Notes from ETNA Summer School 2010
This year ETNA Summer School is jointly organized by Joint Genomic Centre (JGC) and AgroBioInstitute (ABI) which are located at the Department of Biology in Sofia University. After a tour around the facilities, we were given an interesting introduction about the research interests in Bulgaria. Besides rose oil and grapewine(and Black Sea!), this country has a lot more economically important areas. ABI also focused on important crop such as wheat, barley, berries, lactic acid bacteria, thermophile bacteria, honey bee, medicinal herbs, and animal breeding.
The first day is followed by 10 presentations. Most plant-specific talks focused on grapevine genomics and breeding. A plant totally unfamiliar to me. Grapevine or vitis vinifera is grown for wine and table grapes. Wine yard covers 59% of Europe. It’s a perennial crop, grafted and high in genetic diversity, Quality of wine is greatly influenced by environment . The sugar content in the grape is important for fermentation. Although the genome sequences are available, many genes are still unknown and unannotated. Many are unique to the grapevine. It's a highly heterozygous plant. Difficult transformation. It’s an ancient allopolyploid before going through diploidization 2(6+6+7)=38. However, the American grapewine (such as Muscadinia) contains 40 chromosomes. The studies focused on disease resistant, cold or drought tolerant, budding responses and berry development using a combination of transcriptomic (mainly using microarray) and metabolomics.
Metabolomic is an important component of this course. Something new to me. The participants were introduced to basic concepts of metabolomics, sample preparation, detection using GC-MS and most importantly analysing metabolomic data using bioinformatics tools. Every metabolite profile is closely associated to phenotype. For example, different developmental stages of grapewine berry has different concentration of compounds. Metobolomic helps scientists to link the change of metabolites to phenotype such as taste or colour. It's interesting how metabolomic can be integrated with transcriptomic data to produce more biological significant results.
The most interesting talk is epigenetics in plant breeding presented by Prof. Atanasios Tsaftaris. First, he explained the methylation and histone modification mechanisms and some classical examples of plant epigenetics. Epi- means "above" so epigenetics means "above genetics". It's genetics that doesn't follow Mendel's law. I also learn Genetics Imprinting - Expression of only one allele from the parents due to suppression of the other allele caused by methylation. It's now known that epigenetics play an important role in sensing the environment, control of flowering time and seed development. It is also the cause of somaclonal variation in plant tissue culture and why clones in the field don't perform the same. Two years ago, a Nature paper about Arabidopsis epigenome was published but one can't truly appreciate that paper until he/she understand epigenetics and its implication in plant biology. Read this paper!
This summer school has provided me great opportunity to interact with researchers and students. The topic about funding problem was brought up during coffee break. Research funding has been reduced due to economic crisis and I believed it happens everywhere. The grant application criteria in every country are different. In Europe, there's national and EU funding. A national funding is supported by the government. In the Netherlands, the project must be supported by a few private companies before getting grant approval from government. To secure a EU funding, the project must involve two or more countries with a common research interest. In Malaysia, almost all research funding came from the government. Compared to Bulgaria, Malaysia government or universities have been very supportive to postgrad students by providing scholarship and tuition fees waiver. Now I finally have to agree that we have lots of funding and opportunities in Malaysia. It's up to the Malaysian researchers' initiative and creativity to make use of the available resources. So this is one BIG take home message that I wanna tell my colleagues.
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