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家系模型,也称为亲本模型,是遗传评估的经典模型,常用于优良家系的选择和优良亲本的评估。家系分为半同胞家系和全同胞家系,前者可来自种源试验或自由授粉设计,后者多数来自析因交配、双列交配、巢式交配等设计。
1 示例数据
示例数据Pine_provenance.csv共有4个种源,36个半同胞家系。田间试验设计为随机完全区组设计,5个区组,每个小区测量2~6株。
2 统计模型
对于种源-家系试验,典型的统计模型如下:
y=μ+P+F+B+BF+ϵ.
3 分析代码
程序代码(.es)如下:
!RXL !WORKSPACE 2 !OUT !RE !ARG 1 Title: Pine_provenance. #treeid,female,male,prov,block,plot,height,diameter,volume Treeid !I Female !I Male * Prov !I Block * Plot * height diameter volume !*10 Provenance.csv !SKIP 1 !SLN !YHT !DDF 1 !MAXIT 20 !DOPART $1 !PART 1 height ~ mu Prov !f mv, # Specify fixed model !r Female*Block # Specify random model residual units PREDICT Prov Female !present Prov Female VPREDICT F Pheno Female + Female.Block + Residual # sum of variances F Additive Female*4 # Multiply component by 4 H h2i Additive Pheno # Heritability
4 主结果
程序运行的主结果文件(.esr)如下:
... Summary of 914 data records Variable Levels Miss Zero Min Max Distribution or Mn SD Sk Kt Treeid 914 0 0 1 914 Male 2 0 914 0 0 Female 36 0 0 1 36 Prov 4 0 0 1 4 77 267 306 264 Block 5 0 0 1 5 192 187 188 179 168 Plot 240 0 0 1 240 height 1 0 0 4.00 15.20 10.48 1.79 -0.40 0.21 diameter 1 0 0 5.00 31.20 18.31 4.40 -0.24 -0.13 volume 1 0 0 0.03000 4.29300 1.18093 0.66110 0.74 0.71 * This job may use 8 processor cores. * 1 LogL= -935.00 2.477 910 DF 2 LogL= -934.25 2.502 910 DF 3 LogL= -934.12 2.529 910 DF 4 LogL= -934.12 2.527 910 DF 5 LogL= -934.12 2.527 910 DF ... Akaike Information Criterion 1876.24 (assuming 4 parameters). Bayesian Information Criterion 1895.50 Analysis of height Wald F statistics Source of Variation NumDF DenDF F-inc P-inc mu 1 3566.99 Prov 3 10.01 Model_Term Order Gamma Sigma Z_ratio %C Block 5 0.425370E-01 0.107492 1.20 0 P Female 36 0.749901E-01 0.189502 2.26 0 P Female.Block 180 0.782019E-01 0.197618 2.29 0 P Residual_units 914 1.00000 2.52703 19.22 mv 0 effects fitted. Block 5 effects fitted. Female 36 effects fitted. Female.Block 180 effects fitted. Warning: If job runs slow, see if !EQN 2 or !EQN 3 is faster. Finished: Sat Feb 29 10:45:37 2020 LogL Converged prov.HS1/prov.HS
5 遗传力计算
.evp文件里含有遗传力的计算结果,具体如下:
Warning: The analysis was performed on the GAMMA scale.
Check all parameters have been converted to the Sigma scale.
1 Residual 2.5270 0.13147
2 Block 0.10749 0.89924E-01
3 Female 0.18950 0.83980E-01
4 Female.Block 0.19762 0.86236E-01
F Pheno Female + Female.Block + Residual
5 Pheno 2.9141 0.14791
F Additive Female*4
6 Additive 0.75801 0.33592
H h2i Additive Pheno
h2i = Additive 6/Pheno 5 = 0.26011 0.11018
Notice: The parameter estimates are followed by
their approximate standard errors.
6 模型效应值
此模型估计的种源效应值如下:
Model_Term, Class, Solution, StndError
Prov, 10, 0.0 , 0.0
Prov, 11, -1.6656325, 0.3741344
Prov, 12, -0.6237406, 0.3701346
Prov, 13, -1.2201920, 0.3769892
mu, 1, 11.5120637, 0.3619919
模型估算的母本一般配合力或者家系效应值在.ess文件里,部分结果如下:
Model_Term, Class, Solution, StndError
Female, 170, -0.1633745, 0.3433451
Female, 191, -0.0825666, 0.3395366
Female, 192, 0.2459411, 0.3418598
Female, 196, -0.4605941, 0.3072528
Female, 197, 0.3556406, 0.3019308
Female, 198, -0.4505721, 0.3016501
Female, 200, 0.2670928, 0.3065233
Female, 201, -0.1905731, 0.3072727
Female, 202, -0.0289731, 0.2981268
...
7 模型预测
与ASReml类似,Echidna也可进行模型项的预测,本例中,部分的家系预测值(.epv)如下:
Predicted values of height
Notice: Some PREDICT qualifier combinations may not work properly.
---- ---- ---- ---- 1 ---- ---- ---- ----
Block is ignored.
Predicted_Value Stnd_Error Ecode Prov Female
11.42950 0.33923 E 10 191
11.75801 0.34975 E 10 192
9.38584 0.33593 E 11 196
10.20207 0.32912 E 11 197
9.39586 0.32880 E 11 198
10.11352 0.33504 E 11 200
9.65586 0.33591 E 11 201
9.81746 0.32424 E 11 202
10.23119 0.33101 E 11 203
10.13957 0.32423 E 11 204
9.76929 0.33423 E 11 205
9.89575 0.33136 E 11 206
9.70434 0.32851 E 11 207
10.52994 0.32528 E 12 210
10.87955 0.32769 E 12 211
...
与ASreml相比,Echidna的predict功能还不够稳定。
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版权声明:本文为CSDN博主「yzhlinscau」的原创文章,遵循 CC 4.0 BY-SA 版权协议,转载请附上原文出处链接及本声明。
原文链接:https://blog.csdn.net/yzhlinscau/article/details/104569724
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