An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly

Autor: M Y Nawaz, D.J.A. Santos, Andrea Renata da Silva Romero, Diercles Francisco Cardoso, Cedric Gondro, Humberto Tonhati, André Vieira do Nascimento
Přispěvatelé: Universidade Estadual Paulista (Unesp), Michigan State Univ, Univ Guelph, Univ Maryland
Rok vydání: 2021
Předmět:
Zdroj: Web of Science
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
ISSN: 1365-2052
Popis: Made available in DSpace on 2021-06-26T08:03:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-06-09 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database. Sao Paulo State Univ, Dept Anim Sci, BR-14884900 Jaboticabal, Brazil Michigan State Univ, Genet & Genome Sci Program, E Lansing, MI 48823 USA Univ Guelph, Dept Anim Biosci, Guelph, ON N1G 2W1, Canada Univ Maryland, Dept Anim Sci, College Pk, MD 20740 USA Michigan State Univ, Dept Anim Sci, E Lansing, MI 48823 USA Sao Paulo State Univ, Dept Anim Sci, BR-14884900 Jaboticabal, Brazil FAPESP: 2016/21213-0 FAPESP: 2017/10542-6 FAPESP: 2018/25725-1
Databáze: OpenAIRE
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