Number of significant SNPs validated in the Holstein and Jersey validation sets.

<p>The number of SNPs tested in the validation data sets was HTDMY_int 152, HTDMY_slope 76, THI_int 92, THI_slope 42, as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006676#pone-0006676-t002" target="_blank">Table 2</a>. For each trait, the numbers of SNPs significant in the Holstein Validation (HV) are given in the HV row and Holstein discovery (HD) column, the numbers of SNPs significant in the Jersey Validation (JV) are given in the JV row and HD column, and the number of SNPs validated in both the HV and JV data sets are given in the JV row and the HV column. The numbers on the corresponding upper diagonal are the correlation of SNP solutions for SNPs validated in both data sets.</p>*<p>HD Holstein discovery.</p>**<p>HV Holstein Validation.</p>***<p>JV Jersey Validation.</p

Position of significant SNPs in the discovery and validation data sets on chromosome 9.

<p>The position of the putative glycerol-3-phosphate dehydrogenase 1-like gene is indicated.</p

Distribution of environmental variables.

<p>A. Distribution of Temperature humidity index (THI) values in the data. B. Distribution of Herd average daily milk yields (HTDMY) in the data.</p

Number of SNPs significant at P<0.001 by trait and false discovery rates in Holstein Friesian discovery data.

<p>Number of SNPs significant at P<0.001 by trait and false discovery rates in Holstein Friesian discovery data.</p

Location of dairy farms for which milk production data was retrieved and location of weather stations providing climate data.

<p>A. Location of dairy farms and B. Location of weather stations (green pins) supplying data in 2008 to the Australian Bureau of Meteorology (<a href="http://www.bom.gov.au/silo" target="_blank">http://www.bom.gov.au/silo</a>) that were in turn used by the Queensland Department of Environment and Resource Management DataDrill project (<a href="http://www.longpaddock.qld.gov.au/silo" target="_blank">http://www.longpaddock.qld.gov.au/silo</a>) in interpolating meteorological data onto a 5-×5-km grid across Australia. Image created with using <a href="http://www.microsoft.com/maps/isdk/ajax/" target="_blank">http://www.microsoft.com/maps/isdk/ajax/</a> .</p

SNPs for HTDMY_slope and THI_slope validated in the Jersey data set and their effects in the discovery and validation data set.

<p>The effects are the result of inheriting one extra copy of the second allele of the SNP (alleles in alphabetical order and called in top-bottom format). The F-value thresholds were 10.84 (P<0.001) for discovery and 3.85 (P<0.05) for validation. Blank cells indicate non-significance.</p>*<p>Note that the ARS prefix in front of BFGL in the marker names has been removed for clarity.</p

Number of records, mean, standard deviation (SD), heritability estimate (h²) of each trait for the genotyped animals and their 5-generation ancestors.¹

1<p> = similar summary statistics for 19 of the above traits can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen.1004198-Bolormaa2" target="_blank">[8]</a>.</p

Effects of 28 lead SNPs on the individual traits (signed values with |t|>1 are shown).

<p>*  = Group of the lead SNPs that were clustered together as shown on <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen-1004198-g007" target="_blank">Figure 7</a>.</p>2<p> = This SNP order refers SNPs, which are given on <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen-1004198-t004" target="_blank">Table 4</a>.</p

A: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits and multi-trait chi-squared statistic on a region of BTA 5; B: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits when SNP_i along with 28 lead SNPs were simultaneously fitted in the GWAS model.

<p>A: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits and multi-trait chi-squared statistic on a region of BTA 5; B: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits when SNP_i along with 28 lead SNPs were simultaneously fitted in the GWAS model.</p

Number of significant SNPs (<i>P</i><10⁻⁵) in reference population that were also significant in the validation population.

<p>%-same = percentage of SNPs, which have an effect in the same direction in both validation and reference sets.</p