Nucleotide polymorphism in the Adh1 locus region of the wild rice Oryza rufipogon

Abstract

Nucleotide variation in the alcohol dehydrogenase (Adh1) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species. The estimated nucleotide diversity in the Adh1 locus region of O. rufipogon was 0.002, which was one of the lowest values detected in nuclear loci of plant species investigated so far. Tests of neutrality detected significantly negative deviation from the neutral mutation model for the coding region, especially for replacement sites. When each of the ADH1 domains was considered, significance was detected only for the catalytic domain 1. These results suggest purifying selection in the Adh1 coding region. In the phylogenetic tree of Oryza species based on Adh1 variation, cultivated rice O. sativa subspp. japonica and indica were included in the cluster of O. rufipogon. The genetic distance of the Adh1 region between O. rufipogon and O. sativa was as low as the nucleotide diversity of O. rufipogon. These results imply that O. rufipogon and O. sativa cannot be classified based on the nucleotide variation of Adh1. No replacement divergence between O. rufipogon and the other three A-genome species (O. glumaepatula, O. barthii and O. meridionalis) were detected, indicating that ADH1 is conserved in the A-genome species. On the other hand, between O. rufipogon and the E-genome species O. australiensis, replacement changes were detected only in the catalytic domain 1. The difference in replacement substitutions between the A- and E-genome species may be related to adaptive changes in the ADH1 domains, reflecting environmental differences where the species encounter anaerobic stress.

DNA polymorphism in the blast disease resistance gene Pita of the wild rice Oryza rufipogon and its related species

“…The Pita sequences of O. meridionalis were determined by two independent sequencing experiments. The present findings were inconsistent with a prior phylogenetic tree based not only on sequence variations in Adh1 and Adh2 (Yoshida et al, 2004;Yoshida and Miyashita, 2005), but also on RFLP, RAPD (Ishii et al, 1996;Bautista et al, 2001), and SINE insertion polymorphisms (Cheng et al, 2002), which sug- (Supplementary fig. 2).…”

“…The shape of the tree within the sequence type A was star-like. These results supported the hypothesis that O. rufipogon recently expanded into tropical and subtropical regions (Barbier et al, 1991;Yoshida et al, 2004;Miyashita et al, 2005;Yoshida and Miyashita, 2005).…”

“…Therefore, we employed the amino acid distance analysis of Miyata et al (1979) to estimate whether the observed nucleotide differences between O. rufipogon and O. officinalis at replacement sites of Pita could be related to physicochemical differences. The analysis revealed that the number of nonconserved amino acid differences in the Pita was 73, which was 52% of the total number of amino acid differences in the Pita (Supplementary table 2 (Yoshida et al, 2004;Miyashita et al, 2005;Yoshida and Miyashita, 2005). As observed in the Adh2 and 10 nuclear loci (Tang et al, 2006), a dimorphic pattern was also detected in O. rufipogon Pita.…”

The Evolution of Sex-Independent Transmission Ratio Distortion Involving Multiple Allelic Interactions at a Single Locus in Rice

“…(C133A) for u w , and from 6.75 3 10 À3 (P139) to 8.66 3 10 À3 (F06) for p, which is comparable to the values for the nucleotide diversity previously reported in nuclear genes of rice (Yoshida et al 2004; Zhu et al 2007). At these five loci, the estimates of u w and p were lower in the S 6 and S 6 a carriers than those in the S 6 n carriers (Table 3 and Figure 4B).…”

Comparative Analysis of Rice Genome Sequence to Understand the Molecular Basis of Genome Evolution

“…Ge et al [8] were the first to sequence two genes (Adh1 and Adh2) from 31 accessions representing all 23 rice species; they reported the phylogenetic relationships among the different Oryza species that are determined from the sequence polymorphisms. Yoshida et al [44,45] have investigated the nucleotide diversity in the Adh1 and Adh2 gene regions of O. rufipogon in order to clarify the mechanisms by which DNA variation is maintained.…”