This is Denis Murphy again, from the University of Glamorgan, UK. 

Two main points I’d like to raise:

1. About genomics in general. Together with our international colleagues, we are working on several projects aimed at the annotation of whole genome sequences in a variety of plant species from the model Arabidopsis to large commercial crops such as oil palm. We are also trying to analyze the genomes of crop pathogens, such as the fungal Ganoderma spp that infect oil palm crops.

As I stated in my previous message (nr. 25), it is very important that we do not underestimate the difficulty in moving beyond the generation of raw sequence data to extracting truly accurate and useful information/knowledge from such data. For example, although the human genome was sequenced well over a decade ago and has since been the subject of billions of dollars of research, we are still at the very early stages of exploiting it for significant medical advances. In contrast, crop and livestock genomes are still being sequenced and the amount of research funding to analyze/exploit the data is tiny compared to the biomedical sector so we must be patient.

With next generation technologies it is now relatively straightforward to get BGI or one of the many private companies to sequence a given genome. However, the analysis of such data is quite another matter. Unfortunately we have recently seen several cases where genome sequences have been published in peer-reviewed journals where the annotation/analysis is far from robust. In too many cases, relatively out dated or poorly performing bioinformatics tools are used and the result is an analysis that is at best incomplete and at worst misleading. If such a basic method as gene annotation has yet to be perfected in a way that can be used widely in the community, we are surely a long way off from direct use of such tools in many developing country (DC) crops, especially so called ‘orphan crops’.

2. What is the present and future impacts of genomics? Genomics is already having a useful impact in some areas of breeding, especially in development of molecular markers. There are also other exciting tools like association genetics, targeting induced local lesions in genomes (TILLING) and phenomics that show great promise but have yet to impact much on DC crops. The small number of specific examples of genomics in practical DC applications mentioned so far in this conference underlies the fact that these are very much emerging technologies for the future. For this reason, it is essential that DC scientists and agronomists are trained in the nature and potential of genomics tools so that they can eventually apply them to their own crops in the longer term. I personally think that genomics could be a game changer in breeding – but not just yet.

Professor Denis J Murphy, 
University of Glamorgan, CF37 4AT, 
United Kingdom 
email: dmurphy2 (at) glam.ac.uk
website: http://staff.glam.ac.uk/users/184 
Google Scholar outputs: http://scholar.google.co.uk/citations?hl=en&user=GQc6wQsu-BkC

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