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S De Smet - One of the best experts on this subject based on the ideXlab platform.

  • effect of linseed feeding at similar linoleic acid levels on the fatty acid composition of double muscled Belgian Blue young bulls
    Meat Science, 2004
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, L Haak, An Balcaen, S De Smet
    Abstract:

    The effect of including linseed [extruded (EL) or crushed (CL)] instead of whole soybeans (S) in the finishing diet of double-muscled Belgian Blue young bulls on the fatty acid composition of the longissimus thoracis, triceps brachii and subcutaneous fat was investigated. The dietary supply of C18:2n-6 was similar in the three diets, while in the EL and CL diet the supply of C18:3n-3 was equal. No effects of diet on the saturated, monounsaturated and branched chain fatty acids were found. Including linseed in place of whole soybeans increased the total intramuscular n-3 fatty acid content significantly, mainly as C18:3n-3, while no significant effect on the total and individual n-6 fatty acid incorporation was observed in the intramuscular fat. As a consequence of the higher n-3 content, the n-6/n-3 ratio was decreased by linseed feeding. In contrast with the intramuscular fat, the subcutaneous fat showed a significantly increased C18:3n-3 proportion accompanied by a significantly decreased C18:2n-6 proportion when linseed was fed. Diet did not influence the c9t11CLA content in the intramuscular or the subcutaneous fat.

  • meat quality fatty acid composition and flavour analysis in Belgian retail beef
    Meat Science, 2003
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, An Balcaen, P Dirinck, A De Winne, S De Smet
    Abstract:

    The objective of this study was to evaluate the differences in biochemical, sensorial and quality characteristics of retail beef in Belgium. Four types of beef (Belgian Blue double-muscled, Limousin, Irish and Argentine) and two different muscles (longissimus lumborum and semimembranosus) were bought at the retail level and compared with regard to colour, shear force, collagen content, fatty acid analysis, taste panel evaluation as well as flavour analysis. Belgian Blue and Limousin beef had a paler colour, lower collagen and intramuscular fat contents. Fatty acid profiles were significantly different between the four types, with significantly higher PUFA/SFA and n-6/n-3 ratios for Belgiam Blue and Limousin beef compared to Argentine and Irish beef. There were significant differences between the meat types for taste panel tenderness and shear force, however both measurements did not fully correspond. Flavour analysis by gas chromatography-mass spectrometry as well as sensory analysis demonstrated that Irish and Argentine beef had a higher flavour intensity related to higher contents of volatile compounds. Differences in tenderness and flavour between the meat types were probably affected by differences in ageing time, related to import vs local production of meat.

  • perimysial collagen crosslinking and meat tenderness in Belgian Blue double muscled cattle
    Meat Science, 2002
    Co-Authors: T M Ngapo, S De Smet, P Berge, J Culioli, Eric Dransfield, E Claeys
    Abstract:

    The relationship between intramuscular collagen and five collagen crosslink concentrations, and the tenderness of meat from Belgian Blue normal, heterozygous double-muscled (DM) and homozygous DM cattle was investigated using M. semitendinosus (St) and M. gluteobiceps (Gb). The histidinohydroxymerodesmosine (HHMD) concentration (per mol collagen) in St was less in DM animals than normal animals. Concentrations (per gram of wet meat) of HHMD and Erlich chromogen (EC) in Gb, and HHMD, EC, dihydroxylysinorleucine (DHLNL) and hydroxylysinorleucine (HLNL) in St were also lower in DM animals than normal animals. Shear force of raw meat was significantly greater in normal animals than DM for both muscles; cooked meat shear force was greater in the normal animals for the Gb muscles only, showing a good correlation with sarcomere length. Most correlations between shear force and collagen or crosslink concentrations were not significant and those that were highly significant were generally weak.

  • effect of double muscling in Belgian Blue young bulls on the intramuscular fatty acid composition with emphasis on conjugated linoleic acid and polyunsaturated fatty acids
    Animal Science, 2001
    Co-Authors: Katleen Raes, S De Smet, Daniel Demeyer
    Abstract:

    The effect of double-muscling (DM) genotype (double-muscling, mh/mh; heterozygous, mh/+; normal, +/+) of Belgian Blue (BB) young bulls on the intramuscular fatty acid composition, in particular conjugated linoleic acid (CLA) and polyunsaturated fatty acids (PUFA) was examined in five different muscles. The relative fatty acid composition showed only minor differences between muscles within genotypes. However, the DM genotype had a large effect on both the intramuscular total fatty acid content and on the relative fatty acid composition. Across muscles, the mh/mh animals had a lower total fatty acid content compared with the +/+animals (907 v: 2656 mg/100 g muscle; P P P P

  • effect of double muscling in Belgian Blue young bulls on the intramuscular fatty acid composition with emphasis on conjugated linoleic acid and polyunsaturated fatty acids
    Animal Science, 2001
    Co-Authors: Katleen Raes, S De Smet, Daniel Demeyer
    Abstract:

    The effect of double-muscling (DM) genotype (double-muscling, mh/mh; heterozygous, mh/+; normal, +/+) of Belgian Blue (BB) young bulls on the intramuscular fatty acid composition, in particular conjugated linoleic acid (CLA) and polyunsaturated fatty acids (PUFA) was examined in five different muscles. The relative fatty acid composition showed only minor differences between muscles within genotypes. However, the DM genotype had a large effect on both the intramuscular total fatty acid content and on the relative fatty acid composition. Across muscles, the mh/mh animals had a lower total fatty acid content compared with the +/+animals (907 v: 2656 mg/100 g muscle; P < 0·01) and a higher PUFA proportion in total fatty acids (27·5 v 11·3 g/100 g total fatty acids; P < 0001), resulting in a higher PUFA/saturated fatty acid ratio (0·55 v 0·18; P < 0·01) and a lower n-6/n-3 ratio (5·34 v. 6·17; P < 0·01). The heterozygous genotype was intermediate between the two homozygous genotypes. The relative CLA content was similar in the mh/mh and +/+ genotypes and approximated 0·4 to 0·5 g/100 g total fatty acids. From the data it is further suggested that differences in the metabolism of the n-3 and n-6 fatty acids could exist between DM genotypes.

Daniel Demeyer - One of the best experts on this subject based on the ideXlab platform.

  • effect of linseed feeding at similar linoleic acid levels on the fatty acid composition of double muscled Belgian Blue young bulls
    Meat Science, 2004
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, L Haak, An Balcaen, S De Smet
    Abstract:

    The effect of including linseed [extruded (EL) or crushed (CL)] instead of whole soybeans (S) in the finishing diet of double-muscled Belgian Blue young bulls on the fatty acid composition of the longissimus thoracis, triceps brachii and subcutaneous fat was investigated. The dietary supply of C18:2n-6 was similar in the three diets, while in the EL and CL diet the supply of C18:3n-3 was equal. No effects of diet on the saturated, monounsaturated and branched chain fatty acids were found. Including linseed in place of whole soybeans increased the total intramuscular n-3 fatty acid content significantly, mainly as C18:3n-3, while no significant effect on the total and individual n-6 fatty acid incorporation was observed in the intramuscular fat. As a consequence of the higher n-3 content, the n-6/n-3 ratio was decreased by linseed feeding. In contrast with the intramuscular fat, the subcutaneous fat showed a significantly increased C18:3n-3 proportion accompanied by a significantly decreased C18:2n-6 proportion when linseed was fed. Diet did not influence the c9t11CLA content in the intramuscular or the subcutaneous fat.

  • meat quality fatty acid composition and flavour analysis in Belgian retail beef
    Meat Science, 2003
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, An Balcaen, P Dirinck, A De Winne, S De Smet
    Abstract:

    The objective of this study was to evaluate the differences in biochemical, sensorial and quality characteristics of retail beef in Belgium. Four types of beef (Belgian Blue double-muscled, Limousin, Irish and Argentine) and two different muscles (longissimus lumborum and semimembranosus) were bought at the retail level and compared with regard to colour, shear force, collagen content, fatty acid analysis, taste panel evaluation as well as flavour analysis. Belgian Blue and Limousin beef had a paler colour, lower collagen and intramuscular fat contents. Fatty acid profiles were significantly different between the four types, with significantly higher PUFA/SFA and n-6/n-3 ratios for Belgiam Blue and Limousin beef compared to Argentine and Irish beef. There were significant differences between the meat types for taste panel tenderness and shear force, however both measurements did not fully correspond. Flavour analysis by gas chromatography-mass spectrometry as well as sensory analysis demonstrated that Irish and Argentine beef had a higher flavour intensity related to higher contents of volatile compounds. Differences in tenderness and flavour between the meat types were probably affected by differences in ageing time, related to import vs local production of meat.

  • effect of double muscling in Belgian Blue young bulls on the intramuscular fatty acid composition with emphasis on conjugated linoleic acid and polyunsaturated fatty acids
    Animal Science, 2001
    Co-Authors: Katleen Raes, S De Smet, Daniel Demeyer
    Abstract:

    The effect of double-muscling (DM) genotype (double-muscling, mh/mh; heterozygous, mh/+; normal, +/+) of Belgian Blue (BB) young bulls on the intramuscular fatty acid composition, in particular conjugated linoleic acid (CLA) and polyunsaturated fatty acids (PUFA) was examined in five different muscles. The relative fatty acid composition showed only minor differences between muscles within genotypes. However, the DM genotype had a large effect on both the intramuscular total fatty acid content and on the relative fatty acid composition. Across muscles, the mh/mh animals had a lower total fatty acid content compared with the +/+animals (907 v: 2656 mg/100 g muscle; P P P P

  • effect of double muscling in Belgian Blue young bulls on the intramuscular fatty acid composition with emphasis on conjugated linoleic acid and polyunsaturated fatty acids
    Animal Science, 2001
    Co-Authors: Katleen Raes, S De Smet, Daniel Demeyer
    Abstract:

    The effect of double-muscling (DM) genotype (double-muscling, mh/mh; heterozygous, mh/+; normal, +/+) of Belgian Blue (BB) young bulls on the intramuscular fatty acid composition, in particular conjugated linoleic acid (CLA) and polyunsaturated fatty acids (PUFA) was examined in five different muscles. The relative fatty acid composition showed only minor differences between muscles within genotypes. However, the DM genotype had a large effect on both the intramuscular total fatty acid content and on the relative fatty acid composition. Across muscles, the mh/mh animals had a lower total fatty acid content compared with the +/+animals (907 v: 2656 mg/100 g muscle; P < 0·01) and a higher PUFA proportion in total fatty acids (27·5 v 11·3 g/100 g total fatty acids; P < 0001), resulting in a higher PUFA/saturated fatty acid ratio (0·55 v 0·18; P < 0·01) and a lower n-6/n-3 ratio (5·34 v. 6·17; P < 0·01). The heterozygous genotype was intermediate between the two homozygous genotypes. The relative CLA content was similar in the mh/mh and +/+ genotypes and approximated 0·4 to 0·5 g/100 g total fatty acids. From the data it is further suggested that differences in the metabolism of the n-3 and n-6 fatty acids could exist between DM genotypes.

  • early post mortem conditions and the calpain calpastatin system in relation to tenderness of double muscled beef
    Meat Science, 1997
    Co-Authors: D Steen, S De Smet, L Uytterhaegen, E Claeys, Daniel Demeyer
    Abstract:

    Abstract Early post mortem temperature, pH, sarcomere length, colour, water holding capacity, calpain/calpastatin activities and myofibrillar protein concentrations (semi-quantative SDS-PAGE), measured at different times post mortem on 153 double-muscled Belgian Blue White bulls, were related to shear force (SF) measurements. The M. longissimus thoracis tenderised up to 8 days post mortem. SF was slightly correlated with temperature at 3 h post mortem (r = 0.20, p = 0.015), but not with pH early post mortem. Higher ultimate pH values measured at 24 h post mortem were related to darker meat, lower cooking losses and shorter sarcomere lengths. Sarcomere length was significantly related to SF, even after 12 days of ageing, suggesting that proteolytic activity was not able to overcome shortening. Up to 12 days post mortem, calpastatin and m-calpain activities were significantly correlated with SF suggesting a considerable role of calpains in meat tenderization of double-muscled Belgian Blue White bulls, although at 24 h post mortem, μ-calpain could no longer be detected. Titin, nebulin, filamin and troponin-T were degraded during the ageing period. Troponin-T was degraded by 80% between day 1 and 8. At 8 days post mortem its concentration was significantly correlated with 30 kDa (r = 0.63, p = 0.00), shear force (r = 0.39, p = 0.00), calpastatin activity at 1 day post mortem (r = 0.29, p = 0.01) and with the m-calpain/ calpastatin activity ratio at 1 day post mortem (r = −0.43, p = 0.00).

Katleen Raes - One of the best experts on this subject based on the ideXlab platform.

  • effect of linseed feeding at similar linoleic acid levels on the fatty acid composition of double muscled Belgian Blue young bulls
    Meat Science, 2004
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, L Haak, An Balcaen, S De Smet
    Abstract:

    The effect of including linseed [extruded (EL) or crushed (CL)] instead of whole soybeans (S) in the finishing diet of double-muscled Belgian Blue young bulls on the fatty acid composition of the longissimus thoracis, triceps brachii and subcutaneous fat was investigated. The dietary supply of C18:2n-6 was similar in the three diets, while in the EL and CL diet the supply of C18:3n-3 was equal. No effects of diet on the saturated, monounsaturated and branched chain fatty acids were found. Including linseed in place of whole soybeans increased the total intramuscular n-3 fatty acid content significantly, mainly as C18:3n-3, while no significant effect on the total and individual n-6 fatty acid incorporation was observed in the intramuscular fat. As a consequence of the higher n-3 content, the n-6/n-3 ratio was decreased by linseed feeding. In contrast with the intramuscular fat, the subcutaneous fat showed a significantly increased C18:3n-3 proportion accompanied by a significantly decreased C18:2n-6 proportion when linseed was fed. Diet did not influence the c9t11CLA content in the intramuscular or the subcutaneous fat.

  • meat quality fatty acid composition and flavour analysis in Belgian retail beef
    Meat Science, 2003
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, An Balcaen, P Dirinck, A De Winne, S De Smet
    Abstract:

    The objective of this study was to evaluate the differences in biochemical, sensorial and quality characteristics of retail beef in Belgium. Four types of beef (Belgian Blue double-muscled, Limousin, Irish and Argentine) and two different muscles (longissimus lumborum and semimembranosus) were bought at the retail level and compared with regard to colour, shear force, collagen content, fatty acid analysis, taste panel evaluation as well as flavour analysis. Belgian Blue and Limousin beef had a paler colour, lower collagen and intramuscular fat contents. Fatty acid profiles were significantly different between the four types, with significantly higher PUFA/SFA and n-6/n-3 ratios for Belgiam Blue and Limousin beef compared to Argentine and Irish beef. There were significant differences between the meat types for taste panel tenderness and shear force, however both measurements did not fully correspond. Flavour analysis by gas chromatography-mass spectrometry as well as sensory analysis demonstrated that Irish and Argentine beef had a higher flavour intensity related to higher contents of volatile compounds. Differences in tenderness and flavour between the meat types were probably affected by differences in ageing time, related to import vs local production of meat.

  • effect of double muscling in Belgian Blue young bulls on the intramuscular fatty acid composition with emphasis on conjugated linoleic acid and polyunsaturated fatty acids
    Animal Science, 2001
    Co-Authors: Katleen Raes, S De Smet, Daniel Demeyer
    Abstract:

    The effect of double-muscling (DM) genotype (double-muscling, mh/mh; heterozygous, mh/+; normal, +/+) of Belgian Blue (BB) young bulls on the intramuscular fatty acid composition, in particular conjugated linoleic acid (CLA) and polyunsaturated fatty acids (PUFA) was examined in five different muscles. The relative fatty acid composition showed only minor differences between muscles within genotypes. However, the DM genotype had a large effect on both the intramuscular total fatty acid content and on the relative fatty acid composition. Across muscles, the mh/mh animals had a lower total fatty acid content compared with the +/+animals (907 v: 2656 mg/100 g muscle; P P P P

  • effect of double muscling in Belgian Blue young bulls on the intramuscular fatty acid composition with emphasis on conjugated linoleic acid and polyunsaturated fatty acids
    Animal Science, 2001
    Co-Authors: Katleen Raes, S De Smet, Daniel Demeyer
    Abstract:

    The effect of double-muscling (DM) genotype (double-muscling, mh/mh; heterozygous, mh/+; normal, +/+) of Belgian Blue (BB) young bulls on the intramuscular fatty acid composition, in particular conjugated linoleic acid (CLA) and polyunsaturated fatty acids (PUFA) was examined in five different muscles. The relative fatty acid composition showed only minor differences between muscles within genotypes. However, the DM genotype had a large effect on both the intramuscular total fatty acid content and on the relative fatty acid composition. Across muscles, the mh/mh animals had a lower total fatty acid content compared with the +/+animals (907 v: 2656 mg/100 g muscle; P < 0·01) and a higher PUFA proportion in total fatty acids (27·5 v 11·3 g/100 g total fatty acids; P < 0001), resulting in a higher PUFA/saturated fatty acid ratio (0·55 v 0·18; P < 0·01) and a lower n-6/n-3 ratio (5·34 v. 6·17; P < 0·01). The heterozygous genotype was intermediate between the two homozygous genotypes. The relative CLA content was similar in the mh/mh and +/+ genotypes and approximated 0·4 to 0·5 g/100 g total fatty acids. From the data it is further suggested that differences in the metabolism of the n-3 and n-6 fatty acids could exist between DM genotypes.

E Claeys - One of the best experts on this subject based on the ideXlab platform.

  • effect of linseed feeding at similar linoleic acid levels on the fatty acid composition of double muscled Belgian Blue young bulls
    Meat Science, 2004
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, L Haak, An Balcaen, S De Smet
    Abstract:

    The effect of including linseed [extruded (EL) or crushed (CL)] instead of whole soybeans (S) in the finishing diet of double-muscled Belgian Blue young bulls on the fatty acid composition of the longissimus thoracis, triceps brachii and subcutaneous fat was investigated. The dietary supply of C18:2n-6 was similar in the three diets, while in the EL and CL diet the supply of C18:3n-3 was equal. No effects of diet on the saturated, monounsaturated and branched chain fatty acids were found. Including linseed in place of whole soybeans increased the total intramuscular n-3 fatty acid content significantly, mainly as C18:3n-3, while no significant effect on the total and individual n-6 fatty acid incorporation was observed in the intramuscular fat. As a consequence of the higher n-3 content, the n-6/n-3 ratio was decreased by linseed feeding. In contrast with the intramuscular fat, the subcutaneous fat showed a significantly increased C18:3n-3 proportion accompanied by a significantly decreased C18:2n-6 proportion when linseed was fed. Diet did not influence the c9t11CLA content in the intramuscular or the subcutaneous fat.

  • meat quality fatty acid composition and flavour analysis in Belgian retail beef
    Meat Science, 2003
    Co-Authors: Katleen Raes, Daniel Demeyer, E Claeys, An Balcaen, P Dirinck, A De Winne, S De Smet
    Abstract:

    The objective of this study was to evaluate the differences in biochemical, sensorial and quality characteristics of retail beef in Belgium. Four types of beef (Belgian Blue double-muscled, Limousin, Irish and Argentine) and two different muscles (longissimus lumborum and semimembranosus) were bought at the retail level and compared with regard to colour, shear force, collagen content, fatty acid analysis, taste panel evaluation as well as flavour analysis. Belgian Blue and Limousin beef had a paler colour, lower collagen and intramuscular fat contents. Fatty acid profiles were significantly different between the four types, with significantly higher PUFA/SFA and n-6/n-3 ratios for Belgiam Blue and Limousin beef compared to Argentine and Irish beef. There were significant differences between the meat types for taste panel tenderness and shear force, however both measurements did not fully correspond. Flavour analysis by gas chromatography-mass spectrometry as well as sensory analysis demonstrated that Irish and Argentine beef had a higher flavour intensity related to higher contents of volatile compounds. Differences in tenderness and flavour between the meat types were probably affected by differences in ageing time, related to import vs local production of meat.

  • perimysial collagen crosslinking and meat tenderness in Belgian Blue double muscled cattle
    Meat Science, 2002
    Co-Authors: T M Ngapo, S De Smet, P Berge, J Culioli, Eric Dransfield, E Claeys
    Abstract:

    The relationship between intramuscular collagen and five collagen crosslink concentrations, and the tenderness of meat from Belgian Blue normal, heterozygous double-muscled (DM) and homozygous DM cattle was investigated using M. semitendinosus (St) and M. gluteobiceps (Gb). The histidinohydroxymerodesmosine (HHMD) concentration (per mol collagen) in St was less in DM animals than normal animals. Concentrations (per gram of wet meat) of HHMD and Erlich chromogen (EC) in Gb, and HHMD, EC, dihydroxylysinorleucine (DHLNL) and hydroxylysinorleucine (HLNL) in St were also lower in DM animals than normal animals. Shear force of raw meat was significantly greater in normal animals than DM for both muscles; cooked meat shear force was greater in the normal animals for the Gb muscles only, showing a good correlation with sarcomere length. Most correlations between shear force and collagen or crosslink concentrations were not significant and those that were highly significant were generally weak.

  • early post mortem conditions and the calpain calpastatin system in relation to tenderness of double muscled beef
    Meat Science, 1997
    Co-Authors: D Steen, S De Smet, L Uytterhaegen, E Claeys, Daniel Demeyer
    Abstract:

    Abstract Early post mortem temperature, pH, sarcomere length, colour, water holding capacity, calpain/calpastatin activities and myofibrillar protein concentrations (semi-quantative SDS-PAGE), measured at different times post mortem on 153 double-muscled Belgian Blue White bulls, were related to shear force (SF) measurements. The M. longissimus thoracis tenderised up to 8 days post mortem. SF was slightly correlated with temperature at 3 h post mortem (r = 0.20, p = 0.015), but not with pH early post mortem. Higher ultimate pH values measured at 24 h post mortem were related to darker meat, lower cooking losses and shorter sarcomere lengths. Sarcomere length was significantly related to SF, even after 12 days of ageing, suggesting that proteolytic activity was not able to overcome shortening. Up to 12 days post mortem, calpastatin and m-calpain activities were significantly correlated with SF suggesting a considerable role of calpains in meat tenderization of double-muscled Belgian Blue White bulls, although at 24 h post mortem, μ-calpain could no longer be detected. Titin, nebulin, filamin and troponin-T were degraded during the ageing period. Troponin-T was degraded by 80% between day 1 and 8. At 8 days post mortem its concentration was significantly correlated with 30 kDa (r = 0.63, p = 0.00), shear force (r = 0.39, p = 0.00), calpastatin activity at 1 day post mortem (r = 0.29, p = 0.01) and with the m-calpain/ calpastatin activity ratio at 1 day post mortem (r = −0.43, p = 0.00).

Tom Druet - One of the best experts on this subject based on the ideXlab platform.

  • Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle
    Genetics Selection Evolution, 2017
    Co-Authors: Marina Solé, Ann-stephan Gori, Pierre Faux, Amandine Bertrand, Frédéric Farnir, Mathieu Gautier, Tom Druet
    Abstract:

    Background : Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods. Results :When using 600 K single nucleotide polymorphisms (SNPs), the inbreeding coefficient (probability of sampling an HBD locus in an individual) was on average 0.303 (ranging from 0.258 to 0.375). HBD-classes associated to historical ancestors (with small segments ≤ 200 kb) accounted for 21.6% of the genome length (71.4% of the total length of the genome in HBD segments), whereas classes associated to more recent ancestors accounted for only 22.6% of the total length of the genome in HBD segments. However, these recent classes presented more individual variation than more ancient classes. Although inbreeding coefficients obtained with low SNP densities (7 and 32 K) were much lower (0.060 and 0.093), they were highly correlated with those obtained at higher density (r = 0.934 and 0.975, respectively), indicating that they captured most of the individual variation. At higher SNP density, smaller HBD segments are identified and, thus, more past generations can be explored. We observed very high correlations between our estimates and those based on homozygosity (r = 0.95) or on runs-of-homozygosity (r = 0.95). As expected, pedigree-based estimates were mainly correlated with recent HBD-classes (r = 0.56). Conclusions : Although we observed high levels of autozygosity associated with small HBD segments in BBB cattle, recent inbreeding accounted for most of the individual variation. Recent autozygosity can be captured efficiently with low-density SNP arrays and relatively simple models (e.g., two HBD classes). The HMM framework provides local HBD probabilities that are still useful at lower SNP densities.

  • MOESM5 of Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle
    2017
    Co-Authors: Marina Solé, Ann-stephan Gori, Pierre Faux, Amandine Bertrand, Frédéric Farnir, Mathieu Gautier, Tom Druet
    Abstract:

    Additional file 5. Table S1. Correlation coefficients between inbreeding coefficients estimated with different methods for the 634 Belgian Blue sires and using the 50 K panel. The table reports the correlations between all inbreeding coefficients estimated with different methods using the 50 K panel. Table S2. Correlation coefficients between inbreeding coefficients estimated with different methods for the 634 Belgian Blue sires and using the LD panel. The table reports the correlations between all inbreeding coefficients estimated with different methods using the LD panel

  • MOESM1 of Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle
    2017
    Co-Authors: Marina Solé, Ann-stephan Gori, Pierre Faux, Amandine Bertrand, Frédéric Farnir, Mathieu Gautier, Tom Druet
    Abstract:

    Additional file 1. Figure S1. Trend per year of birth of individual inbreeding coefficients in the 634 Belgian Blue sires. Inbreeding coefficients were estimated with the Mix14R model (13 HBD-classes model with pre-defined R k rates) using the BovineHD genotyping panel. (a) Trend for genomic inbreeding coefficients estimated using all HBD classes; (b) trend for genomic inbreeding coefficients estimated with the most recent HBD classes (R k  ≤ 32) and (c) trend obtained with pedigree-based estimates

  • Belgian Blue Cattle
    2016
    Co-Authors: Tom Druet, Michel Georges, Carole Charlier
    Abstract:

    Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattl

  • genome wide next generation dna and rna sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class h gene pigh and causes arthrogryposis in Belgian Blue cattle
    BMC Genomics, 2015
    Co-Authors: Arnaud Sartelet, Nico Tamma, Corinne Fasquelle, Wouter Coppieters, Michel Georges, Tom Druet, Eric Pailhoux, Christophe Richard, Latifa Karim, Carole Charlier
    Abstract:

    Cattle populations are characterized by regular outburst of genetic defects as a result of the extensive use of elite sires. The causative genes and mutations can nowadays be rapidly identified by means of genome-wide association studies combined with next generation DNA sequencing, provided that the causative mutations are conventional loss-of-function variants. We show in this work how the combined use of next generation DNA and RNA sequencing allows for the rapid identification of otherwise difficult to identify splice-site variants. We report the use of haplotype-based association mapping to identify a locus on bovine chromosome 10 that underlies autosomal recessive arthrogryposis in Belgian Blue Cattle. We identify 31 candidate mutations by resequencing the genome of four cases and 15 controls at ~10-fold depth. By analyzing RNA-Seq data from a carrier fetus, we observe skipping of the second exon of the PIGH gene, which we confirm by RT-PCR to be fully penetrant in tissues from affected calves. We identify - amongst the 31 candidate variants - a C-to-G transversion in the first intron of the PIGH gene (c211-10C > G) that is predicted to affect its acceptor splice-site. The resulting PIGH protein is likely to be non-functional as it lacks essential domains, and hence to cause arthrogryposis. This work illustrates how the growing arsenal of genome exploration tools continues to accelerate the identification of an even broader range of disease causing mutations, therefore improving the management and control of genetic defects in livestock.