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Luca Fontanesi - One of the best experts on this subject based on the ideXlab platform.

  • twenty years of artificial Directional Selection have shaped the genome of the italian large white pig breed
    Animal Genetics, 2016
    Co-Authors: G Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Vincenzo Russo, Maurizio Gallo, L Buttazzoni, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years of artificial Directional Selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the Selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the Selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a Directional Selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.

  • Twenty years of artificial Directional Selection have shaped the genome of the Italian Large White pig breed.
    Animal Genetics, 2015
    Co-Authors: G Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Vincenzo Russo, Maurizio Gallo, L Buttazzoni, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years of artificial Directional Selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the Selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni 

Sunjin Moon - One of the best experts on this subject based on the ideXlab platform.

  • a genome wide scan for signatures of Directional Selection in domesticated pigs
    BMC Genomics, 2015
    Co-Authors: Sunjin Moon, Woori Kwak, Wonhyong Chung, Samsun Sung, Taesung Park, M A M Groenen, Rasmus Nielsen
    Abstract:

    Animal domestication involved drastic phenotypic changes driven by strong artificial Selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial Selection during pig domestication. Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of Directional Selection by detecting selective sweeps using an F ST-based approach that detects Directional Selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under Selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of Directional Selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong Selection include loci involved in behaviorial traits in domesticated pigs including tameness. We show that a significant proportion of Selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of Selection during domestication in pigs.

Tetsuo Miyake - One of the best experts on this subject based on the ideXlab platform.

  • The novel Directional Selection based on complex discrete wavelet transform
    2014 International Conference on Wavelet Analysis and Pattern Recognition, 2014
    Co-Authors: Takeshi Kato, Zhong Zhang, Hiroshi Toda, Takashi Imamura, Tetsuo Miyake
    Abstract:

    This paper proposes the novel Directional Selection based on the complex discrete wavelet transform (CDWT). CDWT is known as a very useful image processing method because of shift-invariant property. Another property of the CDWT is the Directional Selection that can detect the edges with different direction in images and the Directional Selection is expected as a geometric feature extraction method. However, the Directional Selection of the CDWT does not offer various Directional features. Therefore, we propose the novel Directional Selection based on the CDWT and the Directional filters We design the Directional filters that can offers many Directional features references from the curvelet transform and the contourlet Transform.

  • Design of Directional Selection for three-dimensional complex discrete wavelet transform
    Sixth International Conference on Machine Vision (ICMV 2013), 2013
    Co-Authors: Takeshi Kato, Zhong Zhang, Hiroshi Toda, Takashi Imamura, Tetsuo Miyake, Yasuhiro Ishikawa
    Abstract:

    In this paper, we propose the novel design method of Directional Selection for three-dimensional complex discrete wavelet transform (3D-CDWT) (hereafter, all abbreviations will be written with capital letters). Previously, the complex discrete wavelet transform has been able to extract Directional edges from images using the Directional Selection property. This can be applied to shape and texture analysis. However the angular range of each Directional edge is still unclear and the angular ranges are fixed. Thus, it is difficult to be applied to image processing. Therefore, we firstly clarify the angular range of Directional edges by using frequency characteristics. Secondly, we propose a design method for the angular range of Directional edges with a desirable angular range. As a result, we can clarify the angular ranges of Directional edges and it is possible to obtain the Directional edges with arbitrary angular range.

  • The principle and evaluation method of Directional Selection of complex wavelet transform
    2013 International Conference on Wavelet Analysis and Pattern Recognition, 2013
    Co-Authors: Takeshi Kato, Zhong Zhang, Hiroshi Toda, Takashi Imamura, Tetsuo Miyake
    Abstract:

    Previously, Discrete wavelet Transform(DWT) is well known for useful image processing method. Complex Discrete Wavelet Transform(CDWT) is one of the DWT and has the function called Directional Selection. This is the expected to be applied into shape and texture analysis. But the principle of Directional Selection is still not clear. In this paper, we consider the principle of Directional Selection. After that, we propose the evaluation method for Directional Selection based on the principle. Finally, we confirm the validity of evaluation method.

  • a novel design method for Directional Selection based on 2 dimensional complex wavelet packet transform
    International Journal of Wavelets Multiresolution and Information Processing, 2013
    Co-Authors: Takeshi Kato, Zhong Zhang, Hiroshi Toda, Takashi Imamura, Tetsuo Miyake
    Abstract:

    In this paper, we propose a design method for Directional Selection in the two-dimensional complex wavelet packet transform (2D-CWPT). Current two-dimensional complex discrete wavelet transforms (2D-CDWT) can extract Directional components from images, but the number of directions is small, and the directions and resolutions are fixed. Thus the current 2D-CDWTs are not flexible enough. In this study, we propose a new design method of the Directional filters that can detect desirable direction components. Additionally flexible Directional Selection is achieved because the Directional filters are added to the 2D-CWPT. Finally, the proposed method is applied to defect detection in semiconductor wafer circuits and an encouraging result is obtained.

  • A novel design method for Directional Selection of 2-Dimensional Complex Wavelet Packet Transform
    2012 International Conference on Wavelet Analysis and Pattern Recognition, 2012
    Co-Authors: Takeshi Kato, Zhong Zhang, Hiroshi Toda, Takashi Imamura, Tetsuo Miyake
    Abstract:

    In this paper, we propose a design method for Directional Selection in the 2-Dimensional Complex Wavelet Packet Transform. Previous 2-Dimensional Complex Discrete Wavelet Transforms break up direction components, but the number of directions is small, and the directions and resolutions are fixed. So, they are not flexible enough. In this study, we propose a new design method that can detect desirable directions and resolutions. Finally, the proposed method is applied to defect detection in semiconductor wafer circuits in order to validate the proposed method.

Joel G Kingsolver - One of the best experts on this subject based on the ideXlab platform.

  • phenotypic Selection in natural populations what limits Directional Selection
    The American Naturalist, 2011
    Co-Authors: Joel G Kingsolver, Sarah E Diamond
    Abstract:

    AbstractStudies of phenotypic Selection document Directional Selection in many natural populations. What factors reduce total Directional Selection and the cumulative evolutionary responses to Selection? We combine two data sets for phenotypic Selection, representing more than 4,600 distinct estimates of Selection from 143 studies, to evaluate the potential roles of fitness trade-offs, indirect (correlated) Selection, temporally varying Selection, and stabilizing Selection for reducing net Directional Selection and cumulative responses to Selection. We detected little evidence that trade-offs among different fitness components reduced total Directional Selection in most study systems. Comparisons of Selection gradients and Selection differentials suggest that correlated Selection frequently reduced total Selection on size but not on other types of traits. The direction of Selection on a trait often changes over time in many temporally replicated studies, but these fluctuations have limited impact in reduc...

  • strength and tempo of Directional Selection in the wild
    Proceedings of the National Academy of Sciences of the United States of America, 2001
    Co-Authors: Hopi E Hoekstra, Jonathan M Hoekstra, David Berrigan, Sacha Vignieri, A Hoang, C E Hill, Peter Beerli, Joel G Kingsolver
    Abstract:

    Directional Selection is a major force driving adaptation and evolutionary change. However, the distribution, strength, and tempo of phenotypic Selection acting on quantitative traits in natural populations remain unclear across different study systems. We reviewed the literature (1984–1997) that reported the strength of Directional Selection as indexed by standardized linear Selection gradients (β). We asked how strong are viability and sexual Selection, and whether strength of Selection is correlated with the time scale over which it was measured. Estimates of the magnitude of Directional Selection (|β|) were exponentially distributed, with few estimates greater than 0.50 and most estimates less than 0.15. Sexual Selection (measured by mating success) appeared stronger than viability Selection (measured by survival). Viability Selection that was measured over short periods (days) was typically stronger than Selection measured over longer periods (months and years), but the strength of sexual Selection did not vary with duration of Selection episodes; as a result, sexual Selection was stronger than viability Selection over longer time scales (months and years), but not over short time scales (days).

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

  • twenty years of artificial Directional Selection have shaped the genome of the italian large white pig breed
    Animal Genetics, 2016
    Co-Authors: G Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Vincenzo Russo, Maurizio Gallo, L Buttazzoni, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years of artificial Directional Selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the Selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the Selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a Directional Selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.

  • Twenty years of artificial Directional Selection have shaped the genome of the Italian Large White pig breed.
    Animal Genetics, 2015
    Co-Authors: G Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Vincenzo Russo, Maurizio Gallo, L Buttazzoni, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years of artificial Directional Selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the Selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni