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These QTLs were also detected with single trait analysis.
Only two minor QTLs (CHR3 and 8) were detected in Set 2 (Table 4), of which CHR3 was not significant in single trait analysis.
CHR7 was a consistent QTL over Set 1 and Set 2, which was not detected as a significant QTL with single trait analysis.
It seems that more consistent minor QTLs were detected in the multi-trait analyses although one has to be aware that the statistical assumptions are stronger for the multi-trait analysis, which may cause more false positive than single trait analysis.
A multiple traits instead of single trait analysis may be a promising way to take correlations among these traits into consideration.
No epistatic effect was detected based on single trait analysis.
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The statistical power via single trait-analysis and combined traits analyses was the same (data not shown).
In the rest of the paper, we demonstrate how a locus, previously hidden in conventional single-trait analysis, can now be detected via our multivariate technique.
A novel locus, hidden in the original single-trait analysis, was detected, where the rare allele showed significantly higher response to P. syringae pv.
Compared with single-trait analysis, joint mapping addresses more questions and has advantages for power of QTL detection and precision of parameter estimation.
A single-trait analysis of mastitis using unweighted EBV was also performed for comparative purposes.
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