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Muhammad Luqman Aslam - One of the best experts on this subject based on the ideXlab platform.

  • genome wide candidate regions for selective sweeps revealed through massive parallel sequencing of dna across ten turkey populations
    BMC Genetics, 2014
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Fozia Nasreen, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Steven G Schroeder, M A M Groenen
    Abstract:

    The domestic turkey (Meleagris gallopavo) is an important Agricultural Species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated Species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these Species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated Species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.

  • whole genome snp discovery and analysis of genetic diversity in turkey meleagris gallopavo
    BMC Genomics, 2012
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Martin G Elferink, Robert C Fleischer, Steven G Schroeder
    Abstract:

    The turkey (Meleagris gallopavo) is an important Agricultural Species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock Species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock Species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.

  • genetic variances heritabilities and maternal effects on body weight breast meat yield meat quality traits and the shape of the growth curve in turkey birds
    BMC Genetics, 2011
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, B J Ducro, A L J Vereijken, M A M Groenen
    Abstract:

    Background Turkey is an important Agricultural Species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds.

Steven G Schroeder - One of the best experts on this subject based on the ideXlab platform.

  • genome wide candidate regions for selective sweeps revealed through massive parallel sequencing of dna across ten turkey populations
    BMC Genetics, 2014
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Fozia Nasreen, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Steven G Schroeder, M A M Groenen
    Abstract:

    The domestic turkey (Meleagris gallopavo) is an important Agricultural Species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated Species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these Species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated Species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.

  • whole genome snp discovery and analysis of genetic diversity in turkey meleagris gallopavo
    BMC Genomics, 2012
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Martin G Elferink, Robert C Fleischer, Steven G Schroeder
    Abstract:

    The turkey (Meleagris gallopavo) is an important Agricultural Species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock Species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock Species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.

J W M Bastiaansen - One of the best experts on this subject based on the ideXlab platform.

  • genome wide candidate regions for selective sweeps revealed through massive parallel sequencing of dna across ten turkey populations
    BMC Genetics, 2014
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Fozia Nasreen, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Steven G Schroeder, M A M Groenen
    Abstract:

    The domestic turkey (Meleagris gallopavo) is an important Agricultural Species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated Species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these Species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated Species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.

  • whole genome snp discovery and analysis of genetic diversity in turkey meleagris gallopavo
    BMC Genomics, 2012
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Martin G Elferink, Robert C Fleischer, Steven G Schroeder
    Abstract:

    The turkey (Meleagris gallopavo) is an important Agricultural Species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock Species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock Species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.

  • genetic variances heritabilities and maternal effects on body weight breast meat yield meat quality traits and the shape of the growth curve in turkey birds
    BMC Genetics, 2011
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, B J Ducro, A L J Vereijken, M A M Groenen
    Abstract:

    Background Turkey is an important Agricultural Species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds.

Richard P M A Crooijmans - One of the best experts on this subject based on the ideXlab platform.

  • genome wide candidate regions for selective sweeps revealed through massive parallel sequencing of dna across ten turkey populations
    BMC Genetics, 2014
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Fozia Nasreen, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Steven G Schroeder, M A M Groenen
    Abstract:

    The domestic turkey (Meleagris gallopavo) is an important Agricultural Species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated Species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these Species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated Species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.

  • whole genome snp discovery and analysis of genetic diversity in turkey meleagris gallopavo
    BMC Genomics, 2012
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Martin G Elferink, Robert C Fleischer, Steven G Schroeder
    Abstract:

    The turkey (Meleagris gallopavo) is an important Agricultural Species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock Species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock Species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.

  • genetic variances heritabilities and maternal effects on body weight breast meat yield meat quality traits and the shape of the growth curve in turkey birds
    BMC Genetics, 2011
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, B J Ducro, A L J Vereijken, M A M Groenen
    Abstract:

    Background Turkey is an important Agricultural Species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds.

M A M Groenen - One of the best experts on this subject based on the ideXlab platform.

  • genome wide candidate regions for selective sweeps revealed through massive parallel sequencing of dna across ten turkey populations
    BMC Genetics, 2014
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, Hendrikjan Megens, Fozia Nasreen, Le Ann Blomberg, Curtis P Van Tassell, Tad S Sonstegard, Steven G Schroeder, M A M Groenen
    Abstract:

    The domestic turkey (Meleagris gallopavo) is an important Agricultural Species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated Species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these Species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated Species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation.

  • genetic variances heritabilities and maternal effects on body weight breast meat yield meat quality traits and the shape of the growth curve in turkey birds
    BMC Genetics, 2011
    Co-Authors: Muhammad Luqman Aslam, J W M Bastiaansen, Richard P M A Crooijmans, B J Ducro, A L J Vereijken, M A M Groenen
    Abstract:

    Background Turkey is an important Agricultural Species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds.