Table 3

Values of π (prior) used in the Bayesian analysis in the sires

S.S. in Sires

Total

SSR

SSR/2

SSRx2


Milk Yield

370

40,668

0.0091

0.0045

0.0182


Fat Yield

370

40,668

0.0091

0.0045

0.0182


Protein Yield

385

40,668

0.0095

0.0047

0.0189


Fat %

216

40,668

0.0053

0.0027

0.0106


Protein %

229

40,668

0.0056

0.0028

0.0113


SCS

9

40,668

0.0002

0.0001

0.0004


Fat % = fat percentage; Protein % = protein percentage; SCS = somatic cell score; S.S. in Sires = number of significant SNPs from the single SNP regression model in the sires for a particular trait; Total = total number of SNPs in the analysis; SSR = value of π based on the number of significant SNPs from the single SNP regression model in the sires (i.e. for milk yield, 370/40668 = 0.0091); SSR/2 = half the value of π than that of the SSR prior; SSRx2 = twice the value of π than that of the SSR prior

For the Bayesian analysis three different priors were used for each trait; these priors represent the proportion of SNPs believed to affect the particular trait. The SSR prior for a trait is calculated by dividing the total number of significant SNPs from the single SNP regression analysis in the sires by the total number of SNPs in the analysis (i.e. 40,668). The other two priors, SSR/2 and SSRx2 are simply the half and double the SSR prior respectively

Meredith et al. BMC Genetics 2012 13:21   doi:10.1186/1471-2156-13-21

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