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. 2019 Jul 17;10:673. doi: 10.3389/fgene.2019.00673

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Copyright © 2019 Ye, Gao, Zheng, Chen, Teng, Yuan, Zhang, Chen, Zhang, Li and Zhang

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Impact of the linkage disequilibrium (LD)-based marker pruning of selected or remaining variants on prediction accuracy. R-squared of LD less than 0.1 was fixed to prune selected (or remaining) variants, and then the remaining (or selected) variants that were pruned with different R-squared cutoffs of LD (0.99, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, and 0.1) for GBLUP were merged. The red line is the prediction accuracy of GBLUP with all markers of imputed WGS data. The predictive ability was assessed by the Pearson correlation between the predicted genetic values and the observed phenotypes corrected for fixed effect(s) per trait. These traits were average daily gain (ADG), intestine length (IL), breast muscle weight (BMW), residual feed intake (RFI), body weight in 91 days (BW91), and average daily feed intake (ADFI).