Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance.

Authors: Zhao, Huanhuan¹ (AUTHOR) huan.zhao@agriculture.vic.gov.au, MacLeod, Iona M^1,2 (AUTHOR), Keeble-Gagnere, Gabriel¹ (AUTHOR), Barbulescu, Denise M¹ (AUTHOR), Tibbits, Josquin F¹ (AUTHOR), Kaur, Sukhjiwan¹ (AUTHOR), Hayden, Matthew^1,2 (AUTHOR) matthew.hayden@agriculture.vic.gov.au

Source: BMC Genomics. 3/4/2025, Vol. 26 Issue 1, p1-13. 13p.

Subject Terms: *WHOLE genome sequencing, *GENOME-wide association studies, *LIFE sciences, *GERMPLASM, *CANOLA

Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle

Authors: Xiang, Ruidong, Fang, Lingzhao, Liu, Shuli, Macleod, Iona M., Liu, Zhiqian, Breen, Edmond J., Gao, Yahui, Liu, George E., Tenesa, Albert, Mason, Brett A., Chamberlain, Amanda J., Wray, Naomi R., Goddard, Michael E.

Source: In Cell Genomics 11 October 2023 3(10)

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

Authors: Dorji, Jigme ^{1, 2, *}, MacLeod, Iona M. ², Chamberlain, Amanda J. ², Vander Jagt, Christy J. ², Ho, Phuong N. ², Khansefid, Majid ², Mason, Brett A. ², Prowse-Wilkins, Claire P. ^{2, 3}, Marett, Leah C. ^{3, 4}, Wales, William J. ^{3, 4}, Cocks, Benjamin G. ^{1, 2}, Pryce, Jennie E. ^{1, 2}, Daetwyler, Hans D. ^{1, 2}

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

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

Mitochondrial sequence variants: testing imputation accuracy and their association with dairy cattle milk traits.

Authors: Dorji, Jigme, Chamberlain, Amanda J., Reich, Coralie M., VanderJagt, Christy J., Nguyen, Tuan V., Daetwyler, Hans D., MacLeod, Iona M.

Source: Genetics Selection Evolution; 9/12/2024, Vol. 56 Issue 1, p1-9, 9p

Subject Terms: MITOCHONDRIAL DNA, PEARSON correlation (Statistics), SINGLE nucleotide polymorphisms, GENOME-wide association studies, DAIRY cattle

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

Using expression data to fine map QTL associated with fertility in dairy cattle.

Authors: van den Berg, Irene, Chamberlain, Amanda J., MacLeod, Iona M., Nguyen, Tuan V., Goddard, Mike E., Xiang, Ruidong, Mason, Brett, Meier, Susanne, Phyn, Claire V. C., Burke, Chris R., Pryce, Jennie E.

Source: Genetics Selection Evolution; 6/6/2024, Vol. 56 Issue 1, p1-18, 18p

Subject Terms: GENE expression, DAIRY cattle, CATTLE fertility, GENETIC engineering, DNA copy number variations, GENOME-wide association studies, ALLELES

Geographic Terms: NEW Zealand, AUSTRALIA

Genomic Prediction Using Prior Quantitative Trait Loci Information Reveals a Large Reservoir of Underutilised Blackleg Resistance in Diverse Canola (Brassica napus L.) Lines

Authors: Fikere, Mulusew, Barbulescu, Denise M., Malmberg, Michelle M., Shi, Fan, Koh, Joshua C.O., Slater, Anthony T., MacLeod, Iona M., Bowman, Phillip J., Salisbury, Phillip A., Spangenberg, German C., Cogan, Noel O.I., Daetwyler, Hans D.

Source: The œplant genome. 11(2):1-16

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100093374857.0x000001&indx=1&recIds=ETOCvdc_100093374857.0x000001

Two-Variance-Component Model Improves Genetic Prediction in Family Datasets

Authors: Tucker, George, Loh, Po-Ru, MacLeod, Iona M., Hayes, Ben J., Goddard, Michael E., Berger, Bonnie, Price, Alkes L.

Source: In The American Journal of Human Genetics 5 November 2015 97(5):677-690

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

Authors: Dorji, Jigme, Vander Jagt, Christy J., Garner, Josie B., Marett, Leah C., Mason, Brett A., Reich, Coralie M., Xiang, Ruidong, Clark, Emily L., Cocks, Benjamin G., Chamberlain, Amanda J., MacLeod, Iona M., Daetwyler, Hans D.

Source: BMC genomics. 21(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100177571125.0x000001&indx=1&recIds=ETOCvdc_100177571125.0x000001

Effect direction meta-analysis of GWAS identifies extreme, prevalent and shared pleiotropy in a large mammal

Authors: Xiang, Ruidong, van den Berg, Irene, MacLeod, Iona M., Daetwyler, Hans D., Goddard, Michael E.

Source: Communications biology. 3(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164505616.0x000001&indx=1&recIds=ETOCvdc_100164505616.0x000001

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

Authors: Larkin, Denis M., Daetwyler, Hans D., Hernandez, Alvaro G., Wright, Chris L., Hetrick, Lorie A., Boucek, Lisa, Bachman, Sharon L., Band, Mark R., Akraiko, Tatsiana V., Cohen-Zinder, Miri, Thimmapuram, Jyothi, Macleod, Iona M., Harkins, Timothy T., McCague, Jennifer E., Goddard, Michael E., Hayes, Ben J., Lewin, Harris A.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2012 May . 109(20), 7693-7698.

Access URL: https://www.jstor.org/stable/41592733

Fine-mapping sequence mutations with a major effect on oligosaccharide content in bovine milk

Authors: Liu, Zhiqian, Wang, Tingting, Pryce, Jennie E., MacLeod, Iona M., Hayes, Ben J., Chamberlain, Amanda J., Jagt, Christy Vander, Reich, Coralie M., Mason, Brett A., Rochfort, Simone, Cocks, Benjamin G.

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_100131279822.0x000001&indx=1&recIds=ETOCvdc_100131279822.0x000001

Genomic prediction based on selected variants from imputed whole-genome sequence data in Australian sheep populations

Authors: Moghaddar, Nasir, Khansefid, Majid, van der Werf, Julius H. J., Bolormaa, Sunduimijid, Duijvesteijn, Naomi, Clark, Samuel A., Swan, Andrew A., Daetwyler, Hans D., MacLeod, Iona M.

Source: Genetics, selection, evolution. 51(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129444088.0x000001&indx=1&recIds=ETOCvdc_100129444088.0x000001

Accuracy of imputation to whole-genome sequence in sheep

Authors: Bolormaa, Sunduimijid, Chamberlain, Amanda J., Khansefid, Majid, Stothard, Paul, Swan, Andrew A., Mason, Brett, Prowse-Wilkins, Claire P., Duijvesteijn, Naomi, Moghaddar, Nasir, van der Werf, Julius H., Daetwyler, Hans D., MacLeod, Iona M.

Source: Genetics, selection, evolution. 51(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100128469465.0x000001&indx=1&recIds=ETOCvdc_100128469465.0x000001

The impact of QTL sharing and properties on multi-breed GWAS in cattle: a simulation study.

Authors: van den Berg, Irene¹ (AUTHOR) irene.vandenberg@agriculture.vic.gov.au, MacLeod, Iona M.^1,2 (AUTHOR)

Source: Animal Production Science. 2023, Vol. 63 Issue 10/11, p996-1007. 12p.

Subject Terms: *CATTLE breeds, *GENOME-wide association studies, *CATTLE breeding, *DAIRY cattle, *GENE frequency, *CATTLE

Use of dry-matter intake recorded at multiple time periods during lactation increases the accuracy of genomic prediction for dry-matter intake and residual feed intake in dairy cattle.

Authors: Bolormaa, Sunduimijid, Haile-Mariam, Mekonnen, Marett, Leah C., Miglior, Filippo, Baes, Christine F., Schenkel, Flavio S., Connor, Erin E., Manzanilla-Pech, Coralia I. V., Wall, Eileen, Coffey, Mike P., Goddard, Michael E., MacLeod, Iona M., Pryce, Jennie E.

Source: Animal Production Science; 2023, Vol. 63 Issue 10/11, p1113-1125, 13p

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

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

Source: BMC genomics. 19(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127150011.0x000001&indx=1&recIds=ETOCvdc_100127150011.0x000001

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

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

Authors: Bolormaa, Sunduimijid, MacLeod, Iona M., Khansefid, Majid, Marett, Leah C., Wales, William J., Miglior, Filippo, Baes, Christine F., Schenkel, Flavio S., Connor, Erin E., Manzanilla-Pech, Coralia I. V., Stothard, Paul, Herman, Emily, Nieuwhof, Gert J., Goddard, Michael E., Pryce, Jennie E.

Source: Genetics Selection Evolution; 9/6/2022, Vol. 54 Issue 1, p1-17, 17p

Subject Terms: GENETIC variation, SINGLE nucleotide polymorphisms, PHENOTYPES, GENOME-wide association studies, HERITABILITY, GENETIC correlations, HEIFERS