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While the improvement in prediction reliability for the milk protein and fertility traits was statistically significant using haploblocks rather than individual SNPs, for mastitis the improved prediction reliability was observed only when D′≥0.45.
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A third reason why imputed sequence information did not improve prediction reliability could be parameterization of the BSSVS model.
This suggests that pre-selecting SNPs and treating them as fixed effects or giving them a high prior might improve prediction reliability.
Certainly, large-scale investigations of miRNA target binding via Argonaute CLIP-Seq in corresponding cell lines would improve prediction reliability [80], and traditional techniques such as overexpression, reporter assays and site mutation may be needed in future to verify some of the critical miRNA target relationships.
One way forward is improved prediction.
Fig. 9 Improved prediction accuracy.
Averaged over the 15 traits, including the X chromosome improved the prediction reliability by 0.5% points.
Information on pH and CEC improved the prediction reliability of KS and the MRC: pH might influence soil structure (Hodnett & Tomasella, 2002; Tóth et al., 2012), which is closely correlated to water retention close to saturation and saturated hydraulic conductivity, and CEC is related to the clay mineralogy and forms of organic matter (Bruand, 2004; Botula Manyala Ilanga et al., 2013).
Including PSD instead of FAO_MOD texture classes did not improve the prediction reliability but the number of final groups in the model decreased.
The use of haplotype blocks improved the prediction reliabilities, even when selection focused on only a group of haplotype blocks.
High-density genomic data may improve reliability even more by improving predictions.
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