It makes the Line x Tester Genetic Analysis. It also estimates the general and specific combinatory ability effects and the line and tester genetic contribution.
lineXtester(replications, lines, testers, y)
| replications | Replications |
|---|---|
| lines | Lines |
| testers | Testers |
| y | Variable, response |
return anova(formula = Y ~ Replications + Treatments).
where the
Treatments contains parents, crosses and crosses vs Parents.
The crosses
contains Lines, Testers and its interaction .
ANOVA with parents and crosses
ANOVA for line X tester analysis
ANOVA for line X tester analysis including parents
GCA Effects: Lines
Effects, Testers Effects and SCA Effects.
Standard Errors for Combining
Ability Effects.
Genetic Components.
...
Proportional
contribution of lines, testers and their interactions to total variance
Biometrical Methods in Quantitative Genetic Analysis, Singh, Chaudhary. 1979. Hierarchial and factorial mating designs for quantitative genetic analysis in tetrasomic potato. R. Ortis; A.Golmirzaie. Theor Appl Genet (2002) 104:675-679
# see structure line by testers library(agricolae) # example 1 data(heterosis) site1<-subset(heterosis,heterosis[,1]==1) output1<-with(site1,lineXtester(Replication, Female, Male, v2))#> #> ANALYSIS LINE x TESTER: v2 #> #> ANOVA with parents and crosses #> ============================== #> Df Sum Sq Mean Sq F value Pr(>F) #> Replications 2 0.002674074 0.001337037 0.088 0.9159 #> Treatments 35 29.135740741 0.832449735 54.763 0.0000 #> Parents 11 21.221688889 1.929244444 126.917 0.0000 #> Parents vs. Crosses 1 1.692474074 1.692474074 111.341 0.0000 #> Crosses 23 6.221577778 0.270503382 17.795 0.0000 #> Error 70 1.064059259 0.015200847 #> Total 107 30.202474074 #> #> ANOVA for line X tester analysis #> ================================ #> Df Sum Sq Mean Sq F value Pr(>F) #> Lines 7 4.3497111 0.62138730 9.078 0.0003 #> Testers 2 0.9135444 0.45677222 6.673 0.0092 #> Lines X Testers 14 0.9583222 0.06845159 4.503 0.0000 #> Error 70 1.0640593 0.01520085 #> #> ANOVA for line X tester analysis including parents #> ================================================== #> Df Sum Sq Mean Sq F value Pr(>F) #> Replications 2 0.002674074 0.001337037 0.088 0.9159 #> Treatments 35 29.135740741 0.832449735 54.763 0.0000 #> Parents 11 21.221688889 1.929244444 126.917 0.0000 #> Parents vs. Crosses 1 1.692474074 1.692474074 111.341 0.0000 #> Crosses 23 6.221577778 0.270503382 17.795 0.0000 #> Lines 7 4.349711111 0.621387302 9.078 0.0003 #> Testers 2 0.913544444 0.456772222 6.673 0.0092 #> Lines X Testers 14 0.958322222 0.068451587 4.503 0.0000 #> Error 70 1.064059259 0.015200847 #> Total 107 30.202474074 #> #> GCA Effects: #> =========== #> Lines Effects: #> Achirana LT-8 MF-I MF-II Serrana TPS-2 TPS-25 TPS-7 #> 0.143 -0.346 -0.134 -0.169 0.394 -0.016 0.321 -0.194 #> #> Testers Effects: #> TPS-13 TPS-67 TS-15 #> 0.104 0.052 -0.156 #> #> SCA Effects: #> =========== #> Testers #> Lines TPS-13 TPS-67 TS-15 #> Achirana -0.010 0.002 0.008 #> LT-8 0.186 -0.042 -0.144 #> MF-I -0.059 0.070 -0.011 #> MF-II -0.021 0.055 -0.034 #> Serrana -0.241 0.008 0.233 #> TPS-2 -0.044 0.101 -0.057 #> TPS-25 0.136 -0.259 0.123 #> TPS-7 0.054 0.064 -0.118 #> #> Standard Errors for Combining Ability Effects: #> ============================================= #> S.E. (gca for line) : 0.04109724 #> S.E. (gca for tester) : 0.02516682 #> S.E. (sca effect) : 0.0711825 #> S.E. (gi - gj)line : 0.05812027 #> S.E. (gi - gj)tester : 0.03559125 #> S.E. (sij - skl)tester: 0.1006673 #> #> Genetic Components: #> ================== #> Cov H.S. (line) : 0.0614373 #> Cov H.S. (tester) : 0.01618003 #> Cov H.S. (average): 0.004651843 #> Cov F.S. (average): 0.1223343 #> F = 0, Adittive genetic variance: 0.01860737 #> F = 1, Adittive genetic variance: 0.009303686 #> F = 0, Variance due to Dominance: 0.03550049 #> F = 1, Variance due to Dominance: 0.01775025 #> #> Proportional contribution of lines, testers #> and their interactions to total variance #> =========================================== #> Contributions of lines : 69.91331 #> Contributions of testers: 14.68349 #> Contributions of lxt : 15.4032#> 'data.frame': 92 obs. of 4 variables: #> $ replication: int 1 2 3 4 1 2 3 4 1 2 ... #> $ line : int 1 1 1 1 1 1 1 1 1 1 ... #> $ tester : int 6 6 6 6 7 7 7 7 8 8 ... #> $ yield : num 74.4 70.9 60.9 68 91.8 ...#> #> ANALYSIS LINE x TESTER: yield #> #> ANOVA with parents and crosses #> ============================== #> Df Sum Sq Mean Sq F value Pr(>F) #> Replications 3 83.00012 27.66671 0.304 0.8224 #> Treatments 22 32553.20239 1479.69102 16.249 0.0000 #> Parents 7 6299.88519 899.98360 9.883 0.0000 #> Parents vs. Crosses 1 53.66287 53.66287 0.589 0.4455 #> Crosses 14 26199.65433 1871.40388 20.551 0.0000 #> Error 66 6010.03298 91.06111 #> Total 91 38646.23549 #> #> ANOVA for line X tester analysis #> ================================ #> Df Sum Sq Mean Sq F value Pr(>F) #> Lines 4 10318.361 2579.59035 1.457 0.3009 #> Testers 2 1718.926 859.46289 0.485 0.6327 #> Lines X Testers 8 14162.367 1770.29589 19.441 0.0000 #> Error 66 6010.033 91.06111 #> #> ANOVA for line X tester analysis including parents #> ================================================== #> Df Sum Sq Mean Sq F value Pr(>F) #> Replications 3 83.00012 27.66671 0.304 0.8224 #> Treatments 22 32553.20239 1479.69102 16.249 0.0000 #> Parents 7 6299.88519 899.98360 9.883 0.0000 #> Parents vs. Crosses 1 53.66287 53.66287 0.589 0.4455 #> Crosses 14 26199.65433 1871.40388 20.551 0.0000 #> Lines 4 10318.36140 2579.59035 1.457 0.3009 #> Testers 2 1718.92577 859.46289 0.485 0.6327 #> Lines X Testers 8 14162.36716 1770.29589 19.441 0.0000 #> Error 66 6010.03298 91.06111 #> Total 91 38646.23549 #> #> GCA Effects: #> =========== #> Lines Effects: #> 1 2 3 4 5 #> -9.960 -0.718 23.817 -13.870 0.732 #> #> Testers Effects: #> 6 7 8 #> 0.292 6.404 -6.697 #> #> SCA Effects: #> =========== #> Testers #> Lines 6 7 8 #> 1 -8.019 24.959 -16.940 #> 2 -12.546 5.717 6.828 #> 3 -9.461 -4.918 14.378 #> 4 33.136 -14.321 -18.815 #> 5 -3.111 -11.438 14.548 #> #> Standard Errors for Combining Ability Effects: #> ============================================= #> S.E. (gca for line) : 2.75471 #> S.E. (gca for tester) : 2.133789 #> S.E. (sca effect) : 4.771297 #> S.E. (gi - gj)line : 3.895748 #> S.E. (gi - gj)tester : 3.017633 #> S.E. (sij - skl)tester: 6.747633 #> #> Genetic Components: #> ================== #> Cov H.S. (line) : 67.4412 #> Cov H.S. (tester) : -45.54165 #> Cov H.S. (average): 2.680894 #> Cov F.S. (average): 411.3472 #> F = 0, Adittive genetic variance: 10.72357 #> F = 1, Adittive genetic variance: 5.361787 #> F = 0, Variance due to Dominance: 839.6174 #> F = 1, Variance due to Dominance: 419.8087 #> #> Proportional contribution of lines, testers #> and their interactions to total variance #> =========================================== #> Contributions of lines : 39.38358 #> Contributions of testers: 6.560872 #> Contributions of lxt : 54.05555