International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)


A13. Expressed Sequence Tags (ESTs) as Universal Markers for Comparative Mapping

Yasushi Kondo,1 Dominique Simon-Chazottes,2 Andrew S. McCallion,3 Gregor J. Stewart,3 R. Wayne Davies,3 Gabor Gyapay,4 Tadao Serikawa5 and Jean-Louis Guénet2
1Advanced Medical Research Department, Tanabe Seiyaku Co., Ltd., Kashima 3-chomAe, Yodogawa-ku, Osaka 532-8505, Japan
2Unité de Génétique des Mammifères, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
3Laboratory of , Dumbarton road, Glasgow University, United Kingdom
4Genethon, 1 avenue de l'Internationale, 91000 Evry, France
5Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan

Simple Sequence Repeats (microsatellites) have greatly contributed to the rapid development of high density genetic maps in several mammalian species. These markers have several important advantages: i) they are abundant, ii) they are evenly distributed over the whole genome, iii) they are amenable to PCR technology; iv) finally, they exhibit a relatively high level of polymorphism within a given species when compared to other genomic sequences. In man and more recently in mouse and rat, the use of such molecular markers has greatly facilitated the establishment of very dense maps based on the use of cellular radiation hybrids. In the mouse, the use of inter-specific or inter-subspecific crosses and the possibility of breeding very large progeny has made possible the establishment of high density linkage maps with an average resolution as low as 0.1 cM. Unfortunately, microsatellite markers are relatively species specific and accordingly cannot be used reliably for comparative mapping.

To circumvent this species specificity other types of molecular markers, designed from transcribed sequences, have been used in an attempt at establishing landmarks for comparative mapping. These are for example the Comparative Anchor Tagged Sequences (or CATS) and the Traced Orthologous Amplified Sequences Tags (or TOASTs). Both these sequences have proven very useful and highly reliable but, unlike the microsatellites, they have the drawback of being poorly abundant and their value for comparative mapping thus appears limited.

Expressed Sequence Tags (or ESTs), which are single-pass sequences from the ends of cDNA clones, have been reported as potentially interesting molecular markers and, because they represent transcribed sequences with presumptive homology in other species, their potential value for comparative mapping has recently been demonstrated. ESTs are extremely abundant in the human and various rodent species (over 1,000,000 human EST and over 400,000 mouse ESTs are stored in the various databases).

We demonstrated that a substantial proportion of these ESTs can be used efficiently for the mapping of orthologous sequences and appear as highly valuable for the precise determination of synteny edges between man, mouse, rat and presumably many other species.


Abstracts * Officers * Bylaws * Application Form * Meeting Calendar * Contact Information * Home * Resources * News and Views * Membership

Base url http://imgs.org
Last modified: Saturday, November 3, 2012