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3. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

Author

Bickhart, Derek M, Xu, Lingyang, Hutchison, Jana L, Cole, John B, Null, Daniel J, Schroeder, Steven G, Song, Jiuzhou, Garcia, Jose Fernando, Sonstegard, Tad S, Van Tassell, Curtis P, Schnabel, Robert D, Taylor, Jeremy F, Lewin, Harris A, and Liu, George E

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Animals, Breeding, Cattle, DNA Copy Number Variations, Gene Duplication, Genome, Multigene Family, Polymorphism, Genetic, cattle genome, population sequencing, copy number variation, taurine, indicine, Plant Biology & Botany
Abstract

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1 Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.

Published
2016

7. Author response for '<scp>NUAK1</scp> governs centrosome replication in pancreatic cancer via <scp>MYPT1</scp> / <scp>PP1β</scp> and <scp>GSK3β</scp> ‐dependent regulation of <scp>PLK4</scp>'

Author

null Declan Whyte, null George Skalka, null Peter Walsh, null Ania Wilczynska, null Nikki R. Paul, null Claire Mitchell, null Colin Nixon, null William Clarke, null Martin Bushell, null Jennifer P. Morton, null Daniel J. Murphy, and null Nathiya Muthalagu

Published
2023
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14. Author response for 'Implementing GitHub Actions continuous integration to reduce error rates in ecological data collection'

Author

null Albert Y. Kim, null Valentine Herrmann, null Ross Bareto, null Brianna Calkins, null Erika Gonzalez‐Akre, null Daniel J. Johnson, null Jennifer A. Jordan, null Lukas Magee, null Ian R. McGregor, null Nicolle Montero, null Karl Novak, null Teagan Rogers, null Jessica Shue, and null Kristina J. Anderson‐Teixeira

Published
2022
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18. Author response for 'Treetop: A Shiny‐based Application and R package for Extracting Forest Information from LiDAR data for Ecologists and Conservationists'

Author

null Carlos Alberto Silva, null Andrew T. Hudak, null Lee A. Vierling, null Ruben Valbuena, null Adrian Cardil, null Midhun Mohan, null Danilo Roberti Alves de Almeida, null Eben N. Broadbent, null Angelica M. Almeyda Zambrano, null Ben Wilkinson, null Ajay Sharma, null Jason B. Drake, null Paul B. Medley, null Jason G. Vogel, null Gabriel Atticciati Prata, null Jeff W. Atkins, null Caio Hamamura, null Daniel J. Jonson, and null Carine Klauberg

Published
2022
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20. Author response for 'Improving landscape‐scale productivity estimates by integrating trait‐based models and remotely‐sensed foliar‐trait and canopy‐structural data'

Author

null Daniel J. Wieczynski, null Sandra Díaz, null Sandra M. Durán, null Nikolaos M. Fyllas, null Norma Salinas, null Roberta E. Martin, null Alexander Shenkin, null Miles R. Silman, null Gregory P. Asner, null Lisa Patrick Bentley, null Yadvinder Malhi, null Brian J. Enquist, and null Van M. Savage

Published
2022
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26. Author response for 'A randomised, open label, active comparator trial assessing the effects of 26 weeks of liraglutide or sitagliptin on cardiovascular function in young obese adults with type 2 diabetes'

Author

null David R. Webb, null Zin Zin Htike, null Daniel J. Swarbrick, null Emer M. Brady, null Laura J. Gray, null John Biglands, null Gaurav S. Gulsin, null Joseph Henson, null Kamlesh Khunti, null Gerry P. McCann, null Helen L. Waller, null M'Balu A Webb, null Jack Sargent, null Thomas Yates, null Francesco Zaccardi, and null Melanie J. Davies

Published
2020
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27. Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle

Author

Fang, Lingzhao, primary, Zhou, Yang, additional, Liu, Shuli, additional, Jiang, Jicai, additional, Bickhart, Derek M., additional, Null, Daniel J., additional, Li, Bingjie, additional, Schroeder, Steven G., additional, Rosen, Benjamin D., additional, Cole, John B., additional, Van Tassell, Curtis P., additional, Ma, Li, additional, and Liu, George E., additional

Published
2019
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28. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits

Author

Fang, Lingzhao, primary, Zhou, Yang, additional, Liu, Shuli, additional, Jiang, Jicai, additional, Bickhart, Derek M., additional, Null, Daniel J., additional, Li, Bingjie, additional, Schroeder, Steven G., additional, Rosen, Benjamin D., additional, Cole, John B., additional, Van Tassell, Curtis P., additional, Ma, Li, additional, and Liu, George E., additional

Published
2019
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30. Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor

Author

Porto-Neto, Laercio R., primary, Bickhart, Derek M., additional, Landaeta-Hernandez, Antonio J., additional, Utsunomiya, Yuri T., additional, Pagan, Melvin, additional, Jimenez, Esbal, additional, Hansen, Peter J., additional, Dikmen, Serdal, additional, Schroeder, Steven G., additional, Kim, Eui-Soo, additional, Sun, Jiajie, additional, Crespo, Edward, additional, Amati, Norman, additional, Cole, John B., additional, Null, Daniel J., additional, Garcia, Jose F., additional, Reverter, Antonio, additional, Barendse, William, additional, and Sonstegard, Tad S., additional

Published
2018
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31. The Larson Blue coat color phenotype in Holsteins: Characteristics and effects on body temperature regulation and production in lactating cows in a hot climate

Author

Dahl, Geoffrey E., Cole, John Bruce, Null, Daniel J., Hansen, Peter James, Uludağ Üniversitesi/Veteriner Fakültesi/Zootekni Anabilim Dalı., Dikmen, Serdal, and A-5731-2018

Subjects
Heat stress disorders, Physiology, Climate, Hot temperature, Coat color, Agriculture, dairy & animal science, Thermoregulation, Heat stress, Body temperature regulation, Genetics, Animals, Lactation, Body temperature, Milk yield, Pigmentation, Animal, Temperature, Agriculture, Bovine, Heat, Milk, Dairy Cows, Holstein-Friesian Cattle, Cattle, Heat injury, Metabolism, Veterinary, Pigment, Florida, Pigments, biological, Female, Seasons, Season, Polymorphisms, Mutations, Hair
Abstract

Here we report a previously undescribed coat color phenotype in Holstein cattle. Larson Blue Holsteins, located on a dairy in south Florida, exhibit a coloration pattern that is similar to that of black and white or red and white Holsteins except that, instead of being black or red, darker regions of the body vary in color from gray to taupe. The Larson Blue phenotype was readily apparent in young calves. The phenotype is not due to inheritance of known mutations causing coat color variation in cattle, including dominant red, Telstar, silver color dilutor, or Dun color. Three variants with moderate effects on the melanophilin (MLPH) gene were identified in 2 Larson blue cows. Despite being lighter in color, there was no difference in daily variation in vaginal temperature between Larson Blue and other Holsteins when recorded during the summer for cows housed in free-stall barns with shade, fans, and sprinklers. Similarly, there was no effect of the Larson Blue phenotype on seasonal variation in milk yield. Therefore, the phenotype confers no advantage in terms of response to heat stress when cattle are housed in facilities with extensive cooling. Agriculture and Food Research Initiative Competitive Grant from the USDA National Institute of Food and Agriculture - 68004-20365 United States Department of Agriculture (USDA) USDA Agricultural Research Service - 1265-31000-096-00 GeneSeek Sue DeNise Zoetis Animal Genetics U.S. Department of Agriculture USDA National Institute of Food and Agriculture NIFA Agricultural Research Service ARS

Published
2017

36. PLAINS CO2 REDUCTION PARTNERSHIP

Author

null Edward N. Steadman, null John A. Harju, null Erin M. O'Leary, null James A. Sorensen, null Daniel J. Daly, null Melanie D. Jensen, and null Thea E. Reikoff

Published
2005
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37. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle

Author

Cochran, Sarah D, Cole, John B, Null, Daniel J, Hansen, Peter J, Cochran, Sarah D, Cole, John B, Null, Daniel J, and Hansen, Peter J

Abstract

Background: Identification of single nucleotide polymorphisms (SNPs) for specific genes involved in reproduction might improve reliability of genomic estimates for these low-heritability traits. Semen from 550 Holstein bulls of high (≥ 1.7; n = 288) or low (≤ −2; n = 262) daughter pregnancy rate (DPR) was genotyped for 434 candidate SNPs using the Sequenom MassARRAY® system. Three types of SNPs were evaluated: SNPs previously reported to be associated with reproductive traits or physically close to genetic markers for reproduction, SNPs in genes that are well known to be involved in reproductive processes, and SNPs in genes that are differentially expressed between physiological conditions in a variety of tissues associated in reproductive function. Eleven reproduction and production traits were analyzed. Results: A total of 40 SNPs were associated (P < 0.05) with DPR. Among these were genes involved in the endocrine system, cell signaling, immune function and inhibition of apoptosis. A total of 10 genes were regulated by estradiol. In addition, 22 SNPs were associated with heifer conception rate, 33 with cow conception rate, 36 with productive life, 34 with net merit, 23 with milk yield, 19 with fat yield, 13 with fat percent, 19 with protein yield, 22 with protein percent, and 13 with somatic cell score. The allele substitution effect for SNPs associated with heifer conception rate, cow conception rate, productive life and net merit were in the same direction as for DPR. Allele substitution effects for several SNPs associated with production traits were in the opposite direction as DPR. Nonetheless, there were 29 SNPs associated with DPR that were not negatively associated with production traits. Conclusion: SNPs in a total of 40 genes associated with DPR were identified as well as SNPs for other traits. It might be feasible to include these SNPs into genomic tests of reproduction and other traits. The genes associated with DPR are likely to be important for under

Published
2013

45. A single nucleotide polymorphism in COQ9affects mitochondrial and ovarian function and fertility in Holstein cows†

Author

Ortega, M. Sofia, Wohlgemuth, Stephanie, Tribulo, Paula, Siqueira, Luiz G. B., Null, Daniel J., Cole, John B., Da Silva, Marcus V., and Hansen, Peter J.

Abstract

A single missense mutation at position 159 of coenzyme Q9 (COQ9) (G→A; rs109301586) has been associated with genetic variation in fertility in Holstein cattle, with the A allele associated with higher fertility. COQ9 is involved in the synthesis of coenzyme COQ10, a component of the electron transport system of the mitochondria. Here we tested whether reproductive phenotype is associated with the mutation and evaluated functional consequences for cellular oxygen metabolism, body weight changes, and ovarian function. The mutation in COQ9modifies predicted tertiary protein structure and affected mitochondrial respiration of peripheral blood mononuclear cells. The A allele was associated with low resting oxygen consumption and high electron transport system capacity. Phenotypic measurements for fertility were evaluated for up to five lactations in a population of 2273 Holstein cows. There were additive effects of the mutation (P <0.05) in favor of the A allele for pregnancy rate, interval from calving to conception, and services per conception. There was no association of genotype with milk production or body weight changes postpartum. The mutation in COQ9affected ovarian function; the A allele was associated with increased mitochondrial DNA copy number in oocytes, and there were overdominance effects for COQ9expression in oocytes, follicle number, and antimullerian hormone concentrations. Overall, results show how a gene involved in mitochondrial function is associated with overall fertility, possibly in part by affecting oocyte quality.A SNP in COQ9was described that changes predicted protein structure, is associated with altered mitochondrial afunction, and that modulates reproductive function in dairy cattle, possibly by regulating oocyte quality.

Published
2017
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46. Review

Author

null Daniel J. Hulsebosch

Subjects
Cultural Studies, History
Published
2010
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49. Status of the Tactical Environment Multiple Systems Evaluation Program (TEMSEP)

Author

null Daniel J., Spohn George, Merkel John F., Dietz Jr., and John N. Bombardt

Subjects
Engineering, SIMPLE (military communications protocol), business.industry, Electromagnetic environment, Range (aeronautics), Systems engineering, Instrumentation (computer programming), Nuclear weapon, business, Electromagnetic interference, Simulation, Technical progress, Electromagnetic pulse
Abstract

This report discusses technical progress made under the Tactical Environment Multiple Systems Evaluation Program (TEMSEP). The long and short range goals of the program are presented with particular emphasis on the topics of instrumentation in an ionizing radiation environment, basic phenomena associated with the electromagnetic pulse (EMP) generation within the nuclear source region, and laboratory simulation of the electromagnetic environment associated with the nearby (endoatmospheric) detonation of a nuclear weapon. Experiments used the AURORA Flash X-Ray Facility as a radiation source. Notable milestones accomplished were the experimental verification of the existence of the boundary layer phenomenon and verification of electromagnetic coupling models for simple structures.

Published
1977
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