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只要知道遗传参数的计算公式,通过AFEchidna的pin函数来求解是非常方便的。
下面以双性状为例,演示遗传相关、遗传力、遗传变异系数、遗传增益等参数的计算:
// bi-trait
res12<-echidna(cbind(h3,h4)~Trait+Trait:Rep,
random=~us(Trait):Fam,
residual=~units.us(Trait),
predict='Fam',mulT=T,
qualifier = '!filter Spacing !select 1',
es0.file="fm.es0")
计算遗传相关,以及性状h3的各种遗传参数:
// genetic parameter
pin(res12, mulp=c(gcor~V3/sqrt(V2*V4),
gcv.h3~100*sqrt(V2)/mup.h3,
h2.h3~4*V2/(V2+V5),
delG.h3m~4*V2/(V2+V5)*(mus.h3-mup.h3),
delG2.h3p~100*4*V2/(V2+V5)*(mus.h3-mup.h3)/mup.h3)
)
)
运行结果:
// results
> pin(res12, mulp=c(gcor~V3/sqrt(V2*V4),
+ gcv.h3~100*sqrt(V2)/mup.h3,
+ h2.h3~V2*4/(V2+V5),
+ delG.h3m~4/(V2+V5)*(mus.h3-mup.h3),
+ delG2.h3p~100*4/(V2+V5)*(mus.h3-mup.h3)/mup.h3)
+ )
variance components are as following:
Term Sigma SE vcS
1 Residual 1.00 0.000 V1
2 us(Trait):Fam;us(Trait) 132.43 56.428 V2
3 us(Trait):Fam;us(Trait) 168.81 75.851 V3
4 us(Trait):Fam;us(Trait) 243.39 115.710 V4
5 units:us(Trait);us(Trait) 1589.10 100.300 V5
6 units:us(Trait);us(Trait) 1964.20 138.080 V6
7 units:us(Trait);us(Trait) 3596.00 226.990 V7
pin formula:
gcor ~ V3/sqrt(V2 * V4)
gcv.h3 ~ 100 * sqrt(V2)/mup.h3
h2.h3 ~ 4 * V2/(V2 + V5)
delG.h3m ~ 4 * V2/(V2 + V5) * (mus.h3 - mup.h3)
delG2.h3p ~ 100 * 4 * V2/(V2 + V5) * (mus.h3 - mup.h3)/mup.h3
Term Estimate SE
1 gcor 0.940 0.0612
11 gcv.h3 4.533 0.9660
12 h2.h3 0.308 0.1250
13 delG.h3m 7.750 3.1560
14 delG2.h3p 3.053 1.2430
上述结果中,gcor为遗传相关,gcv.h3、h2.h3、delG.h3m、delG.h3p分别为性状h3的遗传变异系数、单株遗传力、遗传增益及遗传增益百分比。
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