Proceedings of the XLVI Italian Society of Agricultural Genetics - SIGA Annual Congress

Giardini Naxos, Italy - 18/21 September, 2002

ISBN 88-900622-3-1

Poster Abstract - 4.14

A SYNTENIC APPROACH TO GENE ISOLATION IN MAIZE

PERINI D., GALLAVOTTI A., GATTI E., GIANFRANCESCHI L., SARI GORLA M.

Dipartimento di Genetica e di Biologia dei Microrganismi, Università degli Studi di Milano

male-sterility, pollen, synteny, EST, maize

Recently, a maize gametophytic pollen mutant, GaMS1 (Gametophytic Male Sterile1) has been localized on the short arm of chromosome 2, bin 2.04, and the region containing the mutated genes was restricted to a 0.8 cM interval, delimited by several molecular markers.

Initially, a map-based cloning strategy was adopted to isolate the gene but, due to the lack of molecular markers closer to GaMS1 and to the presence of highly repetitive sequences in this genomic region, we had difficulties in ordering the isolated BAC clones and building the contig of overlapping clones to reconstruct the genomic region of interest.

In order to bypass such obstacles we switched to an alternative strategy, taking advantage of the large amount of information derived from the rice genome sequencing project, which is presently being completed.

We adopted an in silico approach to identify rice sequences homologous to the GaMS1 flanking markers. A BAC contig, mapping on rice chromosome 4, was identified, which contains sequences with high homology to the maize ESTs mapping in the GaMS1 region. Thanks to the availability of a high density map of GaMS1 region and to the physical map of the corresponding rice chromosome area, we could identify a well conserved microscale colinearity between the region on maize chromosome 2 and a portion of the long arm of rice chromosome 4.

To fully exploit the advantages offered by the availability of the complete rice genomic sequence and gene annotation, we compared the rice ESTs present in the contig to identify maize orthologous ESTs –still unmapped– available in the sequence databases. Several homologues genes have been identified and the corresponding maize genomic sequences have been amplified, cloned and sequenced to identify polymorphisms between the parental lines of the segregating population used during the fine mapping of GaMS1. At present some of these ESTs are being mapped to check their position in maize, to confirm the micro syntheny between those two genomic regions and to restrict even further the region containing the mutated gene responsible for the pollen sterile phenotype.