Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes

Abstract

Large regions of genomic colinearity have been demonstrated among grass species by recombinational mapping, but the degree of chromosomal conservation at the sub-centimorgan level has not been extensively investigated. We cloned the rice and sorghum genes homologous to the sh2 locus of maize on bacterial artificial chromosomes (BACs), and observed that a homologue of the maize a1 gene was also present on each of these BACs. In sorghum, we found a direct duplication of a1 homologues separated by about 10 kb. In maize, sh2 and a1 are approximately 140 kb apart and transcribed in the same direction, with sh2 upstream of a1. In rice and sorghum, this arrangement is fully conserved. However, the sh2 and a1 homologues are separated by about 19 kb in both rice and sorghum. We found low-copy-number and repetitive DNAs between the sh2 and a1 homologues of sorghum and rice. The sh2 and a1 homologues cross-hybridized, but the repetitive DNA and most low-copy-number sequences between these genes did not. These results indicate that maize, sorghum, and rice have conserved gene order and composition in the sh2-a1 region, but have acquired extensive qualitative and quantitative differences in the sequences between these genes.

Figure 1

Restriction maps of regions containing sh2 and a1 homologues from maize, sorghum, and rice. Arrows indicate predicted transcripts and transcriptional orientations. Transcript sizes in sorghum and rice are approximations based on the analogous maize transcripts. The sorghum and rice maps are drawn to scale, while the gap in the maize map indicates about 100 kb of additional DNA not shown. Within the sorghum or rice maps, all sites for the mapped enzymes are indicated, except HpaI and NsiI sites in rice. The mapped segments in rice and sorghum are from central portions (32 kb and 45 kb, respectively) of the much larger (130 kb and 80 kb, respectively) BAC inserts. B, BamHI; C, ClaI; H, HpaI; N, NsiI; P, PacI; Pm, PmeI; S, SacI; Sn, SnaBI; X, XhoI.

Figure 2

Sequence confirmations and comparisons for the rice and sorghum homologues of the maize sh2 and a1 loci. Boxes indicate exons, relative to the maize genes, and vertical lines connect identical nucleotides. (A) sh2 comparisons, showing overlap between maize and sorghum (nt 1–394) and between maize and rice (nt 245–500). The different regions of overlap with the maize sequences are due to the different fragments sequenced in each species. (B) a1 comparisons, showing overlap between maize, sorghum, and rice (nt 1–600).

Figure 3

Organization of repetitive and conserved sequences in the sh2-a1 regions of sorghum and rice. The arrows above the bars indicate predicted transcripts, their orientations, and their approximate sizes. The fill indicates copy number, as determined by gel blot hybridization to total genomic DNA. The asterisks within the bars indicate fragments that cross-hybridized between these regions of the sorghum and rice BACs. The mapped segments in rice and sorghum are from central portions (30 kb and 45 kb, respectively) of the much larger (130 kb and 80 kb, respectively) BAC inserts. These maps have some different sites shown than does the map in Fig. 1. B, BamHI; C, ClaI; E, EcoRI; H, HindIII; M, MluI; N, NheI; Nc, NcoI; P, PmeI; S, SacI; Sn, SnaBI; V, EcoRV; X, XhoI.