotypes in a real-world setting are always a subtle interplay between the genome and the environment. Understanding the diversity of environments in which your species exists can help in the search for traits of interest, and in being mindful of the response of genetic elements to different stimuli. Tim Sutton gave an insightful presentation about efforts to breed crops tolerant to high levels of boron, a common problem in Australian soils. Effective markers were found for boron tolerance in existing cultivars. However, these usually were associated with boron transporters with reduced efficiency, which when present in plants grown in low boron regions (also important growing regions) resulted in tissue boron deficiency, poor growth, and survivability. This is a classic example where understanding the mechanism through which a desirable trait can be conferred by genetic improvement can help when trying to foresee limitations or undesirable side effects that may arise from how the trait responds to a different environment, and therefore deploy our breeding resources appropriately. When undertaking programmes of discovery and application for genetic improvements of agriculturally important species, having an understanding the spectrum of environments under which the available subspecies of interest exist acts as a powerful guide for selecting germplasm for phenotypic screening and maximising the chances of identifying strong quantitative genetic traits that can be applied appropriately in our existing agricultural landscape.

          Of course this doesn’t cover all the interesting topics and insights that came through from the conference. The talk by Si Lok from the Hong Kong Centre for Genomic Sciences was music to my ears. So often you don’t see the technical skill and dedication that goes into generating these vast datasets, but Si Lok made a point of detailing how good labs do good research, and the underlying motivators for these behaviours. His mantra “QA/QC is a lifestyle” was drummed out, and interestingly, he claims this leads to greater harmony in his lab. This stems from the psychology that technicians are stressed if they fear what they are doing may fail and they could be held accountable. Those of us familiar with the wet lab know this feeling, but as he explains, if the protocol is clear, robust, and followed to the letter, then the technician is free from suspicion should any issues arise. After all, says Si Lok, “Collaborative NGS research should be fun”.
          I also found the presentations from Dave Edwards and Jacqui Batley from University of Queensland on applications of skim GBS in mapping crosses using SGSAutoSNP quite exciting.  Not only is this a powerful and flexible new approach to mapping in species where the genomic references are poor or absent, the data generated enable structural validation of existing references, and picks up a fair number of assembly mistakes in the process. In an era where the options for whole genome structural analysis are expanding, this is an excellent informatics tool that doesn’t require any additional hardware investment for those already in possession of Illumina sequencing technology

          Hopefully this is just the beginning for PAGAsia, and we're excited to see it return bigger and better in 2014!

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