Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.

Abstract. Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies. Results: The maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size. Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.

Bibliographic Details

Main Authors:	MOKRY, F. B., BUZANSKAS, M. E., MUDADU, M. de A., GROSSI, D. do A., HIGA, R. H., VENTURA, R. V., LIMA, A. O. de, SARGOLZAEI, M., MEIRELLES, S. L. C., SCHENKEL, F. S., SILVA, M. V. G. B. da, NICIURA, S. C. M., ALENCAR, M. M. de, MINARI, D. P., REGITANO, L. C. de A.
Other Authors:	FABIANA BARICHELLO MOKRY, UFSCar; MARCOS ELI BUZANSKAS, FCAV/Unesp; MAURICIO DE ALVARENGA MUDADU, CPPSE; DANIELA DO AMARAL GROSSI, University of Guelph; ROBERTO HIROSHI HIGA, CNPTIA; RICARDO VIEIRA VENTURA, University of Guelph; ANDRESSA OLIVIERA DE LIMA, UFSCar; MENDI SARGOLZAEI, University of Guelph; SARAH LUGUNA CONCEIÇÃO MEIRELLES, UFV; FLÁVIO SCHRAMM SCHENKEL, University of Guelph; MARCOS VINICIUS GUALBERTO BARBOSA DA SILVA, CNPGL; SIMONE CRISTINA MÉO NICIURA, CPPSE; MAURICIO MELLO DE ALENCAR, CPPSE; DANÍSIO PRADO MUNARI, FCAV/Unesp; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE.
Format:	Artigo de periódico biblioteca
Language:	English eng
Published:	2014-12-22
Subjects:	Polimorfismo de nucleotídeo único, Genome wide association studies, Desequilíbrio de ligação, Gado de corte, Beef cattle, Single nucleotide polymorphism, Linkage disequilibrium,
Online Access:	http://www.alice.cnptia.embrapa.br/alice/handle/doc/1003463
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