GENE IDENTIFICATION IN A COMPLEX CHROMOSOMAL CONTINUUM BY LOCAL GENOMIC CROSS-REFERENCING

Most higher plants have complex genomes containing large quantities of repetitive DNA interspersed with low-copy-number sequences. Many of t hese repetitive DNAs are mobile and have homology to RNAs in various c ell types. This can make it difficult to identify the genes in a long chromosomal continuum. It was decided to use genic sequence conservati on and grass genome co-linearity as tools for gene identification. A b acterial artificial chromosome (BAG) clone containing sorghum genomic DNA was selected using a maize Adh1 probe. The 165 kb sorghum BAC was tested for hybridization to a set of clones representing the contiguou s 280 kb of DNA flanking maize Adh1. None of the repetitive maize DNAs hybridized, but most of the low-copy-number sequences did. A low-copy -number sequence that did cross-hybridize was found to be a gene, whil e one that did not was found to be a low-copy-number retrotransposon t hat was named Reina. Regions of crosshybridization were co-linear betw een the two genomes, but closer together in the smaller sorghum genome . These results indicate that local genomic cross-referencing by hybri dization of orthologous clones can be an efficient and rapid technique for gene identification and studies of genome organization.