MOESM2 of Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

Additional file 2: Table S1. Comparison of genetic correlations between traits and SNP-based correlations (777K, AWM and 206 common genes). The data summarize the comparison between genetic correlations and SNP-based correlations across the three beef cattle breeds

MOESM3 of Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

Additional file 3: Figure S2. (A) Number of overlapping SNPs. (B) Overlapping pathways. The figure represents the number of overlapping SNPs and pathways identified across the three beef cattle breeds

MOESM5 of Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds

Additional file 5: Table S3. Description of the genes that overlap with the QTL for Warner-bratzler shear force (WBSF) according to the Cattle QTLdb

Loss in calving rate in matings between carrier sires and daughters of carrier sires.

*<p>p<0.05, **p<0.01 and ***p<0.001 versus control group (t-test). Haplotypes with significant negative effects on conception rate in both heifers and adult cows in matings at risk are shown in bold type. Nb: number. a: no mating at risk was observed between carriers of these haplotypes and daughters of carrier bulls during the period of time studied (see methods).</p

List of regions displaying significant deficit of homozygotes.

<p>Homoz: homozygote, freq: frequency. Only regions with Chi-square test p-values lower than 10⁻⁴ are shown except HH2 (italic), previously reported by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065550#pone.0065550-VanRaden1" target="_blank">[13]</a>.</p

List of candidate mutations for embryonic lethal defects.

*<p>: mutations with damaging predicted effect on the structure and function of the protein. In bold are shown the strongest candidate mutations for each haplotype. Mutation g.49942403T>C, predicted to affect BCAR3 splicing, was not retained as a plausible causative mutation since deficiency in BCAR3 is not lethal in mouse <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065550#pone.0065550-Near1" target="_blank">[17]</a>. MIS18A p.C13Y substitution was also not retained as a plausible causative mutation as described in the manuscript.</p

Genetic population structure prediction.

<p>Genetic population structure predicted by STRUCTURE software for the 3 main dairy breeds (Fig 7A) and for the 8 breeds (Fig 7B).</p

Distribution of SVs based on their type and size.

<p>Histogram summarizing the distribution of SVs based on their type and size. Inversions are highlighted in blue, deletions in red and tandem duplications in green.</p

Results of PCA analysis.

<p>PCA analysis results were shown for the 3 main dairy breeds (Fig 6A) and for the 8 breeds (Fig 6B).</p

MOESM2 of Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Additional file 2. Size distribution of small insertions and deletions identified by GATK. Total number of small insertions and deletions and their distribution by size are indicated