Principal component analysis of 1,543 animals genotyped with 43,043 SNPs.

Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: Application in cattle breeds

BERTOLINI, FRANCESCA
GALIMBERTI, GIULIANO
CALO', DANIELA GIOVANNA
SCHIAVO, GIUSEPPINA
FONTANESI, LUCA
Matassino, D.

January 2015

The genetic identification of the population of origin of individuals, including animals, has severa...

Principal component analysis of European wolves using 67K single nucleotide polymorphism markers.

Astrid V. Stronen (469967)
Bogumiła Jędrzejewska (469968)
Cino Pertoldi (469969)
Ditte Demontis (469970)
Ettore Randi (42572)
Magdalena Niedziałkowska (469971)
Małgorzata Pilot (154642)
Vadim E. Sidorovich (154644)
Ihor Dykyy (469972)
Josip Kusak (469973)
Elena Tsingarska (469974)
Ilpo Kojola (469975)
Alexandros A. Karamanlidis (180358)
Aivars Ornicans (469976)
Vladimir A. Lobkov (469977)
Vitalii Dumenko (469978)
Sylwia D. Czarnomska (469979)

October 2013

Principal component analysis of European wolves using 67K single nucleotide polymorphism (SNP) ma...

Genetic structure of the Brazilian Gir population.

Amanda Marchi Maiorano (5586707)
Daniela Lino Lourenco (3694603)
Shogo Tsuruta (5586710)
Alejandra Maria Toro Ospina (5586713)
Nedenia Bonvino Stafuzza (790336)
Yutaka Masuda (5586716)
Anibal Eugenio Vercesi Filho (5586719)
Joslaine Noely dos Santos Goncalves Cyrillo (5586722)
Rogério Abdallah Curi (5586725)
Josineudson Augusto II de Vasconcelos Silva (5586728)

August 2018

(a) Eigenvalues of principal component analysis (PCA). (b) PCA scatter-plots of the first two pri...

Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs and 8 Australian cattle dogs (‘Dataset B’).

Kylie M. Cairns (5367911)
Laura M. Shannon (428052)
Janice Koler-Matznick (5367914)
J. William O. Ballard (3342590)
Adam R. Boyko (145817)

June 2018

Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW din...

Clustering of animals based on principal component analysis of allele sharing.

James W. Kijas (147570)
James E. Miller (147575)
Tracy Hadfield (147583)
Russell McCulloch (147590)
Elsa Garcia-Gamez (5648821)
Laercio R. Porto Neto (147600)
Noelle Cockett (147607)

July 2012

Individual animals were plotted for the first (PCA1) and second (PCA2) principal components using...

Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes and 5 NGSD.

Kylie M. Cairns (5367911)
Laura M. Shannon (428052)
Janice Koler-Matznick (5367914)
J. William O. Ballard (3342590)
Adam R. Boyko (145817)

June 2018

Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW din...

Phylogram of the inferred relationships between 74 cattle breeds.

Jared E. Decker (534281)
Stephanie D. McKay (236279)
Megan M. Rolf (544071)
JaeWoo Kim (544072)
Antonio Molina Alcalá (544073)
Tad S. Sonstegard (175161)
Olivier Hanotte (89422)
Anders Götherström (216373)
Christopher M. Seabury (194409)
Lisa Praharani (544074)
Masroor Ellahi Babar (544075)
Luciana Correia de Almeida Regitano (544076)
Mehmet Ali Yildiz (544077)
Michael P. Heaton (186097)
Wan-Sheng Liu (200939)
Chu-Zhao Lei (380116)
James M. Reecy (121998)
Muhammad Saif-Ur-Rehman (544078)
Robert D. Schnabel (194392)
Jeremy F. Taylor (179789)

March 2014

Breeds were colored according to their geographic origin; black: Africa, green: Asia, red: North ...

Phylogram of the inferred relationships between 134 cattle breeds.

Jared E. Decker (534281)
Stephanie D. McKay (236279)
Megan M. Rolf (544071)
JaeWoo Kim (544072)
Antonio Molina Alcalá (544073)
Tad S. Sonstegard (175161)
Olivier Hanotte (89422)
Anders Götherström (216373)
Christopher M. Seabury (194409)
Lisa Praharani (544074)
Masroor Ellahi Babar (544075)
Luciana Correia de Almeida Regitano (544076)
Mehmet Ali Yildiz (544077)
Michael P. Heaton (186097)
Wan-Sheng Liu (200939)
Chu-Zhao Lei (380116)
James M. Reecy (121998)
Muhammad Saif-Ur-Rehman (544078)
Robert D. Schnabel (194392)
Jeremy F. Taylor (179789)

March 2014

Breeds were colored according to their geographic origin; black: Africa, green: Asia, red: North ...

Genetic relationship between Gulf Coast Native and 12 other breeds.

James W. Kijas (147570)
James E. Miller (147575)
Tracy Hadfield (147583)
Russell McCulloch (147590)
Elsa Garcia-Gamez (5648821)
Laercio R. Porto Neto (147600)
Noelle Cockett (147607)

July 2012

Individuals were clustered using PCA of allele sharing and plotted for PCA1 and 2 (A) and ...

Principal component analyses for n = 48 Nordic dogs with 15 648 single nucleotide polymorphism markers.

Astrid V. Stronen (469967)
Elina Salmela (95614)
Birna K. Baldursdóttir (4059688)
Peer Berg (3212316)
Ingvild S. Espelien (4059685)
Kirsi Järvi (4059682)
Henrik Jensen (214354)
Torsten N. Kristensen (357531)
Claudia Melis (713509)
Tommaso Manenti (761778)
Hannes Lohi (102236)
Cino Pertoldi (469969)

June 2017

Norwegian Buhund (n = 10), Norrbottenspets (n = 12), Norwegian Lundehund (n = 17), and Icelandic ...

Principal component analysis on the log10 (count+1) of each of the most abundant genera (present at >0.1%) identified for each animal.

Daniel Hand (278401)
Corrin Wallis (278402)
Alison Colyer (278403)
Charles W. Penn (161371)

January 2013

Each point is labelled with the dog ID followed by the mother ID and is coloured according to the...

Tracing cattle breeds with principal components analysis ancestry informative SNPs.

Jamey Lewis
Zafiris Abas
Christos Dadousis
Dimitrios Lykidis
Peristera Paschou
Petros Drineas

The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine geneti...

Genetic differentiation of the studied horse breeds visualized using principal components analysis (A) and FST-based cladogram (B).

Artur Gurgul (825970)
Igor Jasielczuk (825972)
Ewelina Semik-Gurgul (5880599)
Klaudia Pawlina-Tyszko (4814556)
Monika Stefaniuk-Szmukier (3908575)
Tomasz Szmatoła (4585621)
Grażyna Polak (6278210)
Iwona Tomczyk-Wrona (6278213)
Monika Bugno-Poniewierska (3908578)

January 2019

Principal components analysis was performed based on SNP genotypes. The cladogram was created based ...

Principal Component Analysis (PCA) based on genotype data for four German warmblood horse breeds.

Wietje Nolte (6635660)
Georg Thaller (151783)
Christa Kuehn (82445)

April 2019

Based on a genomic relationship matrix, eigenvalues were calculated and the first two components use...

The two leading principal components of the analysis with the genotype data with 601,455 SNPs for 282 animals.

Ngoc-Thuy Ha (5662534)
Josef Johann Gross (705718)
Annette van Dorland (705719)
Jens Tetens (132258)
Georg Thaller (151783)
Martin Schlather (166743)
Rupert Bruckmaier (705720)
Henner Simianer (118732)

March 2015

The first and second principal components explain 8.7% and 1.4% of the total variation, respectiv...

Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: Application in cattle breeds

BERTOLINI, FRANCESCA
GALIMBERTI, GIULIANO
CALO', DANIELA GIOVANNA
SCHIAVO, GIUSEPPINA
FONTANESI, LUCA
Matassino, D.

January 2015

The genetic identification of the population of origin of individuals, including animals, has severa...

Principal component analysis of European wolves using 67K single nucleotide polymorphism markers.

Astrid V. Stronen (469967)
Bogumiła Jędrzejewska (469968)
Cino Pertoldi (469969)
Ditte Demontis (469970)
Ettore Randi (42572)
Magdalena Niedziałkowska (469971)
Małgorzata Pilot (154642)
Vadim E. Sidorovich (154644)
Ihor Dykyy (469972)
Josip Kusak (469973)
Elena Tsingarska (469974)
Ilpo Kojola (469975)
Alexandros A. Karamanlidis (180358)
Aivars Ornicans (469976)
Vladimir A. Lobkov (469977)
Vitalii Dumenko (469978)
Sylwia D. Czarnomska (469979)

October 2013

Principal component analysis of European wolves using 67K single nucleotide polymorphism (SNP) ma...

Genetic structure of the Brazilian Gir population.

Amanda Marchi Maiorano (5586707)
Daniela Lino Lourenco (3694603)
Shogo Tsuruta (5586710)
Alejandra Maria Toro Ospina (5586713)
Nedenia Bonvino Stafuzza (790336)
Yutaka Masuda (5586716)
Anibal Eugenio Vercesi Filho (5586719)
Joslaine Noely dos Santos Goncalves Cyrillo (5586722)
Rogério Abdallah Curi (5586725)
Josineudson Augusto II de Vasconcelos Silva (5586728)

August 2018

(a) Eigenvalues of principal component analysis (PCA). (b) PCA scatter-plots of the first two pri...

Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes, 5 NGSD, 8 Borneo village dogs, 9 Vietnam village dogs, 10 Portugal village dogs and 8 Australian cattle dogs (‘Dataset B’).

Kylie M. Cairns (5367911)
Laura M. Shannon (428052)
Janice Koler-Matznick (5367914)
J. William O. Ballard (3342590)
Adam R. Boyko (145817)

June 2018

Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW din...

Clustering of animals based on principal component analysis of allele sharing.

James W. Kijas (147570)
James E. Miller (147575)
Tracy Hadfield (147583)
Russell McCulloch (147590)
Elsa Garcia-Gamez (5648821)
Laercio R. Porto Neto (147600)
Noelle Cockett (147607)

July 2012

Individual animals were plotted for the first (PCA1) and second (PCA2) principal components using...

Principal components analysis (PCA) based upon filtered whole genome SNP genotypes (58,512 sites) for 23 dingoes and 5 NGSD.

Kylie M. Cairns (5367911)
Laura M. Shannon (428052)
Janice Koler-Matznick (5367914)
J. William O. Ballard (3342590)
Adam R. Boyko (145817)

June 2018

Colours represent population clusters: red for SE dingoes, purple for FI dingoes, blue for NW din...

Phylogram of the inferred relationships between 74 cattle breeds.

Jared E. Decker (534281)
Stephanie D. McKay (236279)
Megan M. Rolf (544071)
JaeWoo Kim (544072)
Antonio Molina Alcalá (544073)
Tad S. Sonstegard (175161)
Olivier Hanotte (89422)
Anders Götherström (216373)
Christopher M. Seabury (194409)
Lisa Praharani (544074)
Masroor Ellahi Babar (544075)
Luciana Correia de Almeida Regitano (544076)
Mehmet Ali Yildiz (544077)
Michael P. Heaton (186097)
Wan-Sheng Liu (200939)
Chu-Zhao Lei (380116)
James M. Reecy (121998)
Muhammad Saif-Ur-Rehman (544078)
Robert D. Schnabel (194392)
Jeremy F. Taylor (179789)

March 2014

Breeds were colored according to their geographic origin; black: Africa, green: Asia, red: North ...

Phylogram of the inferred relationships between 134 cattle breeds.

Jared E. Decker (534281)
Stephanie D. McKay (236279)
Megan M. Rolf (544071)
JaeWoo Kim (544072)
Antonio Molina Alcalá (544073)
Tad S. Sonstegard (175161)
Olivier Hanotte (89422)
Anders Götherström (216373)
Christopher M. Seabury (194409)
Lisa Praharani (544074)
Masroor Ellahi Babar (544075)
Luciana Correia de Almeida Regitano (544076)
Mehmet Ali Yildiz (544077)
Michael P. Heaton (186097)
Wan-Sheng Liu (200939)
Chu-Zhao Lei (380116)
James M. Reecy (121998)
Muhammad Saif-Ur-Rehman (544078)
Robert D. Schnabel (194392)
Jeremy F. Taylor (179789)

March 2014

Breeds were colored according to their geographic origin; black: Africa, green: Asia, red: North ...

Genetic relationship between Gulf Coast Native and 12 other breeds.

James W. Kijas (147570)
James E. Miller (147575)
Tracy Hadfield (147583)
Russell McCulloch (147590)
Elsa Garcia-Gamez (5648821)
Laercio R. Porto Neto (147600)
Noelle Cockett (147607)

July 2012

Individuals were clustered using PCA of allele sharing and plotted for PCA1 and 2 (A) and ...

Principal component analyses for n = 48 Nordic dogs with 15 648 single nucleotide polymorphism markers.

Astrid V. Stronen (469967)
Elina Salmela (95614)
Birna K. Baldursdóttir (4059688)
Peer Berg (3212316)
Ingvild S. Espelien (4059685)
Kirsi Järvi (4059682)
Henrik Jensen (214354)
Torsten N. Kristensen (357531)
Claudia Melis (713509)
Tommaso Manenti (761778)
Hannes Lohi (102236)
Cino Pertoldi (469969)

June 2017

Norwegian Buhund (n = 10), Norrbottenspets (n = 12), Norwegian Lundehund (n = 17), and Icelandic ...

Principal component analysis on the log10 (count+1) of each of the most abundant genera (present at >0.1%) identified for each animal.

Daniel Hand (278401)
Corrin Wallis (278402)
Alison Colyer (278403)
Charles W. Penn (161371)

January 2013

Each point is labelled with the dog ID followed by the mother ID and is coloured according to the...

Tracing cattle breeds with principal components analysis ancestry informative SNPs.

Jamey Lewis
Zafiris Abas
Christos Dadousis
Dimitrios Lykidis
Peristera Paschou
Petros Drineas

The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine geneti...

Genetic differentiation of the studied horse breeds visualized using principal components analysis (A) and FST-based cladogram (B).

Artur Gurgul (825970)
Igor Jasielczuk (825972)
Ewelina Semik-Gurgul (5880599)
Klaudia Pawlina-Tyszko (4814556)
Monika Stefaniuk-Szmukier (3908575)
Tomasz Szmatoła (4585621)
Grażyna Polak (6278210)
Iwona Tomczyk-Wrona (6278213)
Monika Bugno-Poniewierska (3908578)

January 2019

Principal components analysis was performed based on SNP genotypes. The cladogram was created based ...

Principal Component Analysis (PCA) based on genotype data for four German warmblood horse breeds.

Wietje Nolte (6635660)
Georg Thaller (151783)
Christa Kuehn (82445)

April 2019

Based on a genomic relationship matrix, eigenvalues were calculated and the first two components use...

The two leading principal components of the analysis with the genotype data with 601,455 SNPs for 282 animals.

Ngoc-Thuy Ha (5662534)
Josef Johann Gross (705718)
Annette van Dorland (705719)
Jens Tetens (132258)
Georg Thaller (151783)
Martin Schlather (166743)
Rupert Bruckmaier (705720)
Henner Simianer (118732)

March 2015

The first and second principal components explain 8.7% and 1.4% of the total variation, respectiv...

Combined use of principal component analysis and random forests identify population-informative single nucleotide polymorphisms: Application in cattle breeds

BERTOLINI, FRANCESCA
GALIMBERTI, GIULIANO
CALO', DANIELA GIOVANNA
SCHIAVO, GIUSEPPINA
FONTANESI, LUCA
Matassino, D.

January 2015

The genetic identification of the population of origin of individuals, including animals, has severa...

Principal component analysis of European wolves using 67K single nucleotide polymorphism markers.

Astrid V. Stronen (469967)
Bogumiła Jędrzejewska (469968)
Cino Pertoldi (469969)
Ditte Demontis (469970)
Ettore Randi (42572)
Magdalena Niedziałkowska (469971)
Małgorzata Pilot (154642)
Vadim E. Sidorovich (154644)
Ihor Dykyy (469972)
Josip Kusak (469973)
Elena Tsingarska (469974)
Ilpo Kojola (469975)
Alexandros A. Karamanlidis (180358)
Aivars Ornicans (469976)
Vladimir A. Lobkov (469977)
Vitalii Dumenko (469978)
Sylwia D. Czarnomska (469979)

October 2013

Principal component analysis of European wolves using 67K single nucleotide polymorphism (SNP) ma...

Genetic structure of the Brazilian Gir population.

Amanda Marchi Maiorano (5586707)
Daniela Lino Lourenco (3694603)
Shogo Tsuruta (5586710)
Alejandra Maria Toro Ospina (5586713)
Nedenia Bonvino Stafuzza (790336)
Yutaka Masuda (5586716)
Anibal Eugenio Vercesi Filho (5586719)
Joslaine Noely dos Santos Goncalves Cyrillo (5586722)
Rogério Abdallah Curi (5586725)
Josineudson Augusto II de Vasconcelos Silva (5586728)

August 2018

(a) Eigenvalues of principal component analysis (PCA). (b) PCA scatter-plots of the first two pri...

Principal component analysis of 1,543 animals genotyped with 43,043 SNPs.

Abstract

Extracted data

Principal component analysis of 1,543 animals genotyped with 43,043 SNPs.

Abstract

Extracted data

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