Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice

Katherine S Caldwell, Peter Langridge, Wayne Powell

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

The ancestral shared synteny concept has been advocated as an approach to positionally clone genes from complex genomes. However, the unified grass genome model and the study of grasses as a single syntenic genome is a topic of considerable controversy. Hence, more quantitative studies of cereal colinearity at the sequence level are required. This study compared a contiguous 300-kb sequence of the barley (Hordeum vulgare) genome with the colinear region in rice (Oryza sativa). The barley sequence harbors genes involved in endosperm texture, which may be the subject of distinctive evolutionary forces and is located at the extreme telomeric end of the short arm of chromosome 5H. Comparative sequence analysis revealed the presence of five orthologous genes and a complex, postspeciation evolutionary history involving small chromosomal rearrangements, a translocation, numerous gene duplications, and extensive transposon insertion. Discrepancies in gene content and microcolinearity indicate that caution should be exercised in the use of rice as a surrogate for map-based cloning of genes from large genome cereals such as barley.

Original languageEnglish
Pages (from-to)3177-90
Number of pages14
JournalPlant Physiology
Volume136
Issue number2
DOIs
Publication statusPrint publication - Oct 2004
Externally publishedYes

Fingerprint

Hardness
Hordeum
Sequence Analysis
Genome
Genes
Poaceae
Synteny
Endosperm
Gene Duplication
Organism Cloning
Clone Cells
Chromosomes
History
Oryza
Edible Grain

Keywords

  • Arabidopsis/genetics
  • Chromosomes, Artificial, Bacterial
  • Contig Mapping
  • DNA Transposable Elements
  • DNA, Intergenic
  • Evolution, Molecular
  • Gene Expression Regulation, Plant
  • Genes, Plant/genetics
  • Genome, Plant
  • Hordeum/genetics
  • Molecular Sequence Data
  • Oryza/genetics

Cite this

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abstract = "The ancestral shared synteny concept has been advocated as an approach to positionally clone genes from complex genomes. However, the unified grass genome model and the study of grasses as a single syntenic genome is a topic of considerable controversy. Hence, more quantitative studies of cereal colinearity at the sequence level are required. This study compared a contiguous 300-kb sequence of the barley (Hordeum vulgare) genome with the colinear region in rice (Oryza sativa). The barley sequence harbors genes involved in endosperm texture, which may be the subject of distinctive evolutionary forces and is located at the extreme telomeric end of the short arm of chromosome 5H. Comparative sequence analysis revealed the presence of five orthologous genes and a complex, postspeciation evolutionary history involving small chromosomal rearrangements, a translocation, numerous gene duplications, and extensive transposon insertion. Discrepancies in gene content and microcolinearity indicate that caution should be exercised in the use of rice as a surrogate for map-based cloning of genes from large genome cereals such as barley.",
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Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. / Caldwell, Katherine S; Langridge, Peter; Powell, Wayne.

In: Plant Physiology, Vol. 136, No. 2, 10.2004, p. 3177-90.

Research output: Contribution to journalArticle

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