13 results on '"Daetwyler, Hans D."'
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2. Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle
- Author
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Liu, Shuli, Liu, Shuli, Fang, Lingzhao, Zhou, Yang, Santos, Daniel J.A., Xiang, Ruidong, Daetwyler, Hans D., Chamberlain, Amanda J., Cole, John B., Li, Cong-jun, Yu, Ying, Ma, Li, Zhang, Shengli, Liu, George E., Liu, Shuli, Liu, Shuli, Fang, Lingzhao, Zhou, Yang, Santos, Daniel J.A., Xiang, Ruidong, Daetwyler, Hans D., Chamberlain, Amanda J., Cole, John B., Li, Cong-jun, Yu, Ying, Ma, Li, Zhang, Shengli, and Liu, George E.
- Abstract
DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others.
- Published
- 2019
3. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
4. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
5. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
6. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
7. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
8. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
9. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
10. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
11. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
- Author
-
Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., Hayes, Ben J., Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Hurtado Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Morgns S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Bieber, Anna, Purfield, Deidre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassel, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.
- Abstract
Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
- Published
- 2018
12. Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle Supporting Information
- Author
-
Larkin, Denis M, Daetwyler, Hans D, Hernandez, Alvaro G, Wright, Chris L, Hetrick, Lorie A, Boucek, Lisa, Bachman, Sharon, Thimmapuram, Jyothi, Larkin, Denis M, Daetwyler, Hans D, Hernandez, Alvaro G, Wright, Chris L, Hetrick, Lorie A, Boucek, Lisa, Bachman, Sharon, and Thimmapuram, Jyothi
- Abstract
Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set of 15,826 SNPs that overlapped in the sequence-based and BovineSNP50 SNPs showed the accuracy of the sequence-based haplotype reconstruction to be as high as 97%. By using the BovineSNP50 genotypes, the frequencies of Chief alleles on his two haplotypes then were determined in 1,149 of his descendants, and the distribution was compared with the frequencies that would be expected assuming no selection. We identified 49 chromosomal segments in which Chief alleles showed strong evidence of selection. Candidate polymorphisms for traits that have been under selection in the dairy cattle population then were identified by referencing Chief’s DNA sequence within these selected chromosome blocks. Eleven candidate genes were identified with functions related to milk-production, fertility, and disease-resistance traits. These data demonstrate that haplotype reconstruction of an ancestral proband by whole-genome resequencing in combination with high-density SNP genotyping of descendants can be used for rapid, genome-wide identification of the ancestor’s alleles that have been subjected to artificial selection.
- Published
- 2012
13. Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle Supporting Information
- Author
-
Larkin, Denis M, Daetwyler, Hans D, Hernandez, Alvaro G, Wright, Chris L, Hetrick, Lorie A, Boucek, Lisa, Bachman, Sharon, Thimmapuram, Jyothi, Larkin, Denis M, Daetwyler, Hans D, Hernandez, Alvaro G, Wright, Chris L, Hetrick, Lorie A, Boucek, Lisa, Bachman, Sharon, and Thimmapuram, Jyothi
- Abstract
Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set of 15,826 SNPs that overlapped in the sequence-based and BovineSNP50 SNPs showed the accuracy of the sequence-based haplotype reconstruction to be as high as 97%. By using the BovineSNP50 genotypes, the frequencies of Chief alleles on his two haplotypes then were determined in 1,149 of his descendants, and the distribution was compared with the frequencies that would be expected assuming no selection. We identified 49 chromosomal segments in which Chief alleles showed strong evidence of selection. Candidate polymorphisms for traits that have been under selection in the dairy cattle population then were identified by referencing Chief’s DNA sequence within these selected chromosome blocks. Eleven candidate genes were identified with functions related to milk-production, fertility, and disease-resistance traits. These data demonstrate that haplotype reconstruction of an ancestral proband by whole-genome resequencing in combination with high-density SNP genotyping of descendants can be used for rapid, genome-wide identification of the ancestor’s alleles that have been subjected to artificial selection.
- Published
- 2012
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