TA feedback - INRA GTF
- COLONOAK New forests: using molecular approaches to assess colonization of abandoned agricultural surfaces by holm oak (Quercus ilex) - March-April 2014
Applicant: DBN Herbarium and Plant Molecular Laboratory, National Botanic Gardens of Ireland
Duration: May 2013 (10 days)
Feedback: Main scientific achievements: genotyping of more than 350 individuals using 8 chloroplast microsatellites and a set of nuclear microsatellites. These experiments will help us better understand population genetics and dynamics of scots pine cultivated, naturalised and putatively native populations in Ireland.
We still have to analyse the data in order to completely answer this question, in particular we will look for evidence of the presence of native population of scots pine in Ireland using population genetics parameters calculated based on the experiments' results.
This platform is a very intersting tool for population genetics of forest trees, enabling high-throughput analysis of microsatellites markers, med-to-high-throughput genotyping of SNPs and state of the art developments and expertise in Next-Generation-Sequencing. We were totally included in the team, all was very well explained on my arrival, and the team was there for any question/problem. The lab set-up is very welcoming and there is plenty of space for storing samples and to make the experiments.
Applicant: CREAF (Centre for Ecological and Applied Forestry, Spain)
Duration: 17 March - 25 April 2014
Feedback: My stay lasted 6 weeks and we planned the main tasks to be done each week to make sure that at the end of this period I had extracted the DNA from the Holm Oak leaves, developed the SNP markers and genotyped the samples.
I have been at all times supported by the site manager of the TA infrastructure and the rest of the people working at the INRA Genomics Transcriptomics Facility, France (GTF). This support has been crucial, as I had never developed Single Nucleotide Polymorphisms (SNPs); this is the first time that I have used them to genotype trees for parentage analyses. The technical support has been very good, with three technicians available for consulting on different issues of the development and identification of molecular markers, sample genotyping and interpretation of the results.Their expertise was essential to develop the DNA libraries, genotype the samples and learn how to use the different software needed to analyse and interpret the results. Without their support this project could not be carried out.