Table S2. Differential expressed genes within the most significant signatures of selection and QTL regions*. (DOCX 16Â kb

Christelle Hennequet-Antier (79326)

CĂŠcile Berri (4978169)

Elisabeth Bihan-Duval (3578903)

Marie Bourin (1829470)

Maryse Boulay (5144126)

Olivier Demeure (116584)

Simon Boitard (184972)

StĂŠphane Beauclercq (4978166)

BMC Genomics

Figure S5. Manhattan plot of the BF factor testing the association between SNP and ultimate pH of the sartorius (thigh) muscle (SART-pHu). Bayes Factor (BF) comprised between 20 (first horizontal dotted line) and 150 (second horizontal dotted line) indicates strong evidence of QTL and BF higher than 150 indicates very strong evidence of QTL. (PDF 198Â kb

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Additional file 5: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Table S1. Comparison of p-values (in -log10 scale) for different tests rejecting neutral evolution, for the most significant SNP of the 10 regions listed in Table 2. (DOCX 14Â kb

Additional file 6: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Figure S2. Evolution of haplotype cluster frequencies in region hapFLK-1c (Chromosome 1, from 18,755,135 to 29,764,967 bp). A: each panel corresponds to a population, from G0 (top) to G5plus (bottom). For one given genomic position (on the x-axis), each color band corresponds to one haplotype cluster, and the height of this band gives the cluster frequency. The selection scenario described in the text is based on cluster frequencies at the position of the strongest hapFLK signal, which is indicated by the vertical black line. B: Evolution of the dark red, red and green cluster frequencies along generations. As discussed in the text, these clusters are the ones showing the strongest evidence of selection at this locus. (PNG 1614 kb

Cécile Berri (214956)

Stéphane Beauclercq (4978220)

Additional file 2: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Additional file 7: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Elisabeth Le Bihan-Duval

Christelle Hennequet-Antier

Cécile Berri

Stéphane A. Beauclercq

Marie Christine Bourin

Maryse Boulay

Olivier Demeure

Simon Boitard

Crossref

Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

International audienceBackground The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the present study, we took advantage of a unique model of two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle (PM-pHu) in order to decipher the genetic control of this trait. Two complementary approaches were used: detection of selection signatures generated during the first five generations and genome-wide association study for PM-pHu and Sartorius muscle pHu (SART-pHu) at the sixth generation of selection. Results Sixty-three genomic regions showed significant signatures of positive selection. Out of the 10 most significant regions (detected by HapFLK or FLK method with a p-value below 1e-6), 4 were detected as soon as the first generation (G1) and were recovered at each of the four following ones (G2-G5). Another four corresponded to a later onset of selection as they were detected only at G5. In total, 33 SNPs, located in 24 QTL regions, were significantly associated with PM-pHu. For SART-pHu, we detected 18 SNPs located in 10 different regions. These results confirmed a polygenic determinism for these traits and highlighted two major QTL: one for PM-pHu on GGA1 (with a Bayes Factor (BF) of 300) and one for SART-pHu on GGA4 (with a BF of 257). Although selection signatures were enriched in QTL for PM-pHu, several QTL with strong effect haven’t yet responded to selection, suggesting that the divergence between lines might be further increased. Conclusions A few regions of major interest with significant selection signatures and/or strong association with PM-pHu or SART-pHu were evidenced for the first time in chicken. Their gene content suggests several candidates associated with diseases of glycogen storage in humans. The impact of these candidate genes on meat quality and muscle integrity should be further investigated in chicken

Le Bihan-Duval, Elisabeth

Hennequet-Antier, Christelle

Berri, Cécile

Beauclercq, Stéphane

Bourin, Marie Christine

Boulay, Maryse

Demeure, Olivier

Boitard, Simon

HAL Université de Tours

Background

The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the present study, we took advantage of a unique model of two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle (PM-pHu) in order to decipher the genetic control of this trait. Two complementary approaches were used: detection of selection signatures generated during the first five generations and genome-wide association study for PM-pHu and Sartorius muscle pHu (SART-pHu) at the sixth generation of selection.
Results

Sixty-three genomic regions showed significant signatures of positive selection. Out of the 10 most significant regions (detected by HapFLK or FLK method with a p-value below 1e-6), 4 were detected as soon as the first generation (G1) and were recovered at each of the four following ones (G2-G5). Another four corresponded to a later onset of selection as they were detected only at G5. In total, 33 SNPs, located in 24 QTL regions, were significantly associated with PM-pHu. For SART-pHu, we detected 18 SNPs located in 10 different regions. These results confirmed a polygenic determinism for these traits and highlighted two major QTL: one for PM-pHu on GGA1 (with a Bayes Factor (BF) of 300) and one for SART-pHu on GGA4 (with a BF of 257). Although selection signatures were enriched in QTL for PM-pHu, several QTL with strong effect haven’t yet responded to selection, suggesting that the divergence between lines might be further increased.
Conclusions

A few regions of major interest with significant selection signatures and/or strong association with PM-pHu or SART-pHu were evidenced for the first time in chicken. Their gene content suggests several candidates associated with diseases of glycogen storage in humans. The impact of these candidate genes on meat quality and muscle integrity should be further investigated in chicken

le Bihan-Duval, Elisabeth

ProdInra

Figure S1. p-values (in -log10 scale) obtained along the genome when applying FLK to generation 1 (yellow), 2 (green), 3 (blue), 4 (red) or 5 (black) of the selection experiment. Horizontal dotted lines indicate the 5% FDR threshold for each of these generations. Vertical black lines correspond to a change of chromosome, and the numbers below these lines provide the length of the finishing chromosome. (TIFF 1599Â kb

Additional file 1: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Figure S3. Evolution of haplotype cluster frequencies in region hapFLK-2c (Chromosome 2, from 24,502,152 to 33,353,778 bp). A: each panel corresponds to a population, from G0 (top) to G5plus (bottom). For one given genomic position (on the x-axis), each color band corresponds to one haplotype cluster, and the height of this band gives the cluster frequency. The selection scenario described in the text is based on cluster frequencies at the position of the strongest hapFLK signal, which is indicated by the vertical black line. B: Evolution of the light blue and light green cluster frequencies along generations. As discussed in the text, these clusters are the ones showing the strongest evidence of selection at this locus. (PNG 1608 kb

Additional file 3: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

Abstract Background The understanding of the biological determinism of meat ultimate pH, which is strongly related to muscle glycogen content, is a key point for the control of muscle integrity and meat quality in poultry. In the present study, we took advantage of a unique model of two broiler lines divergently selected for the ultimate pH of the pectoralis major muscle (PM-pHu) in order to decipher the genetic control of this trait. Two complementary approaches were used: detection of selection signatures generated during the first five generations and genome-wide association study for PM-pHu and Sartorius muscle pHu (SART-pHu) at the sixth generation of selection. Results Sixty-three genomic regions showed significant signatures of positive selection. Out of the 10 most significant regions (detected by HapFLK or FLK method with a p-value below 1e-6), 4 were detected as soon as the first generation (G1) and were recovered at each of the four following ones (G2-G5). Another four corresponded to a later onset of selection as they were detected only at G5. In total, 33 SNPs, located in 24 QTL regions, were significantly associated with PM-pHu. For SART-pHu, we detected 18 SNPs located in 10 different regions. These results confirmed a polygenic determinism for these traits and highlighted two major QTL: one for PM-pHu on GGA1 (with a Bayes Factor (BF) of 300) and one for SART-pHu on GGA4 (with a BF of 257). Although selection signatures were enriched in QTL for PM-pHu, several QTL with strong effect haven’t yet responded to selection, suggesting that the divergence between lines might be further increased. Conclusions A few regions of major interest with significant selection signatures and/or strong association with PM-pHu or SART-pHu were evidenced for the first time in chicken. Their gene content suggests several candidates associated with diseases of glycogen storage in humans. The impact of these candidate genes on meat quality and muscle integrity should be further investigated in chicken

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Additional file 7: of Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL

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