Additional file 2: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Additional file 2: of Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

Hugo Carignano (4852093)
Dana Roldan (4852078)
MarĂa Beribe (4852099)
MarĂa Raschia (4852102)
Ariel Amadio (3360812)
Juan Nani (4852090)
GerĂłnimo Gutierrez (4852096)
Irene Alvarez (466159)
Karina Trono (466160)
Mario Poli (522376)
Marcos Miretti (77348)

February 2018

Figure S2. Holstein and Jersey crosses population sub-structure. Each point represents the coordinat...

Additional file 5: Table S5. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Yahui Gao (776538)
Jianping Jiang (149448)
Shaohua Yang (143807)
Yali Hou (252579)
George Liu (122581)
Shengli Zhang (110370)
Qin Zhang (58638)
Dongxiao Sun (155488)

March 2017

Functional enrichment of GO and KEGG pathway analysis of genes covered by differential CNVRs. (XLSX ...

Additional file 1: of Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

Wengang Zhang (3594995)
Xue Gao (237216)
Yang Zhang (30734)
Yumin Zhao (476234)
Jiabao Zhang (349829)
Yutang Jia (6109619)
Bo Zhu (118038)
Lingyang Xu (389143)
Lupei Zhang (647384)
Huijiang Gao (628320)
Junya Li (240083)
Yan Chen (4308)

December 2018

Figure S1. Comparison of proportion of polymorphic (Pn). Figure S2. Comparison of minor allele frequ...

Additional file 2: of Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins

Mei Liu (41760)
Lingzhao Fang (4023761)
Shuli Liu (627105)
Michael Pan (5351486)
Eyal Seroussi (31976)
John Cole (392281)
Li Ma (46633)
Hong Chen (108084)
George Liu (122581)

March 2019

Table S1. CNVRs identified in this study and overlapping with QTL, OMIA, and CNVRs in previous studi...

Additional file 1: Table S1. of Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle

Shinji Sasaki (238265)
Toshio Watanabe (151136)
Shota Nishimura (238266)
Yoshikazu Sugimoto (151140)

January 2016

Characterization of cattle autosomal CNVRs based on previously published studies. Table S2 – Detaile...

Additional file 1: Table S1. of Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

Yang Zhou (65942)
Yuri Utsunomiya (3518468)
Lingyang Xu (389143)
El Hay (3540962)
Derek Bickhart (275943)
Pamela Alexandre (3540959)
Benjamin Rosen (791093)
Steven Schroeder (77597)
Roberto Carvalheiro (523642)
Haroldo de Rezende Neves (3540953)
Tad Sonstegard (392288)
Curtis Van Tassell (721067)
JosĂŠ Ferraz (3540971)
Heidge Fukumasu (588307)
Jose Garcia (1371534)
George Liu (122581)

June 2016

Detail information of the CNVs detected with high confidence. Table S2. CNV validation by qPCR. Tabl...

Additional file 9: of Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Joaquim da Silva (3455798)
Poliana Giachetto (3455801)
Luiz da Silva (3455792)
Leandro Cintra (3455804)
Samuel Paiva (184995)
Michel Yamagishi (3455795)
Alexandre Caetano (3455789)

June 2016

CNVRs overlapping with previously detected QTLs from the Bovine QTL Database. (XLSX 2973 kb

Additional file 1: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Yang Zhou (65942)
Erin Connor (3539750)
George Wiggans (392282)
Yongfang Lu (3251994)
Robert Tempelman (5162687)
Steven Schroeder (77597)
Hong Chen (108084)
George Liu (122581)

May 2018

Figure S1. Box plot for dPTA distribution of the 2 feed intake-related phenotypes of RFI and DMI. (P...

Additional file 2: Table S2. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Yahui Gao (776538)
Jianping Jiang (149448)
Shaohua Yang (143807)
Yali Hou (252579)
George Liu (122581)
Shengli Zhang (110370)
Qin Zhang (58638)
Dongxiao Sun (155488)

March 2017

Primers information and confirmation results of the 11 chosen CNVRs by qPCR analysis. (XLSX 14Â kb

Additional file 1: of Genomic predictions combining SNP markers and copy number variations in Nellore cattle

El Hay (3540962)
Yuri Utsunomiya (3518468)
Lingyang Xu (389143)
Yang Zhou (65942)
Haroldo Neves (5343551)
Roberto Carvalheiro (523642)
Derek Bickhart (275943)
Li Ma (46633)
Jose Garcia (1371534)
George Liu (122581)

June 2018

Table S1. Detail information of the CNVs detected with high confidence. (XLSX 37 kb

Additional file 2: of Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

T. Iso-Touru (3409142)
G. Sahana (3409136)
B. Guldbrandtsen (3409133)
M. Lund (3409139)
J. Vilkki (3409145)

March 2016

SNPs with Bonferroni corrected p-values higher than 0.05 (−log10(p) ≥ 8.50) for the fat yield. Colum...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 2: of Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle

Shinji Sasaki (238265)
Toshio Watanabe (151136)
Shota Nishimura (238266)
Yoshikazu Sugimoto (151140)

January 2016

Detection number and mean size of CNVRs in 3, 5, 10, and 15 consecutive SNP windows. (PPTX 53Â kb

Additional file 1: of Characterization of recombination features and the genetic basis in multiple cattle breeds

Botong Shen (822728)
Jicai Jiang (122571)
Eyal Seroussi (31976)
George Liu (122581)
Li Ma (46633)

April 2018

Eight breed- and sex-specific recombination maps for Holstein, Jersey, Brown Swiss, and Ayrshire in ...

Additional file 4: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S13. GWAS using imputed whole genome sequence data. The detailed results of p-values for each ...

Additional file 2: of Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

Hugo Carignano (4852093)
Dana Roldan (4852078)
MarĂa Beribe (4852099)
MarĂa Raschia (4852102)
Ariel Amadio (3360812)
Juan Nani (4852090)
GerĂłnimo Gutierrez (4852096)
Irene Alvarez (466159)
Karina Trono (466160)
Mario Poli (522376)
Marcos Miretti (77348)

February 2018

Figure S2. Holstein and Jersey crosses population sub-structure. Each point represents the coordinat...

Additional file 5: Table S5. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Yahui Gao (776538)
Jianping Jiang (149448)
Shaohua Yang (143807)
Yali Hou (252579)
George Liu (122581)
Shengli Zhang (110370)
Qin Zhang (58638)
Dongxiao Sun (155488)

March 2017

Functional enrichment of GO and KEGG pathway analysis of genes covered by differential CNVRs. (XLSX ...

Additional file 1: of Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

Wengang Zhang (3594995)
Xue Gao (237216)
Yang Zhang (30734)
Yumin Zhao (476234)
Jiabao Zhang (349829)
Yutang Jia (6109619)
Bo Zhu (118038)
Lingyang Xu (389143)
Lupei Zhang (647384)
Huijiang Gao (628320)
Junya Li (240083)
Yan Chen (4308)

December 2018

Figure S1. Comparison of proportion of polymorphic (Pn). Figure S2. Comparison of minor allele frequ...

Additional file 2: of Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins

Mei Liu (41760)
Lingzhao Fang (4023761)
Shuli Liu (627105)
Michael Pan (5351486)
Eyal Seroussi (31976)
John Cole (392281)
Li Ma (46633)
Hong Chen (108084)
George Liu (122581)

March 2019

Table S1. CNVRs identified in this study and overlapping with QTL, OMIA, and CNVRs in previous studi...

Additional file 1: Table S1. of Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle

Shinji Sasaki (238265)
Toshio Watanabe (151136)
Shota Nishimura (238266)
Yoshikazu Sugimoto (151140)

January 2016

Characterization of cattle autosomal CNVRs based on previously published studies. Table S2 – Detaile...

Additional file 1: Table S1. of Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

Yang Zhou (65942)
Yuri Utsunomiya (3518468)
Lingyang Xu (389143)
El Hay (3540962)
Derek Bickhart (275943)
Pamela Alexandre (3540959)
Benjamin Rosen (791093)
Steven Schroeder (77597)
Roberto Carvalheiro (523642)
Haroldo de Rezende Neves (3540953)
Tad Sonstegard (392288)
Curtis Van Tassell (721067)
JosĂŠ Ferraz (3540971)
Heidge Fukumasu (588307)
Jose Garcia (1371534)
George Liu (122581)

June 2016

Detail information of the CNVs detected with high confidence. Table S2. CNV validation by qPCR. Tabl...

Additional file 9: of Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Joaquim da Silva (3455798)
Poliana Giachetto (3455801)
Luiz da Silva (3455792)
Leandro Cintra (3455804)
Samuel Paiva (184995)
Michel Yamagishi (3455795)
Alexandre Caetano (3455789)

June 2016

CNVRs overlapping with previously detected QTLs from the Bovine QTL Database. (XLSX 2973 kb

Additional file 1: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Yang Zhou (65942)
Erin Connor (3539750)
George Wiggans (392282)
Yongfang Lu (3251994)
Robert Tempelman (5162687)
Steven Schroeder (77597)
Hong Chen (108084)
George Liu (122581)

May 2018

Figure S1. Box plot for dPTA distribution of the 2 feed intake-related phenotypes of RFI and DMI. (P...

Additional file 2: Table S2. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Yahui Gao (776538)
Jianping Jiang (149448)
Shaohua Yang (143807)
Yali Hou (252579)
George Liu (122581)
Shengli Zhang (110370)
Qin Zhang (58638)
Dongxiao Sun (155488)

March 2017

Primers information and confirmation results of the 11 chosen CNVRs by qPCR analysis. (XLSX 14Â kb

Additional file 1: of Genomic predictions combining SNP markers and copy number variations in Nellore cattle

El Hay (3540962)
Yuri Utsunomiya (3518468)
Lingyang Xu (389143)
Yang Zhou (65942)
Haroldo Neves (5343551)
Roberto Carvalheiro (523642)
Derek Bickhart (275943)
Li Ma (46633)
Jose Garcia (1371534)
George Liu (122581)

June 2018

Table S1. Detail information of the CNVs detected with high confidence. (XLSX 37 kb

Additional file 2: of Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants

T. Iso-Touru (3409142)
G. Sahana (3409136)
B. Guldbrandtsen (3409133)
M. Lund (3409139)
J. Vilkki (3409145)

March 2016

SNPs with Bonferroni corrected p-values higher than 0.05 (−log10(p) ≥ 8.50) for the fat yield. Colum...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 2: of Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle

Shinji Sasaki (238265)
Toshio Watanabe (151136)
Shota Nishimura (238266)
Yoshikazu Sugimoto (151140)

January 2016

Detection number and mean size of CNVRs in 3, 5, 10, and 15 consecutive SNP windows. (PPTX 53Â kb

Additional file 1: of Characterization of recombination features and the genetic basis in multiple cattle breeds

Botong Shen (822728)
Jicai Jiang (122571)
Eyal Seroussi (31976)
George Liu (122581)
Li Ma (46633)

April 2018

Eight breed- and sex-specific recombination maps for Holstein, Jersey, Brown Swiss, and Ayrshire in ...

Additional file 4: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S13. GWAS using imputed whole genome sequence data. The detailed results of p-values for each ...

Additional file 2: of Genome-wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

Hugo Carignano (4852093)
Dana Roldan (4852078)
MarĂa Beribe (4852099)
MarĂa Raschia (4852102)
Ariel Amadio (3360812)
Juan Nani (4852090)
GerĂłnimo Gutierrez (4852096)
Irene Alvarez (466159)
Karina Trono (466160)
Mario Poli (522376)
Marcos Miretti (77348)

February 2018

Figure S2. Holstein and Jersey crosses population sub-structure. Each point represents the coordinat...

Additional file 5: Table S5. of CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

Yahui Gao (776538)
Jianping Jiang (149448)
Shaohua Yang (143807)
Yali Hou (252579)
George Liu (122581)
Shengli Zhang (110370)
Qin Zhang (58638)
Dongxiao Sun (155488)

March 2017

Functional enrichment of GO and KEGG pathway analysis of genes covered by differential CNVRs. (XLSX ...

Additional file 1: of Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

Wengang Zhang (3594995)
Xue Gao (237216)
Yang Zhang (30734)
Yumin Zhao (476234)
Jiabao Zhang (349829)
Yutang Jia (6109619)
Bo Zhu (118038)
Lingyang Xu (389143)
Lupei Zhang (647384)
Huijiang Gao (628320)
Junya Li (240083)
Yan Chen (4308)

December 2018

Figure S1. Comparison of proportion of polymorphic (Pn). Figure S2. Comparison of minor allele frequ...

Additional file 2: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Abstract

Extracted data

Additional file 2: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Abstract

Extracted data

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