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Table 3 Genomic estimates of narrow-sense heritabilities (h 2) and predictive abilities (r gy ) for the E. benthamii and E. pellita breeding populations using different SNP sampling methods

From: Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus

SNP sampling method

E. benthamii

E. pellita

Number of SNPs

DBH

WV

Number of SNPs

DBH

HT

WV

h 2 (SE)

r gy (SE)

h 2 (SE)

r gy (SE)

h 2 (SE)

r gy (SE)

h 2 (SE)

r gy (SE)

h 2 (SE)

r gy (SE)

All SNPs

13,787

0.267 (0.008)

0.162 (0.044)

0.243 (0.008)

0.146 (0.039)

19,506

0.455 (0.005)

0.441 (0.019)

0.283 (0.008)

0.342 (0.042)

0.418 (0.005)

0.425 (0.028)

Randomly selected

5000

0.250 (0.003)

0.163 (0.004)

0.234 (0.003)

0.148 (0.004)

5000

0.410 (0.006)

0.427 (0.003)

0.269 (0.003)

0.336 (0.002)

0.390 (0.004)

0.416 (0.003)

Randomly selected

3000

0.239 (0.005)

0.153 (0.008)

0.226 (0.004)

0.137 (0.008)

3000

0.385 (0.006)

0.417 (0.003)

0.254 (0.005)

0.328 (0.003)

0.363 (0.006)

0.406 (0.003)

Randomly selected

1500

0.229 (0.005)

0.153 (0.008)

0.217 (0.005)

0.137 (0.008)

1500

0.334 (0.005)

0.397 (0.003)

0.232 (0.004)

0.313 (0.003)

0.322 (0.004)

0.389 (0.003)

Randomly selected

500

0.181 (0.006)

0.104 (0.017)

0.174 (0.005)

0.091 (0.015)

500

0.270 (0.008)

0.364 (0.006)

0.203 (0.003)

0.291 (0.006)

0.264 (0.008)

0.361 (0.006)

Evenly spaced 10 Kbp

10,837

0.264 (0.007)

0.159 (0.046)

0.235 (0.007)

0.141 (0.041)

13,946

0.452 (0.004)

0.436 (0.019)

0.272 (0.009)

0.340 (0.042)

0.415 (0.010)

0.421 (0.028)

Evenly spaced 50 Kbp

6867

0.253 (0.007)

0.153 (0.041)

0.242 (0.006)

0.135 (0.035)

7619

0.472 (0.008)

0.440 (0.021)

0.286 (0.008)

0.339 (0.043)

0.439 (0.008)

0.421 (0.031)

Evenly spaced 100 Kbp

4634

0.252 (0.004)

0.146 (0.044)

0.241 (0.006)

0.141 (0.036)

4846

0.460 (0.006)

0.442 (0.024)

0.287 (0.007)

0.339 (0.041)

0.452 (0.008)

0.432 (0.031)

Evenly spaced 250 Kbp

2281

0.261 (0.004)

0.166 (0.039)

0.258 (0.005)

0.160 (0.029)

2297

0.374 (0.007)

0.414 (0.026)

0.271 (0.005)

0.328 (0.042)

0.360 (0.004)

0.400 (0.030)

Evenly spaced 500 Kbp

1203

0.212 (0.006)

0.131 (0.053)

0.199 (0.004)

0.116 (0.050)

1204

0.326 (0.004)

0.388 (0.026)

0.226 (0.004)

0.306 (0.043)

0.307 (0.005)

0.378 (0.033)

Evenly spaced 1 Mbp

610

0.196 (0.002)

0.111 (0.031)

0.178 (0.003)

0.097 (0.022)

609

0.256 (0.004)

0.364 (0.027)

0.203 (0.004)

0.307 (0.041)

0.260 (0.004)

0.365 (0.029)

Genic regions

7254

0.251 (0.008)

0.163 (0.045)

0.240 (0.006)

0.148 (0.037)

11,212

0.421 (0.007)

0.433 (0.020)

0.269 (0.008)

0.340 (0.042)

0.394 (0.005)

0.426 (0.028)

Intergenic regions

6533

0.253 (0.008)

0.152 (0.046)

0.232 (0.005)

0.131 (0.046)

8294

0.449 (0.007)

0.432 (0.021)

0.289 (0.009)

0.340 (0.041)

0.414 (0.006)

0.410 (0.030)

SNPs in LE (LD-pruning)

10,460

0.274 (0.011)

0.174 (0.043)

0.256 (0.010)

0.161 (0.039)

10,984

0.425 (0.010)

0.426 (0.024)

0.275 (0.007)

0.339 (0.041)

0.404 (0.006)

0.413 (0.031)

  1. DBH, cm (Diameter at Breast Height), HT, m (Total Height) and WV, m 3 (Wood Volume), SE (Standard Error)
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BMC Genomics

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