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Imputation Accuracy using FImpute and BEAGLE Software in Brazilian Synthetic Cattle Breed

Monday, August 18, 2014
Posters (The Westin Bayshore)
Tatiane C S Chud , Univ Estadual Paulista Julio de Mesquita Filho, Jaboticabal, Brazil
Ricardo V Ventura , Beef Improvement Opportunities, Guelph, ON, Canada
Flavio S Schenkel , Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
Roberto Carvalheiro , Universidade Estadual Paulista “Júlio de Mesquita Filho”- UNESP, Faculdade de Cięncias Agrárias e Veterinárias, Jaboticabal, Brazil
Marcos E Buzanskas , Univ Estadual Paulista Julio de Mesquita Filho, Jaboticabal, Brazil
Ismael Urbinati , Univ Estadual Paulista Julio de Mesquita Filho, Jaboticabal, Brazil
Luciana C Almeida Regitano , Embrapa Southeast Livestock, Sao Carlos, Brazil
Cintia R Marcondes , Brazilian Agricultural Research Corporation (Embrapa), Sao Carlos, Brazil
Danísio P. Munari , Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, Brazil
Abstract Text: Genotype imputation was implemented using the software BEAGLE and FImpute in 395 animals from Brazilian synthetic beef cattle genotyped with high-density panel. Imputation accuracy from using different reference and target sets of animals was evaluated. After masking SNPs from the Illumina BovineHD SNP panel, 5 sets of low-density panels were created (9K, 20K, 50K, 80K, and 90K). Genotype concordance rate ranged from 73% to 97% (FImpute) and 64% to 96% (BEAGLE). Allelic R square ranged from 0.54 to 0.96 and 0.40 to 0.94 using FImpute and BEAGLE, respectively. Higher imputation accuracies were obtained when the LD panels were composed of 80K and 90K SNP. FImputeoutperformed BEAGLE in all scenarios with an average increase in accuracy of 3% and reduced run time by 20 to 90 times.

Keywords:

Composite breed

Low-density panels

SNP

See more of: Posters: Beef Cattle Breeding (Group 1)
See more of: Species Breeding: Beef cattle
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