Gene identification in a complex chromosomal continuum by local genomic cross-referencing

Zoya Avramova, Alexander Tikhonov, Phillip SanMiguel, Young Kwan Jin, Changnong Liu, Sung Sick Woo, Rod A. Wing, Jeffrey L. Bennetzen

Research output: Contribution to journalArticlepeer-review

50 Scopus citations

Abstract

Most higher plants have complex genomes containing large quantities of repetitive DNA interspersed with low-copy-number sequences. Many of these repetitive DNAs are mobile and have homology to RNAs in various cell types. This can make it difficult to identify the genes in a long chromosomal continuum. It was decided to use genic sequence conservation and grass genome co-linearity as tools for gens identification. A bacterial artificial chromosome (BAC) 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 contiguous 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, while one that did not was found to be a low-copy-number retrotransposon that was named Reina. Regions of cross-hybridization were co-linear between the two genomes, but closer together in the smaller sorghum genome. These results indicate that local genomic cross-referencing by hybridization of orthologous clones can be an efficient and rapid technique for gene identification and studies of genome organization.
Original languageEnglish (US)
JournalPlant Journal
Volume10
Issue number6
DOIs
StatePublished - Jan 1 1996
Externally publishedYes

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