Mitochondrial protein gene expression and the oxidative phosphorylation pathway associated with feed efficiency and energy balance in dairy cattle

Authors: Dorji, Jigme ^*, MacLeod, Iona M., Chamberlain, Amanda J., Vander Jagt, Christy J., Ho, Phuong N., Khansefid, Majid, Mason, Brett A., Prowse-Wilkins, Claire P., Marett, Leah C., Wales, William J., Cocks, Benjamin G., Pryce, Jennie E., Daetwyler, Hans D.

Source: In Journal of Dairy Science January 2021 104(1):575-587

Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia

Authors: Buggiotti, Laura, Yurchenko, Andrey A, Yudin, Nikolay S, Vander Jagt, Christy J, Vorobieva, Nadezhda V, Kusliy, Mariya A, Vasiliev, Sergei K, Rodionov, Andrey N, Boronetskaya, Oksana I, Zinovieva, Natalia A, Graphodatsky, Alexander S, Daetwyler, Hans D, Larkin, Denis M

Source: Molecular biology and evolution. 38(8):3093-3110

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100130289079.0x000001&indx=1&recIds=ETOCvdc_100130289079.0x000001

Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation.

Authors: Nguyen, Tuan V., Bolormaa, Sunduimijid, Reich, Coralie M., Chamberlain, Amanda J., Vander Jagt, Christy J., Daetwyler, Hans D., MacLeod, Iona M.

Source: Genetics Selection Evolution; 11/15/2024, Vol. 56 Issue 1, p1-14, 14p

Subject Terms: GENOME-wide association studies, X chromosome, GENOTYPES, SINGLE nucleotide polymorphisms, EMPIRICAL research

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

Authors: Xiang, Ruidong, van den Berg, Irene, MacLeo, Iona M., Hayes, Benjamin J., Prowse-Wilkins, Claire P., Wang, Min, Bolormaa, Sunduimijid, Liu, Zhiqian, Rochfort, Simone J., Reich, Coralie M., Mason, Brett A., Vander Jagt, Christy J., Daetwyler, Hans D., Lund, Mogens S., Chamberlain, Amanda J., Goddard, Michael E.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Sep . 116(39), 19398-19408.

Access URL: https://www.jstor.org/stable/26855179

An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle

Authors: Fritz, Sébastien, Hoze, Chris, Rebours, Emmanuelle, Barbat, Anne, Bizard, Méline, Chamberlain, Amanda, Escouflaire, Clémentine, Vander Jagt, Christy, Boussaha, Mekki, Grohs, Cécile, Allais-Bonnet, Aurélie, Philippe, Maëlle, Vallée, Amélie, Amigues, Yves, Hayes, Benjamin J., Boichard, Didier, Capitan, Aurélien

Source: In Journal of Dairy Science July 2018 101(7):6220-6231

Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.

Authors: Cai, Zexi, Iso-Touru, Terhi, Sanchez, Marie-Pierre, Kadri, Naveen, Bouwman, Aniek C., Chitneedi, Praveen Krishna, MacLeod, Iona M., Vander Jagt, Christy J., Chamberlain, Amanda J., Gredler-Grandl, Birgit, Spengeler, Mirjam, Lund, Mogens Sandø, Boichard, Didier, Kühn, Christa, Pausch, Hubert, Vilkki, Johanna, Sahana, Goutam

Source: Genetics Selection Evolution; 7/15/2024, Vol. 56 Issue 1, p1-22, 22p

Subject Terms: LOCUS (Genetics), CATTLE breeds, GENOME-wide association studies, SUSTAINABILITY, DAIRY cattle, BOVINE mastitis

Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle.

Authors: Dorji, Jigme^1,2 (AUTHOR) jigme.dorji@agriculture.vic.gov.au, Vander Jagt, Christy J.² (AUTHOR), Chamberlain, Amanda J.² (AUTHOR), Cocks, Benjamin G.^1,2 (AUTHOR), MacLeod, Iona M.² (AUTHOR) iona.macleod@agriculture.vic.gov.au, Daetwyler, Hans D.^1,2 (AUTHOR)

Source: Scientific Reports. 4/4/2022, Vol. 12 Issue 1, p1-18. 18p.

Subject Terms: *WHOLE genome sequencing, *CATTLE genetics, *HAPLOTYPES, *TAURINE, *CATTLE breeds, *GENETIC variation, *CATTLE breeding, *CATTLE

Geographic Terms: CHINA

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

Authors: Khansefid, Majid, Pryce, Jennie, Bolormaa, Sunduimijid, Chen, Yizhou, Millen, Catriona, Chamberlain, Amanda, Vander Jagt, Christy, Goddard, Michael

Source: BMC genomics. 19(1):1-18

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185395848.0x000001&indx=1&recIds=ETOCvdc_100185395848.0x000001

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Authors: Wang, Min, Hancock, Timothy, Chamberlain, Amanda, Vander Jagt, Christy, Pryce, Jennie, Cocks, Benjamin, Goddard, Mike, Hayes, Benjamin

Source: BMC genomics. 19(1):1-17

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185352203.0x000001&indx=1&recIds=ETOCvdc_100185352203.0x000001

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Authors: Yurchenko, Andrey, Daetwyler, Hans, Yudin, Nikolay, Schnabel, Robert, Vander Jagt, Christy, Soloshenko, Vladimir, Lhasaranov, Bulat, Popov, Ruslan, Taylor, Jeremy, Larkin, Denis

Source: Scientific reports. 8(1):1-16

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100178390370.0x000001&indx=1&recIds=ETOCvdc_100178390370.0x000001

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

Authors: Xiang, Ruidong, Hayes, Ben, Vander Jagt, Christy, MacLeod, Iona, Khansefid, Majid, Bowman, Phil, Yuan, Zehu, Prowse-Wilkins, Claire, Reich, Coralie, Mason, Brett, Garner, Josie, Marett, Leah, Chen, Yizhou, Bolormaa, Sunduimijid, Daetwyler, Hans, Chamberlain, Amanda, Goddard, Michael

Source: BMC genomics. 19(1):1-18

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100166734396.0x000001&indx=1&recIds=ETOCvdc_100166734396.0x000001

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Authors: Bouwman, Aniek, Daetwyler, Hans, Chamberlain, Amanda, Ponce, Carla, Sargolzaei, Mehdi, Schenkel, Flavio, Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus, Bowman, Phil, Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Mogens, Servin, Bertrand, Garrick, Dorian, Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse, Schnabel, Robert, Taylor, Jeremy, Vinkhuyzen, Anna, Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Crowley, John, Bieber, Anna, Purfield, Deirdre, Berry, Donagh, Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassell, Curtis, Fries, Ruedi, Stothard, Paul, Veerkamp, Roel, Boichard, Didier, Goddard, Mike, Hayes, Ben

Source: Nature genetics. 50(3):362-367

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100114614176.0x000001&indx=1&recIds=ETOCvdc_100114614176.0x000001

Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test.

Authors: Dorji, Jigme, Reverter, Antonio, Alexandre, Pamela A., Chamberlain, Amanda J., Vander-Jagt, Christy J., Kijas, James, Porto-Neto, Laercio R.

Source: Genetics Selection Evolution; 2/6/2024, Vol. 56 Issue 1, p1-11, 11p

Subject Terms: CATTLE genetics, ALLELES, LIKELIHOOD ratio tests, WHOLE genome sequencing, X chromosome, CATTLE

Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle.

Authors: Dorji, Jigme^1,2 (AUTHOR) jigme.dorji@agriculture.vic.gov.au, Vander Jagt, Christy J.² (AUTHOR), Garner, Josie B.³ (AUTHOR), Marett, Leah C.³ (AUTHOR), Mason, Brett A.² (AUTHOR), Reich, Coralie M.² (AUTHOR), Xiang, Ruidong^2,4 (AUTHOR), Clark, Emily L.⁵ (AUTHOR), Cocks, Benjamin G.^1,2 (AUTHOR), Chamberlain, Amanda J.² (AUTHOR), MacLeod, Iona M.² (AUTHOR), Daetwyler, Hans D.^1,2 (AUTHOR)

Source: BMC Genomics. 10/19/2020, Vol. 21 Issue 1, p1-17. 17p.

Subject Terms: *PLANT mitochondria, *DAIRY cattle, *MITOCHONDRIAL proteins, *ENERGY metabolism, *PROTEIN expression, *GENOMES

Survey of allele specific expression in bovine muscle

Authors: Guillocheau, Gabriel M., El Hou, Abdelmajid, Meersseman, Cédric, Esquerré, Diane, Rebours, Emmanuelle, Letaief, Rabia, Simao, Morgane, Hypolite, Nicolas, Bourneuf, Emmanuelle, Bruneau, Nicolas, Vaiman, Anne, Vander Jagt, Christy J., Chamberlain, Amanda J., Rocha, Dominique

Source: Scientific reports. 9(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131205390.0x000001&indx=1&recIds=ETOCvdc_100131205390.0x000001

In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.

Authors: Nguyen, Tuan V., Vander Jagt, Christy J., Wang, Jianghui, Daetwyler, Hans D., Xiang, Ruidong, Goddard, Michael E., Nguyen, Loan T., Ross, Elizabeth M., Hayes, Ben J., Chamberlain, Amanda J., MacLeod, Iona M.

Source: Genetics Selection Evolution; 1/31/2023, Vol. 55 Issue 1, p1-15, 15p

Subject Terms: SCIENTIFIC community, LIVESTOCK, CONSORTIA, PRICES, COMMUNITY life, NUCLEOTIDE sequencing

Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle.

Authors: Prowse-Wilkins, Claire P., Lopdell, Thomas J., Xiang, Ruidong, Vander Jagt, Christy J., Littlejohn, Mathew D., Chamberlain, Amanda J., Goddard, Michael E.

Source: BMC Genomics; 12/8/2022, Vol. 23 Issue 1, p1-19, 19p

Subject Terms: GENETIC variation, GENE expression, MAMMARY glands, IMMUNOPRECIPITATION, BINDING sites, CATTLE genetics, CATTLE

Correction to: Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle.

Authors: Dorji, Jigme^1,2 (AUTHOR) jigme.dorji@agriculture.vic.gov.au, Vander Jagt, Christy J.² (AUTHOR), Garner, Josie B.³ (AUTHOR), Marett, Leah C.³ (AUTHOR), Mason, Brett A.² (AUTHOR), Reich, Coralie M.² (AUTHOR), Xiang, Ruidong^2,4 (AUTHOR), Clark, Emily L.⁵ (AUTHOR), Cocks, Benjamin G.^1,2 (AUTHOR), Chamberlain, Amanda J.² (AUTHOR), MacLeod, Iona M.² (AUTHOR), Daetwyler, Hans D.^1,2 (AUTHOR)

Source: BMC Genomics. 4/21/2022, Vol. 23 Issue 1, p1-2. 2p.

Subject Terms: *MITOCHONDRIAL proteins, *DAIRY cattle, *PROTEIN expression, *ENERGY metabolism, *GENES, *GENOMES

Extensive variation between tissues in allele specific expression in an outbred mammal.

Authors: Chamberlain, Amanda J.^1,2, Vander Jagt, Christy J.^1,2, Hayes, Benjamin J.^1,2,3 ben.hayes@ecodev.vic.gov.au, Khansefid, Majid^1,2,4, Marett, Leah C.⁵, Millen, Catriona A.^2,4, Nguyen, Thuy T. T.¹, Goddard, Michael E.^1,4

Source: BMC Genomics. 11/23/2015, Vol. 16, p1-20. 20p. 6 Charts, 6 Graphs.

Subject Terms: *GENE expression in mammals, *ALLELES, *CHROMOSOMES, *RNA sequencing, *NUCLEOTIDE sequencing, *GENES

Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.

Authors: Yuan, Zehu, Sunduimijid, Bolormaa, Xiang, Ruidong, Behrendt, Ralph, Knight, Matthew I., Mason, Brett A., Reich, Coralie M., Prowse-Wilkins, Claire, Vander Jagt, Christy J., Chamberlain, Amanda J., MacLeod, Iona M., Li, Fadi, Yue, Xiangpeng, Daetwyler, Hans D.

Source: Genetics Selection Evolution; 1/18/2021, Vol. 53 Issue 1, p1-14, 14p

Subject Terms: ERECTOR spinae muscles, SHEEP, FALSE discovery rate, SINGLE nucleotide polymorphisms, RNA splicing, LIVER