Comparative DNA sequence analysis of wheat and rice genomes

Abstract

The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions.

Figure 1

Rice–wheat genome relationships. Rice genome view showing the wheat chromosome arm location for the most similar wheat gene sequences. Each colored box represents a rice–wheat gene sequence match at ≥ 80% identity. When the wheat EST mapped to more than one wheat chromosome, the other color-coded locations are positioned adjacent to the first. Homologous wheat chromosome locations are grouped together. Rice BAC/PAC sequences that did not match any wheat sequence as well as redundant matches are omitted. The rice centromere location is indicated by `C'.

Figure 2

Wheat–rice genome relationships. (Left) The wheat C-banding karyotype indicating the positions of deletion breakpoints. (Right) Each deletion bin is color-coded according to the rice chromosome matching a significant number (χ² P < 0.01) of wheat ESTs mapped to that bin. The number of those matches is indicated inside the colored rectangle, and the number of matches to all other rice chromosomes is adjacent. Nonsignificant association with a rice chromosome or insufficient data is indicated by “ns” adjacent to the bin.

Figure 3

Diagrammatic representation of earlier RFLP-based comparative maps (Kurata et al. 1994; Van Deynze et al. 1995c; Sarma et al. 2000) for the rice and wheat genomes. The seven homologous wheat chromosome groups are color-coded by wheat chromosome for comparison with Fig. 1. The overlaid boxes represent the predicted homologous rice chromosome region delineated by anchor loci and are color-coded by rice chromosome for comparison with Fig. 2.