Computational protocol: Genetic Evaluation of Dual-Purpose Buffaloes (Bubalus bubalis) in Colombia Using Principal Component Analysis

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Protocol publication

[…] One-trait models were used for estimating genetic parameters and breeding values with MTDFREML (Multiple trait Derivate-Free Restricted Maximum Likelihood) [].For WW and W12 the random effects were: direct additive genetic (a), maternal additive genetic (m), maternal permanent environmental (pe), and residual effect (ε). The fixed effects were: sex (male or female), number of calving (1 to 14) and contemporary group (farm, year, and birth time: January to April, May to August, or September to December). Age at weighing was used as a covariate (linear effect). The matrix representation of the model is: y=Xβ+Z1a+Z2m+Wpe+ε. With Cov(Z1a, Z2m)=0 Where y is a vector of observations, β is the vector of fixed effects, and ε is the random residual vector. X, Z 1, Z 2, and W are the incidence matrices relating the fixed effects, direct additive genetic effects, maternal additive genetic effects, and maternal permanent environmental effects, respectively.The following formula ht2=(σa2+0.5*σm2+σam)/σp2, by Willham RL [], was used in the estimation of total heritability for WW and W12. Where h 2 t = total heritability σ 2 t = direct additive genetic variance σ 2 m = maternal additive genetic variance σ am = genetic covariance between direct and maternal effects σ 2 p = phenotypic varianceFor W18 and W24 random effects were the additive genetic random (a) and the residual effect (ε). The fixed effects were sex (male or female), number of calving (1 to14), and contemporary group (defined as for WW and W12). The age at weighing was used as a covariate (linear effect).For AFC the random effects were the same as for W18 and W24, and the fixed effect of contemporary group was included (farm, year, and time of first birth: January to April, May to August, or September to December).The matrix representation of the model was: y = XB + Z1a+ Wpe + ε For MY270 the random effects were: additive genetic (a), permanent environmental (pe), and residual effect (ε). The fixed effects were parity (1 to 14) and contemporary group (farm, year, and time of birth: January to April, May to August, or September to December).The matrix representation of the model was: y = XB + Z1a+ Wpe + ε [...] PCA was developed using the BV from 133 males, selected from 961 males with higher than 50% reliability for WW, W12, W18, W24, MY270, AFC, maternal genetic effect for weaning weight (MGWW), and maternal genetic effect for yearling weight (MGW12), data are also available in . All BV were standardized to zero mean and unit variance. To select the number of principal components (PC) that explained the highest percentage of variance only those PC with greater than one eigenvalues were took into account []. The linear correlations of traits with each PC were estimated, and significant traits in each PC were defined. This analysis was conducted using command PCA, FactoMineR library [] of r-project software []. […]

Pipeline specifications

Software tools MTDFREML, FactoMineR
Applications Miscellaneous, GWAS
Organisms Bubalus bubalis