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Table 1 Summary of DNA variation in nine genes involved in panicle development

From: Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice

Gene (bp) Group No. of nucleotide substitutions No. of INDELs π × 10−3 h Hd D
LAX1 (648) Total 1 0 0.76 2 0.491
  Indica 1 0 0.66 2 0.425
  Japonica 1 0 0.14 2 0.091
  Tong-il 1 0 0.62 2 0.400
APO1 (1299) Total 12 3 2.02 3 0.533 −0.146
  Indica 12 3 3.6 3 0.667 1.135
  Japonica 0 0
  Tong-il 2 1 0.62 2 0.400 −0.973
APO2 (1170) Total 13 0 4.83 3 0.536 2.755**
  Indica 13 0 4.33 3 0.602 1.329
  Japonica 0 0
  Tong-il 11 0 3.76 2 0.400 −1.200
DEP1 (1281) Total 19 1 2.78 9 0.723 −1.251
  Indica 9 0 2.38 7 0.854 0.647
  Japonica 11 1 1.49 3 0.267 −1.320
  Tong-il 6 0 2.03 3 0.700 −0.668
FON1 (2985) Total 14 0 2.05 6 0.764 2.820**
  Indica 6 0 0.99 4 0.731 2.321*
  Japonica 12 0 2 3 0.552 2.812**
  Tong-il 10 0 1.34 2 0.400 −1.193
GHD8 (903) Total 16 6 6.16 9 0.812 1.605
  Indica 15 6 4.07 7 0.866 −0.560
  Japonica 11 1 1.54 3 0.495 −1.920*
  Tong-il 11 3 7.13 3 0.800 1.527
GN1a (1706) Total 8 4 1.44 8 0.790 0.948
  Indica 5 2 0.98 6 0.801 0.526
  Japonica 6 3 1.26 4 0.557 0.895
  Tong-il 3 2 1.06 2 0.600 1.573
HD1 (1353) Total 12 9 4.04 9 0.771 3.105**
  Indica 10 8 3.07 6 0.760 1.503
  Japonica 11 4 4.11 4 0.686 3.050***
  Tong-il 12 4 4.08 3 0.700 −1.031
SP1 (1881) Total 20 3 2.11 7 0.679 −0.436
  Indica 7 0 1.33 4 0.696 0.756
  Japonica 17 3 2.44 5 0.538 −0.105
  Tong-il 3 0 0.65 2 0.400 −1.049
  1. S, Number of variable sites; π, Nucleotide diversity; h, Number of haplotypes; Hd, Haplotype diversity; D, Tajima’s D
  2. *, **, and ***, significant at p < 0.05, p < 0.01, and p < 0.001, respectively