List of primers used in this study.

<p>List of primers used in this study.</p

<i>myostatin</i> RT-qPCR transcripts.

<p>(A) Partial structure of the <i>myostatin</i> transcript from Blonde d'Aquitaine (BAB) and wild-type (WT) alleles. At top, the BAB allele contains the 41-bp additional exon (blue) and can be detected on qPCR by the probe 41 (blue) and probe W (black). At bottom, the wild-type allele, without the additional exon can only be detected by the probe W. Relative expression of <i>myostatin</i> transcript from twelve muscle samples detected by the probe W (B) and the probe 41 (C). 1-9: BAB homozygous (<i>G/G</i>) animals. 10: BAB heterozygous (<i>G/T</i>) animal. L3, L5: Limousine homozygous (<i>T/T)</i> animals.</p

<i>myostatin</i> cDNA amplifications.

<p>(A) <i>myostatin</i> mRNA structure. Arrows show the primers used for PCR amplification. (B) PCR products obtained from <i>longissimus dorsi</i> cDNA samples of ten Blonde d'Aquitaine animals (1–10). The predicted size (A) is 1.582-kb. All the amplifications were directly sequenced by the same primers used for PCR amplifications (A). T: PCR assay without sample; M: size marker.</p

Genotyping of the <i>T3811>G3811</i> mutation in European cattle breeds.

<p>Genotyping of the <i>T3811>G3811</i> mutation in European cattle breeds.</p

A Blonde d'Aquitaine bull homozygous for the <i>T3811>G3811</i> mutation exhibiting muscle hypertrophy.

<p>A Blonde d'Aquitaine bull homozygous for the <i>T3811>G3811</i> mutation exhibiting muscle hypertrophy.</p

Residual wild-type transcripts.

<p>(A) Partial sequence at exon2/exon3 junction of <i>myostatin</i> cDNA in Blonde d'Aquitaine (BAB) and normal (WT) cattle. Extra-exonisation in BAB at exon2/exon3 (<i>G/A</i>) junction is indicated (bracket). Two specific primers (PCRWT-F/PCRWT-R and PCRBAB-F/PCRBAB-R, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097399#pone-0097399-t002" target="_blank">Table 2</a>) were used to amplify either the correctly spliced (B) transcript (WT strand) or (C) the transcript with an extra exon (BAB strand). (C) The aberrant transcript was detected at relatively higher levels as compared to the heterozygous <i>G/T</i> animal (line 10) in agreement with real-time RT-qPCR data (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097399#pone-0097399-g006" target="_blank">Fig. 6</a>). Of note, residual correctly spliced transcripts were detected in <i>G/G</i> animals at variable levels ranging from undetectable (lines: 3, 4, 5) to detectable levels (lines: 1, 2, 6, 7, 8, 9) as compared to the <i>G/T</i> heterozygous animal (line 10). T: PCR assay without sample; M: size marker.</p

Aberrant <i>myostatin</i> cDNA.

<p>(A) Nine sequenced Blonde d'Aquitaine (BAB) animals carry a 41-bp additional sequence between the exons 2 and 3. (B) Wild-type <i>myostatin</i> cDNA primary structure at the exon2/exon3 junction (WT). (C) The 41-bp extra exon inclusion leads to a premature termination codon. Therefore, translation predicts a truncated protein lacking the entire bioactive region <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097399#pone.0097399-Wozney1" target="_blank">[2]</a>, encoded by exon 3. The arrow indicates that the extra exon inclusion occurs at the exon2/exon3 junction of the wild-type transcript. Of note, the premature stop codon occurs 29-bp upstream from the exon2/exon3 junction.</p

Deep intronic mutation.

<p>(A) The <i>T>G</i> substitution (arrow) creating a strong 5′ donor splice site (GT, underlined) was found in nine animals at the homozygous (<i>G/G</i>) state. (B) The tenth is heterozygous (<i>T/G</i>). A perfect preexistent 3′ acceptor splice site: AG and its upstream pyrimidine tract are underlined.</p

RFLP-PCR genotyping.

<p>(A) The <i>T>G</i> substitution leads to disappearance of the <i>AflII</i> restriction site in Blonde d'Aquitaine (BAB). (B) PCR amplification products from two BAB animals and one Limousine animal (Lim) were digested either by <i>AflII</i> or by <i>HindIII</i> restriction enzymes. <i>AflII</i> digestion differentiates animals which are homozygous <i>G/G</i> (BAB2, no digestion, one 763-bp fragment), heterozygous <i>T/G</i> (BAB1, three fragments: undigested PCR products corresponding to the mutated allele (763-bp) and PCR products corresponding to the wild-type allele gave two 565-bp and 198-bp fragments) or homozygous <i>T/T</i> (Lim, two fragments: 565-bp and 198-bp). <i>HindIII</i> digestion was used as a cutting control. WT: wild-type; M: size marker.</p

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