CBN-V Video Archives - PS3-02
H.A.P.P.Y. Mapping: A Versatile, Universal and Inexpensive Genome Mapping Technique and Implications for Cassava Genome Mapping

Thangavelu M.¹, A.T. Bankier¹, H.F. Spriggs¹, B.A. Konfortov¹, J.A. Pachebat¹ and P. H Dear^1,2

1. Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH, U.K. www.mrc-lmb.cam.ac.uk

2. Cambridge Genomics Limited, 20 Park Crescent, London W1N 4AL, U.K.

Various genome mapping approaches and technologies have been developed and are being used for constructing DNA-marker linkage maps of plant and other genomes. Certain deficiencies with each of these currently available approaches means that many or most of these are unlikely to offer a realistic means for future large-scale mapping of plant and other agrigenomes. The ability to prepare DNA marker maps rapidly and in an efficient and cost-effective manner is, therefore, of considerable interest to researchers worldwide. HAPPY mapping is a simple, rapid, inexpensive, cloning-free, PCR-based procedure for defining the order and spacing of markers directly on native genomic DNA. The technique is based on analysing the co-segregation of markers amplified in limiting dilutions of randomly sheared high molecular weight genomic DNA. HAPPY mapping has been applied for high-resolution, error-free mapping in a set of phylogenetically diverse genomes including human, Tetraodon, Dictyostelium, and a menagerie of parasite genomes. HAPPY mapping is also being used to assemble the shotgun sequencing data of Cryptosporidium parvum and Dictyostelium discoideum genomes. The procedure has recently been extended for mapping plant chromosomes by reconstructing a HAPPY map of a 1.9 Mbp region around the FCA locus of Arabidopsis thaliana. Spanning around 10% of chromosome 4, and with mean marker spacings of approximately 16 kbp, the map showed excellent agreement both with the STS content of mapped BAC clones spanning this region and with the DNA sequence. Based on our results plants and other organisms we conclude that HAPPY mapping is a uniquely valuable addition to currently available plant genome mapping tools. On the basis of our current knowledge of plant genome architecture, we also argue that HAPPY maps can be made immediately and with little effort for most plant species and, further, that such maps can greatly aid the construction of genome-wide or regional physical maps. Finally, and more importantly, HAPPY mapping offers a unique opportunity to revisit issues in genome mapping and to reassess the hitherto impossible challenges of rapid, efficient and cost-effective mapping of plant and other agrigenomes. A thumbnail scenario for high-density mapping of the cassava genome is presented.