Additional file 6: of Crossed beaks in a local Swiss chicken breed

Additional file 3: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Different genotype concordance metrics. 0, 1, and 2 is the number of non-reference allele. NA is SNP...

Additional file 5: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Number of variants identified by GATK, SAMtools and freebayes in the layer chicken genome. (XLSX 13Â...

Additional file 1: of Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Shaopan Ye (4987505)
Xiaolong Yuan (4987508)
Xiran Lin (4987502)
Ning Gao (153779)
Yuanyu Luo (3402893)
Zanmou Chen (3402890)
Jiaqi Li (220961)
Xiquan Zhang (147066)
Zhe Zhang (81603)

March 2018

Table S1. A pedigree-based genetic relationship matrix among the 24 key individuals. Table S2 A summ...

Additional file 2: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord DrĂśgemĂźller (3428597)
Christine Flury (164251)

March 2018

Phenotype details of Appenzeller Barthuhn chickens with crossed beak and all cases used in the study...

Additional file 4: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord DrĂśgemĂźller (3428597)
Christine Flury (164251)

March 2018

Table with all cases for phenotype description and genetic analyses. (XLSX 12Â kb

Additional file 1: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord Drögemüller (132266)
Christine Flury (164251)

March 2018

Scheme of the breeding trial. In total six breeding units of comparable size, made up the parental g...

Additional file 5: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord DrĂśgemĂźller (3428597)
Christine Flury (164251)

March 2018

Genotypes and diplotypes of Appenzeller Barthuhn and two other Swiss Chicken breeds. Genotypes of 12...

Additional file 6: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

September 2018

Table S5. Unique and shared homozygous segments across all chickens included RCS lines and line 63 c...

Additional file 3: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

November 2018

Table S2. The overlapping positions for 106 identified candidate regions with QTLs related to MD dis...

Additional file 1: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

September 2018

Figure S1. Histogram plot of MD incidence (%) rate. MD resistance in chickens is generally evaluated...

Additional file 9: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Percentage of genotyped individuals having a high relationship ≥ 0.25 (or 0.5) with at least one of ...

Additional file 5: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

September 2018

Table S4. Summary statistics and ROH distributions among 8 diverse inbred lines including lines 63, ...

Additional file 4: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

November 2018

Table S3. The inbreeding coefficient (F) for all 30 samples using 155,216 high quality SNPs. (XLSX 1...

Additional file 1: of Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

Irene Bassano (4055410)
Swee Ong (4055416)
Maximo Sanz-Hernandez (6561398)
Michal Vinkler (3178920)
Adebabay Kebede (6190421)
Olivier Hanotte (89422)
Ebele Onuigbo (6561401)
Mark Fife (3043425)
Paul Kellam (6413)

April 2019

Table S1. List of the inbred lines from the Pirbright Institute (Adapted from http://www.narf.ac.uk/...

Additional file 2: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

November 2018

Table S1. GO analysis for 51 genes in 106 identified candidate regions. (XLSX 20 kb

Additional file 3: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Different genotype concordance metrics. 0, 1, and 2 is the number of non-reference allele. NA is SNP...

Additional file 5: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Number of variants identified by GATK, SAMtools and freebayes in the layer chicken genome. (XLSX 13Â...

Additional file 1: of Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Shaopan Ye (4987505)
Xiaolong Yuan (4987508)
Xiran Lin (4987502)
Ning Gao (153779)
Yuanyu Luo (3402893)
Zanmou Chen (3402890)
Jiaqi Li (220961)
Xiquan Zhang (147066)
Zhe Zhang (81603)

March 2018

Table S1. A pedigree-based genetic relationship matrix among the 24 key individuals. Table S2 A summ...

Additional file 2: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord DrĂśgemĂźller (3428597)
Christine Flury (164251)

March 2018

Phenotype details of Appenzeller Barthuhn chickens with crossed beak and all cases used in the study...

Additional file 4: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord DrĂśgemĂźller (3428597)
Christine Flury (164251)

March 2018

Table with all cases for phenotype description and genetic analyses. (XLSX 12Â kb

Additional file 1: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord Drögemüller (132266)
Christine Flury (164251)

March 2018

Scheme of the breeding trial. In total six breeding units of comparable size, made up the parental g...

Additional file 5: of Crossed beaks in a local Swiss chicken breed

Sara Joller (4913569)
Flurina Bertschinger (4913578)
Erwin Kump (4913563)
Astrid Spiri (4913572)
Alois von Rotz (4913566)
Daniela Schweizer-Gorgas (4913575)
Cord DrĂśgemĂźller (3428597)
Christine Flury (164251)

March 2018

Genotypes and diplotypes of Appenzeller Barthuhn and two other Swiss Chicken breeds. Genotypes of 12...

Additional file 6: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

September 2018

Table S5. Unique and shared homozygous segments across all chickens included RCS lines and line 63 c...

Additional file 3: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

November 2018

Table S2. The overlapping positions for 106 identified candidate regions with QTLs related to MD dis...

Additional file 1: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

September 2018

Figure S1. Histogram plot of MD incidence (%) rate. MD resistance in chickens is generally evaluated...

Additional file 9: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Percentage of genotyped individuals having a high relationship ≥ 0.25 (or 0.5) with at least one of ...

Additional file 5: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

September 2018

Table S4. Summary statistics and ROH distributions among 8 diverse inbred lines including lines 63, ...

Additional file 4: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

November 2018

Table S3. The inbreeding coefficient (F) for all 30 samples using 155,216 high quality SNPs. (XLSX 1...

Additional file 1: of Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

Irene Bassano (4055410)
Swee Ong (4055416)
Maximo Sanz-Hernandez (6561398)
Michal Vinkler (3178920)
Adebabay Kebede (6190421)
Olivier Hanotte (89422)
Ebele Onuigbo (6561401)
Mark Fife (3043425)
Paul Kellam (6413)

April 2019

Table S1. List of the inbred lines from the Pirbright Institute (Adapted from http://www.narf.ac.uk/...

Additional file 2: of Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marekâs disease

Lingyang Xu (389143)
Yanghua He (155475)
Yi Ding (172783)
George Liu (122581)
Huanmin Zhang (41829)
Hans Cheng (3418421)
Robert Taylor (226235)
Jiuzhou Song (41834)

November 2018

Table S1. GO analysis for 51 genes in 106 identified candidate regions. (XLSX 20 kb

Additional file 3: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Different genotype concordance metrics. 0, 1, and 2 is the number of non-reference allele. NA is SNP...

Additional file 5: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

Guiyan Ni (3493136)
Tim Strom (3493133)
Hubert Pausch (151770)
Christian Reimer (766620)
Rudolf Preisinger (118728)
Henner Simianer (118732)
Malena Erbe (493655)

October 2015

Number of variants identified by GATK, SAMtools and freebayes in the layer chicken genome. (XLSX 13Â...

Additional file 1: of Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Shaopan Ye (4987505)
Xiaolong Yuan (4987508)
Xiran Lin (4987502)
Ning Gao (153779)
Yuanyu Luo (3402893)
Zanmou Chen (3402890)
Jiaqi Li (220961)
Xiquan Zhang (147066)
Zhe Zhang (81603)

March 2018

Table S1. A pedigree-based genetic relationship matrix among the 24 key individuals. Table S2 A summ...

Additional file 6: of Crossed beaks in a local Swiss chicken breed

Abstract

Extracted data

Additional file 6: of Crossed beaks in a local Swiss chicken breed

Abstract

Extracted data

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