TABLE 2

Nucleotide diversities at Waxy and 12 flanking genes for O. sativa and O. rufipogon

Silent-site nucleotide diversity (π)
O. sativaO. rufipogon:
GeneaGenomic position (chromosome 6) (Mb)indica (N = 21)temperate japonica (N = 22)tropical japonica (N = 18)aus (N = 6)aromatic (N = 6)All sativa (N = 73)b(N = 9)
1. Hypothetical protein1.5220.002360.000600.002050.001470.000820.002470.00259
2. Hypothetical protein1.5650.002420.000000.000000.000000.000000.000710.00281
3. Receptor-like protein kinase1.6060.001410.000480.001410.000930.001490.001270.00093
4. Expressed protein1.6360.002000.000000.004460.000000.003870.002380.00473
5. Putative glycosyl hydrolase1.6880.002350.000800.003130.001330.000000.003510.00393
6. Hypothetical protein1.7200.000000.000340.001610.000000.003280.001120.00077
7. Waxy1.763–1.7680.005940.001090.000150.002790.003720.005590.02127
8. Transketolase1.8100.000000.000000.000000.000000.000000.000000.00089
9. Hypothetical protein1.8500.005640.001550.002620.000000.005700.008640.00891
10. Expressed protein1.8780.003710.000300.000370.004660.003330.004350.00589
11. Enolase1.9330.004310.004730.007550.001340.000000.009050.00281
12. Kinesin-like protein1.9800.003950.001820.000850.004070.000000.004740.00245
13. Putative ribosome-binding factor2.0200.001500.000190.000220.002190.000000.002030.00194
  • a Numbers refer to nomenclature in Figure 1.

  • b Includes O. sativa variety groups indica, temperate japonica, tropical japonica, aus, and aromatic.