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

• Published in: The Plant journal : for cell and molecular biology 1996-12, Vol.10 (6), p.1163-1168
• Main Authors: Avramova, Zoya, Tikhonov, Alexander, SanMiguel, Phillip, Jin, Young‐Kwan, Liu, Changnong, Woo, Sung‐Sick, Wing, Rod A., Bennetzen, Jeffrey L.
• Format: Article
• Language: English
• Subjects: Alcohol Dehydrogenase - genetics; Amino Acid Sequence; Base Sequence; Biological and medical sciences; Chromosome Mapping - methods; Cloning, Molecular - methods; Conserved Sequence; DNA, Plant - genetics; Fundamental and applied biological sciences. Psychology; Genes, Plant; Genes. Genome; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Nucleic Acid Hybridization; Oryza - genetics; Poaceae - genetics; Repetitive Sequences, Nucleic Acid - genetics; Retroelements - genetics; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Sorghum; Species Specificity; Zea mays; Zea mays - genetics
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1046/j.1365-313X.1996.10061163.x

Summary 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 gene 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.