Development of polymorphic markers in the immune gene complex loci of cattle.

Autor:	Bakshy K; Dairy Forage Research Center, USDA-ARS, Madison, WI 53706., Heimeier D; The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK., Schwartz JC; The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK., Glass EJ; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, Edinburgh, UK., Wilkinson S; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, Edinburgh, UK., Skuce RA; Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland BT4 3SD, UK., Allen AR; Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland BT4 3SD, UK., Young J; Dairy Forage Research Center, USDA-ARS, Madison, WI 53706., McClure JC; Dairy Forage Research Center, USDA-ARS, Madison, WI 53706., Cole JB; Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705., Null DJ; Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705., Hammond JA; The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK., Smith TPL; Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933., Bickhart DM; Dairy Forage Research Center, USDA-ARS, Madison, WI 53706. Electronic address: derek.bickhart@usda.gov.
Jazyk:	angličtina
Zdroj:	Journal of dairy science [J Dairy Sci] 2021 Jun; Vol. 104 (6), pp. 6897-6908. Date of Electronic Publication: 2021 Mar 06.
DOI:	10.3168/jds.2020-19809
Abstrakt:	The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial chromosome inserts spanning 3 of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex, and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole-genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome. (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu