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

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.

Figure 1.

A linear representation of the gene content and organization of the (A) region containing the barley Ha locus and its (B) colinear rice region. Coding sequence is represented by colored boxes, and arrows designate gene orientation. Repetitive sequence is represented by shaded boxes. MITEs are indicted by a vertical bar. tRNA are indicated by double arrowheads.

Figure 2.

Stacked representation of the genome organization of the region containing the Ha locus in barley. Arrows directly on the “base” sequence represent putative genes; designation can be seen in Figure 1. Arrows above and below the base sequence represent the position, orientation, and order of insertion of various transposable elements. Vertical bars illustrate MITES.

Figure 3.

A visual representation of one possible evolutionary scheme between the rice and barley colinear sequences. Evolutionary events move upwards toward present day rice (A and B) and downward toward present day barley (C–I) from the presumed last common ancestor. C, An intra-chromosomal rearrangement results in the repositioning of two conserved gene clusters. D, Translocation involves the relocation of CHS. E to G, Subsequent duplications and a gene inversion generate the individual grain texture genes. A and B, H to I, Independent gene duplications and inversions generate numerous copies of ATPase in both species. The two severely degenerate copies of barley ATPase are not present in this scheme.

Figure 4.

Structure of the genes located within the barley contig, the colinear rice region, and their closest Arabidopsis homologs (also see Table I). Intron phase is indicated by the number above each intron.