Additional file 9: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Additional file 4: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the posterior means of the proportion of genetic variance explained by each 1-Mb S...

Additional file 1: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Andrei Kudinov (6557384)
Natalia Dementieva (6557387)
Olga Mitrofanova (6557390)
Olga Stanishevskaya (6557393)
Elena Fedorova (465219)
Tatiana Larkina (6557402)
Arina Mishina (6557405)
Kirill Plemyashov (5012900)
Darren Griffin (5825045)
Michael Romanov (6557408)

April 2019

Table S1. Basic information for SNP markers per chromosome after quality control. (DOCX 29 kb

Additional file 1: of Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

Mengmeng Zhang (1507543)
Wei Han (151406)
Hui Tang (226667)
Guohui Li (105239)
Minjie Zhang (845494)
Ran Xu (316855)
Yijun Liu (205209)
Tao Yang (184280)
Wenting Li (177115)
Jianmin Zou (752752)
Keliang Wu (147828)

August 2018

Table S1. The distribution of SNPs and average distances between neighboring SNPs. (DOCX 17 kb

Additional file 8: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Table S4. The detailed lists of all the chicken pathways used in the pathway-based association analy...

Additional file 7: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Table S3. The detailed information of each pathway based on the pathway-based association analysis. ...

Additional file 1: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Figure S1. Significance of the pathway (âlog10 (PEMP-value)) versus: (a) the number of significant...

Additional file 2: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Figure S2. Manhattan plots showing the association of all SNPs with beak deformity trait using PLINK...

Additional file 8: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the SNP effect distribution within each significant window for skin percentage (SK...

Additional file 7: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the SNP effect distribution within each significant window for skin weight (SKINW)...

Additional file 1: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Plot of the density of SNPs per Mbp in each autosomal chromosome after filtration. (DOCX 155 kb

Additional file 6: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the SNP effect distribution within each significant window for abdominal fat perce...

Additional file 1: Table S1. of Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens

Guoqiang Yi (489551)
Manman Shen (3151977)
Jingwei Yuan (791540)
Congjiao Sun (617470)
Zhongyi Duan (760043)
Liang Qu (651440)
Taocun Dou (817624)
Meng Ma (2075878)
Jian Lu (51707)
Jun Guo (85069)
Sirui Chen (192925)
Lujiang Qu (114956)
Kehua Wang (535422)
Ning Yang (114965)

October 2015

Summary of genome-wide significant SNPs with respect to nine egg weights by univariate GWAS. Table S...

Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai
Yanyan Sun
Nian Liu
Fuguang Xue
Yunlei Li
Songshan Xu
Jianhua Ye
Lei Zhang
Yu Chen
Jilan Chen

June 2018

Abstract Background Beak deformity, typically expressed as the crossing of upper and lower mandibles...

Additional file 2: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

An excel file with the characterization of all the SNP windows analyzed including the proportion of ...

Additional file 3: of A new chicken 55K SNP genotyping array

Ranran Liu (155385)
Siyuan Xing (4530673)
Jie Wang (16762)
Maiqing Zheng (329297)
Huanxian Cui (2936352)
Richard Crooijmans (512752)
Qinghe Li (221930)
Guiping Zhao (329296)
Jie Wen (121424)

May 2019

The third group of SNPs which related to 861 candidate genes. The information of 861 candidate genes...

Additional file 4: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the posterior means of the proportion of genetic variance explained by each 1-Mb S...

Additional file 1: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Andrei Kudinov (6557384)
Natalia Dementieva (6557387)
Olga Mitrofanova (6557390)
Olga Stanishevskaya (6557393)
Elena Fedorova (465219)
Tatiana Larkina (6557402)
Arina Mishina (6557405)
Kirill Plemyashov (5012900)
Darren Griffin (5825045)
Michael Romanov (6557408)

April 2019

Table S1. Basic information for SNP markers per chromosome after quality control. (DOCX 29 kb

Additional file 1: of Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

Mengmeng Zhang (1507543)
Wei Han (151406)
Hui Tang (226667)
Guohui Li (105239)
Minjie Zhang (845494)
Ran Xu (316855)
Yijun Liu (205209)
Tao Yang (184280)
Wenting Li (177115)
Jianmin Zou (752752)
Keliang Wu (147828)

August 2018

Table S1. The distribution of SNPs and average distances between neighboring SNPs. (DOCX 17 kb

Additional file 8: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Table S4. The detailed lists of all the chicken pathways used in the pathway-based association analy...

Additional file 7: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Table S3. The detailed information of each pathway based on the pathway-based association analysis. ...

Additional file 1: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Figure S1. Significance of the pathway (âlog10 (PEMP-value)) versus: (a) the number of significant...

Additional file 2: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai (555291)
Yanyan Sun (351971)
Nian Liu (29935)
Fuguang Xue (3506771)
Yunlei Li (3168603)
Songshan Xu (5467700)
Jianhua Ye (5467697)
Lei Zhang (38117)
Yu Chen (4211599)
Jilan Chen (329299)

June 2018

Figure S2. Manhattan plots showing the association of all SNPs with beak deformity trait using PLINK...

Additional file 8: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the SNP effect distribution within each significant window for skin percentage (SK...

Additional file 7: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the SNP effect distribution within each significant window for skin weight (SKINW)...

Additional file 1: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Plot of the density of SNPs per Mbp in each autosomal chromosome after filtration. (DOCX 155 kb

Additional file 6: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the SNP effect distribution within each significant window for abdominal fat perce...

Additional file 1: Table S1. of Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens

Guoqiang Yi (489551)
Manman Shen (3151977)
Jingwei Yuan (791540)
Congjiao Sun (617470)
Zhongyi Duan (760043)
Liang Qu (651440)
Taocun Dou (817624)
Meng Ma (2075878)
Jian Lu (51707)
Jun Guo (85069)
Sirui Chen (192925)
Lujiang Qu (114956)
Kehua Wang (535422)
Ning Yang (114965)

October 2015

Summary of genome-wide significant SNPs with respect to nine egg weights by univariate GWAS. Table S...

Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Hao Bai
Yanyan Sun
Nian Liu
Fuguang Xue
Yunlei Li
Songshan Xu
Jianhua Ye
Lei Zhang
Yu Chen
Jilan Chen

June 2018

Abstract Background Beak deformity, typically expressed as the crossing of upper and lower mandibles...

Additional file 2: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

An excel file with the characterization of all the SNP windows analyzed including the proportion of ...

Additional file 3: of A new chicken 55K SNP genotyping array

Ranran Liu (155385)
Siyuan Xing (4530673)
Jie Wang (16762)
Maiqing Zheng (329297)
Huanxian Cui (2936352)
Richard Crooijmans (512752)
Qinghe Li (221930)
Guiping Zhao (329296)
Jie Wen (121424)

May 2019

The third group of SNPs which related to 861 candidate genes. The information of 861 candidate genes...

Additional file 4: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

Manhattan plot of the posterior means of the proportion of genetic variance explained by each 1-Mb S...

Additional file 1: of Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

Andrei Kudinov (6557384)
Natalia Dementieva (6557387)
Olga Mitrofanova (6557390)
Olga Stanishevskaya (6557393)
Elena Fedorova (465219)
Tatiana Larkina (6557402)
Arina Mishina (6557405)
Kirill Plemyashov (5012900)
Darren Griffin (5825045)
Michael Romanov (6557408)

April 2019

Table S1. Basic information for SNP markers per chromosome after quality control. (DOCX 29 kb

Additional file 1: of Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

Mengmeng Zhang (1507543)
Wei Han (151406)
Hui Tang (226667)
Guohui Li (105239)
Minjie Zhang (845494)
Ran Xu (316855)
Yijun Liu (205209)
Tao Yang (184280)
Wenting Li (177115)
Jianmin Zou (752752)
Keliang Wu (147828)

August 2018

Table S1. The distribution of SNPs and average distances between neighboring SNPs. (DOCX 17 kb

Additional file 9: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Abstract

Extracted data

Additional file 9: of Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays

Abstract

Extracted data

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