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


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)
Pages (from-to)1163-1168
Number of pages6
JournalPlant Journal
Issue number6
StatePublished - Dec 1996

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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