Imputation of molecular markers in Canchim Cattle

• Grant number: 12/21891-8
• Support Opportunities: Scholarships in Brazil - Master
• Start date: January 01, 2013
• End date: February 28, 2014
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Danísio Prado Munari
• Grantee: Tatiane Cristina Seleguim Chud
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated scholarship(s): 13/02175-2 - Imputation of molecular markers in Canchim cattle, BE.EP.MS

Abstract

The development of new panels to genotyping in high density, containing thousands SNPS (single nucleotide polymorphisms) markers made the genomic selection an attractive and promising selections method. However, these dense marker panels are expensive, complicating the genotyping of all selection candidates. A strategy to reduce these costs would be using low-density marker panels, combined with the use of imputation methods. Imputation consists of predicting missing genotypes in animals genotyped with a low density panel by using information from a reference population genotyped with a higher density panel. Thus, the goal of the study will be compare imputation methods in Canchim Cattle aiming future application of imputed markers for genomic selection. Genomic information from 400 Canchim Cattle animals, obtained by high density panels (777,962 markers) will be used. The animals will be divided in two different groups, called reference and imputation population. For the imputation group low-density marker panels in different scenarios will be simulated. The imputation of genotypes will be conducted by two softwares; FImpute (version 2) and BEAGLE. To determine accuracy imputation, imputed genotypes will be compared with the true markers present in original HD panels.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

CHUD, TATIANE C. S.; VENTURA, RICARDO V.; SCHENKEL, FLAVIO S.; CARVALHEIRO, ROBERTO; BUZANSKAS, MARCOS E.; ROSA, JAQUELINE O.; MUDADU, MAURICIO DE ALVARENGA; DA SILVA, MARCOS VINICIUS G. B.; MOKRY, FABIANA B.; MARCONDES, CINTIA R.; et al. Strategies for genotype imputation in composite beef cattle. BMC GENETICS, v. 16, AUG 7 2015. (13/19335-2, 12/21891-8)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

CHUD, Tatiane Cristina Seleguim. Metodologias e estratégias de imputação de marcadores genéticos em bovinos da raça Cachim. 2014. Master's Dissertation - Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal Jaboticabal.