Algorithm of Term Elimination for Optimization.

<p>Algorithm of Term Elimination for Optimization.</p

Data statistics of Robust04 and GOV2.

<p>Data statistics of Robust04 and GOV2.</p

P@20 scores of various methods.

<p>P@20 scores of various methods.</p

Examples of General negative language model.

<p>Examples of General negative language model.</p

MAP performance of RM-KL for all collections when M = 30.

<p>MAP performance of RM-KL for all collections when M = 30.</p

Posterior density of five test statistics.

<p>The distributions of five test statistics on the X chromosome (red line), empirical distributions of Fst, Tajima's D (black line) and XPCLR (yellow line) from 5000 permutation tests, and the distributions of XPEHH, iHS and XPCLR on all autosomes (black line), respectively. Tajima's D and iHS are for Landrace, XPEHH, XPCLR and Fst are for breed pair of Landrace-Yorkshire only.</p

Summary of selection footprints detected by three between-population methods in different pig breed pairs.

1<p>L-S represents breed pair of Landrace and Songliao, Y represents Yorkshire.</p>2<p>The number of selection footprints (selection region for Fst) separately identified in two breeds for one breed pair in brackets.</p

Identification of Selection Footprints on the X Chromosome in Pig

<div><p>Identifying footprints of selection can provide a straightforward insight into the mechanism of artificial selection and further dig out the causal genes related to important traits. In this study, three between-population and two within-population approaches, the Cross Population Extend Haplotype Homozygosity Test (XPEHH), the Cross Population Composite Likelihood Ratio (XPCLR), the F-statistics (Fst), the Integrated Haplotype Score (iHS) and the Tajima's D, were implemented to detect the selection footprints on the X chromosome in three pig breeds using Illumina Porcine60K SNP chip. In the detection of selection footprints using between-population methods, 11, 11 and 7 potential selection regions with length of 15.62 Mb, 12.32 Mb and 9.38 Mb were identified in Landrace, Chinese Songliao and Yorkshire by XPEHH, respectively, and 16, 13 and 17 potential selection regions with length of 15.20 Mb, 13.00 Mb and 19.21 Mb by XPCLR, 4, 2 and 4 potential selection regions with length of 3.20 Mb, 1.60 Mb and 3.20 Mb by Fst. For within-population methods, 7, 10 and 9 potential selection regions with length of 8.12 Mb, 8.40 Mb and 9.99 Mb were identified in Landrace, Chinese Songliao and Yorkshire by iHS, and 4, 3 and 2 potential selection regions with length of 3.20 Mb, 2.40 Mb and 1.60 Mb by Tajima's D. Moreover, the selection regions from different methods were partly overlapped, especially the regions around 22 ∼25 Mb were detected under selection in Landrace and Yorkshire while no selection in Chinese Songliao by all three between-population methods. Only quite few overlap of selection regions identified by between-population and within-population methods were found. Bioinformatics analysis showed that the genes relevant with meat quality, reproduction and immune were found in potential selection regions. In addition, three out of five significant SNPs associated with hematological traits reported in our genome-wide association study were harbored in potential selection regions.</p></div

Selection regions harboring SNPs associated hematological traits reported by Wang et al. (2012).

<p>Selection regions harboring SNPs associated hematological traits reported by Wang et al. (2012).</p

Overlap of selection regions (Mb) from five methods in three pig breeds.

<p>Overlap of selection regions (Mb) from five methods in three pig breeds.</p