Presentation is loading. Please wait.

Presentation is loading. Please wait.

Christopher Roberts Supervisor: Dr. Luis Mur (former IBS) and Dr. Ian Armstead (formerly IGER) Institute of Biological, Environmental.

Similar presentations


Presentation on theme: "Christopher Roberts Supervisor: Dr. Luis Mur (former IBS) and Dr. Ian Armstead (formerly IGER) Institute of Biological, Environmental."— Presentation transcript:

1 Christopher Roberts Supervisor: Dr. Luis Mur (former IBS) and Dr. Ian Armstead (formerly IGER) Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Introduction In spite of evolutionary divergence and the pressures of domestication, there’s been a noticeable conservation of genetic synteny between related plant species. From the angles of both evolutionary genetics and plant breeding, there’s been considerable interest in defining these interrelationships. Comparative studies will continue to be of great use in transferring information from the model species to the crop species, as physically ordered complete genome sequence are only available for rice (Oryza sativa) and Arabidopsis thaliana, both of which have relatively small genomes. Using rice as an anchor, DNA sequences from both crop and model species can be aligned with the annotated rice pseudomolecules, creating heat maps (Armstead et al 2007) ‘Hot spots’ within the genomes may be revealed where gene sequences are well or poorly conserved between species, making it possible to establish an overall picture of gene similarities, and observe where genes with differing levels of conservation are clustered. The wild grass species Brachypodium distachyon has recently gained favor as a new model system for grass crop genomics research because it possesses a suite of biological traits desired in a model system. It has a small genome (380 Mbp), low degree of repetitive DNA, availability of diploid ecotypes, self fertility promoting inbreeding, transformability, small stature, and a moderately rapid life cycle. (Garvin et al 2008) The aim of this project was to compare the genomes of Rice and Brachapodium, developing heat maps based on array intensity scores obtained from Rice Affymetrix microarrays probed with genomic DNA from Brachypodium accessions Bd21 and Bd3-1, produced as part of their on going Brachypodium project by the Mur Group collaborated with Nottingham Arabidopsis Stock Centre (NASC). Materials and Method Sequence alignments were performed using standalone MegaBLAST obtained from NCBI, BLAST FTP site (ftp://ftp.ncbi.nih.gov/blast/executables/release/) with default settings except for a window size of 16 (-W 16), maximum expectation value of 1 × (-e 1e-010) and alignment output (-D 3). Colour coded moving windows (MWs) of 100 genes along each pseudomolecule where used (in Excel) to generate the ‘heat maps’ consisting of 10 colours (blue


Download ppt "Christopher Roberts Supervisor: Dr. Luis Mur (former IBS) and Dr. Ian Armstead (formerly IGER) Institute of Biological, Environmental."

Similar presentations


Ads by Google