Additional file 10: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

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 8: of A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle

Terhi Iso-Touru (505133)
Christine Wurmser (151766)
Heli Venhoranta (236269)
Maya Hiltpold (6581882)
Tujia Savolainen (6581885)
Anu Sironen (403686)
Konrad Fischer (6581888)
Krzysztof Flisikowski (133283)
Ruedi Fries (151786)
Alejandro Vicente-Carrillo (3119754)
Manuel Alvarez-Rodriguez (3665020)
Szabolcs Nagy (2231290)
Mervi Mutikainen (6581891)
Jaana Peippo (4805769)
Juhani Taponen (236295)
Goutam Sahana (126076)
Bernt Guldbrandtsen (340532)
Henri Simonen (6581894)
Heriberto Rodriguez-Martinez (3119748)
Magnus Andersson (236322)
Hubert Pausch (151770)

April 2019

Candidate causal variants compatible with recessive inheritance of asthenospermia. Functional conseq...

Additional file 2: 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

Table S1. Primer information for CNV validation. Table S2. Characteristics of CNV and their overlapp...

Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902...

Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 ...

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb

Additional file 6: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 5: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S3. 2âĂâ2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 4: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S2. Splicing junction annotation analysis using BAM files generated by different alignment sof...

Genome variants associated with RNA splicing variations in bovine are extensive shared between tissues

Xiang, R
Hayes, BJ
Vander Jagt, CJ
MacLeod, IM
Khansefid, M
Bowman, PJ
Yuan, Z
Prowse-Wilkins, CP
Reich, CM
Mason, BA
Garner, JB
Marett, LC
Chen, Y
Bolormaa, S
Daetwyler, HD
Chamberlain, AJ
Goddard, ME

July 2018

BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate ...

Additional file 2: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Figure S1. Gene coverage uniformity plots for each tissue type for a) all genes, b) 500 highest expr...

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang
Ben J. Hayes
Christy J. Vander Jagt
Iona M. MacLeod
Majid Khansefid
Phil J. Bowman
Zehu Yuan
Claire P. Prowse-Wilkins
Coralie M. Reich
Brett A. Mason
Josie B. Garner
Leah C. Marett
Yizhou Chen
Sunduimijid Bolormaa
Hans D. Daetwyler
Amanda J. Chamberlain
Michael E. Goddard

July 2018

Abstract Background Mammalian phenotypes are shaped by numerous genome variants, many of which may r...

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 5: Table S4. of Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

Hubert Pausch (151770)
Reiner Emmerling (167481)
Birgit Gredler-Grandl (4584202)
Ruedi Fries (151786)
Hans Daetwyler (3525329)
Michael Goddard (3398153)

November 2017

Characteristics of 25 QTL in three breeds analysed. Frequency of 25 QTL in the BV, FV and HOL cattle...

Additional file 8: of Genome changes due to artificial selection in U.S. Holstein cattle

Li Ma (46633)
Tad Sonstegard (392288)
John Cole (392281)
Curtis VanTassell (6323411)
George Wiggans (392282)
Brian Crooker (3529250)
Cheng Tan (293674)
Dzianis Prakapenka (3142692)
George Liu (122581)
Yang Da (89805)

February 2019

Table S1. Genome regions with signature of selection detected by long-range frequency differences in...

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 8: of A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle

Terhi Iso-Touru (505133)
Christine Wurmser (151766)
Heli Venhoranta (236269)
Maya Hiltpold (6581882)
Tujia Savolainen (6581885)
Anu Sironen (403686)
Konrad Fischer (6581888)
Krzysztof Flisikowski (133283)
Ruedi Fries (151786)
Alejandro Vicente-Carrillo (3119754)
Manuel Alvarez-Rodriguez (3665020)
Szabolcs Nagy (2231290)
Mervi Mutikainen (6581891)
Jaana Peippo (4805769)
Juhani Taponen (236295)
Goutam Sahana (126076)
Bernt Guldbrandtsen (340532)
Henri Simonen (6581894)
Heriberto Rodriguez-Martinez (3119748)
Magnus Andersson (236322)
Hubert Pausch (151770)

April 2019

Candidate causal variants compatible with recessive inheritance of asthenospermia. Functional conseq...

Additional file 2: 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

Table S1. Primer information for CNV validation. Table S2. Characteristics of CNV and their overlapp...

Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902...

Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 ...

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb

Additional file 6: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 5: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S3. 2âĂâ2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 4: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Table S2. Splicing junction annotation analysis using BAM files generated by different alignment sof...

Genome variants associated with RNA splicing variations in bovine are extensive shared between tissues

Xiang, R
Hayes, BJ
Vander Jagt, CJ
MacLeod, IM
Khansefid, M
Bowman, PJ
Yuan, Z
Prowse-Wilkins, CP
Reich, CM
Mason, BA
Garner, JB
Marett, LC
Chen, Y
Bolormaa, S
Daetwyler, HD
Chamberlain, AJ
Goddard, ME

July 2018

BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate ...

Additional file 2: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Figure S1. Gene coverage uniformity plots for each tissue type for a) all genes, b) 500 highest expr...

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang
Ben J. Hayes
Christy J. Vander Jagt
Iona M. MacLeod
Majid Khansefid
Phil J. Bowman
Zehu Yuan
Claire P. Prowse-Wilkins
Coralie M. Reich
Brett A. Mason
Josie B. Garner
Leah C. Marett
Yizhou Chen
Sunduimijid Bolormaa
Hans D. Daetwyler
Amanda J. Chamberlain
Michael E. Goddard

July 2018

Abstract Background Mammalian phenotypes are shaped by numerous genome variants, many of which may r...

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 5: Table S4. of Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

Hubert Pausch (151770)
Reiner Emmerling (167481)
Birgit Gredler-Grandl (4584202)
Ruedi Fries (151786)
Hans Daetwyler (3525329)
Michael Goddard (3398153)

November 2017

Characteristics of 25 QTL in three breeds analysed. Frequency of 25 QTL in the BV, FV and HOL cattle...

Additional file 8: of Genome changes due to artificial selection in U.S. Holstein cattle

Li Ma (46633)
Tad Sonstegard (392288)
John Cole (392281)
Curtis VanTassell (6323411)
George Wiggans (392282)
Brian Crooker (3529250)
Cheng Tan (293674)
Dzianis Prakapenka (3142692)
George Liu (122581)
Yang Da (89805)

February 2019

Table S1. Genome regions with signature of selection detected by long-range frequency differences in...

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 8: of A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle

Terhi Iso-Touru (505133)
Christine Wurmser (151766)
Heli Venhoranta (236269)
Maya Hiltpold (6581882)
Tujia Savolainen (6581885)
Anu Sironen (403686)
Konrad Fischer (6581888)
Krzysztof Flisikowski (133283)
Ruedi Fries (151786)
Alejandro Vicente-Carrillo (3119754)
Manuel Alvarez-Rodriguez (3665020)
Szabolcs Nagy (2231290)
Mervi Mutikainen (6581891)
Jaana Peippo (4805769)
Juhani Taponen (236295)
Goutam Sahana (126076)
Bernt Guldbrandtsen (340532)
Henri Simonen (6581894)
Heriberto Rodriguez-Martinez (3119748)
Magnus Andersson (236322)
Hubert Pausch (151770)

April 2019

Candidate causal variants compatible with recessive inheritance of asthenospermia. Functional conseq...

Additional file 2: 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

Table S1. Primer information for CNV validation. Table S2. Characteristics of CNV and their overlapp...

Additional file 10: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Abstract

Extracted data

Additional file 10: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Abstract

Extracted data

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