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Table 4 Summary of DNA polymorphism and diversity estimates in the about 1000 bp of 11 candidate genes

From: Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne

Parameters Entire region Non-coding Coding regions
    All sites Synonymous Non-synonymous
EST1 (bp) 949 33 916   
Indels (sites) 57 12 45   
SNP sites 107 0 107 25 82
Polymorphic sites in %a 12.0 0 12.3 12.0 12.6
θ/bpb 0.0297 0 0.0301   
Tajima's Db -0.0676ns - -0.0676ns   
EST6 (bp) 936 95 841   
Indels (sites) 67 0 67   
SNP sites 247 17 230 71c 137c
Polymorphic sites in % 28.4 17.9 29.7 40.3 22.0
θ/bp 0.0793 0.0553 0.0829   
Tajima's D -0.4662ns 0.0302ns -0.5024ns   
EST7 (bp) 1036 0 1036   
Indels (sites) 13   13   
SNP sites 277   277 57c 183c
Polymorphic sites in % 27.1   27.1 27.1 22.9
θ/bp 0.0791   0.0791   
Tajima's D -0.3672ns   -0.3672ns   
EST26 (bp) 1030 0 1030   
Indels (sites) 0   0   
SNP sites 16   16 6 10
Polymorphic sites in % 1.6   1.6 2.6 1.3
θ/bp 0.00365   0.00365 0.0060 0.0030
Tajima's D 0.0986ns   0.0986ns   
EST31 (bp) 943 0 943   
Indels (sites) 0   0   
SNP sites 20   20 0 20
Polymorphic sites in % 2.1   2.1 0 2.7
θ/bp 0.0050   0.0050 0 0.0064
Tajima's D 1.1385ns   1.1385ns   
EST45 (bp) 1056 309 747   
Indels (sites) 87 0 87   
SNP sites 258 91 167 32c 107c
Polymorphic sites in % 26.6 29.4 22.4 21.8 21.7
θ/bp 0.0756 0.0896 0.0691   
Tajima's D -0.4209ns -0.3269ns -0.4715ns   
EST13 (bp) 959 326 633   
Indels (sites) 9 5 4   
SNP sites 9 2 7 3 4
Polymorphic sites in % 0.9 6.2 1.1 2.2 0.8
θ/bp 0.0022 0.0015 0.0026 0.0051 0.0020
Tajima's D 0.8068ns 1.0927ns 0.5250ns   
EST24 (bp) 985 385 600   
Indels (sites) 11 7 4   
SNP sites 37 25 12 8 4
Polymorphic sites in % 3.8 6.6 2.0 6.1 0.9
θ/bp 0.0089 0.0160 0.0047 0.0144 0.0020
Tajima's D 1.1897ns 1.1556ns 1.0406ns   
EST28 (bp) 1019 398 621   
Indels (sites) 58 58 0   
SNP sites 63 33 30 20 10
Polymorphic sites in % 6.6 9.7 4.8 14.8 2.1
θ/bp 0.0154 0.0228 0.0114 0.0347 0.0049
Tajima's D 0.8363ns 1.3632ns 0.1900ns   
EST39 (bp) 977 257 720   
Indels (sites) 28 23 5   
SNP sites 52 13 39 24c 10c
Polymorphic sites in % 5.5 5.4 5.5 12.8 1.9
θ/bp 0.0130 0.0138 0.0138   
Tajima's D 2.1562* 0.9752ns 2.4360*   
EST40 (bp) 1085 371 712   
Indels (sites) 2 0 2   
SNP sites 9 2 7 1 6
Polymorphic sites in % 0.8 0.5 1.0 0.6 1.1
θ/bp 0.0020 0.0013 0.0023 0.0013 0.0027
Tajima's D -0.1300ns 1.2987ns -0.7024ns   
  1. a Polymorphic sites in percentage measured as polymorphic sites in the target region divided by the total nucleotides in the region excluding indels. Synonymous (non-synonymous) polymorphic sites in percentage measured as synonymous (non-synonymous) mutation sites divided by synonymous (non-synonymous) sites.
  2. b θ Watterson's estimator; π nucleotide diversity per site; D Tajimas's D: *, ** significant at P = 0.05 and 0.01 level; ns non-significant.
  3. c A number of synonymous and non-synonymous mutations were not included due to some codons with multiple and complex evolutionary path.