The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4

Abstract

A 2.3-centimorgan (cM) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced, revealing the presence of 33 putative genes, including several apparently involved in disease resistance. Fourteen of the genes were confirmed by identifying the corresponding transcripts. Five genes, spanning 1.9 cM of the region, cross-hybridized with maize genomic DNA and were genetically mapped in maize, revealing a stretch of colinearity with maize chromosome 4. The Adh1 gene marked one significant interruption. This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. Several other genes, most notably genes similar to known disease resistance genes, showed no cross-hybridization with maize genomic DNA, suggesting sequence divergence or absence of these sequences in maize, which is in contrast to several other well-conserved genes, including Adh1 and Adh2. These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations. Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner-like element, which is new to rice. In contrast to maize, retroelements are less frequent in rice. Only 14.4% of this genome segment consist of retroelements. Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements, accounting for 18.8% of the total repetitive DNA.

Figure 1.

Genetic and Physical Map of Rice Chromosome 11S around the Adh1 and Adh2 Loci and Genetic Map of the Corresponding Regions of Maize Chromosomes 1 and 4. (A) Genetic map of rice 11S. Map positions of markers are shown in centimorgans (http://www.dna.affrc.go.jp:84/publicdata/geneticmap98/chr11pre.html). (B) Physical map of the 339,485-bp segment of rice 11S. Genes indicated in red have been genetically mapped on maize chromosome 4, as shown in (C). The RZ53 map position is from Ahn and Tanksley (1993). Genes shown in yellow do not cross-hybridize with maize genomic DNA. Blue indicates the Adh1 gene; its position on the genetic map of maize chromosome 1 has been inferred from published information (MaizeDB; http://www.agron.missouri.edu/). The gene indicated in white has not been hybridized with maize genomic DNA. MAPK, mitogen-activated protein kinase; PIK, phosphatidylinositol 4-kinase. (C) Segments of maize chromosomes 1 and 4 containing maize homologs of rice chromosome 11 genes identified in (B).

Figure 2.

Gene and Repetitive Element Map of the 339,485-bp Segment of Rice Chromosome 11S. Positions of genes reported in Table 1 and transposable/repetitive elements reported in Table 2 are shown. Arrows indicate direction of transcription. MITEs (Wessler et al., 1995) are indicated with colored stars. Different classes of MITEs are shown in different colors (R. Tarchini, unpublished results). NBS, nucleotide binding site.