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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations

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Author(s):
Melo, Thaise P. [1] ; Takada, Luciana [1] ; Baldi, Fernando [1] ; Oliveira, Henrique N. [1] ; Dias, Marina M. [1] ; Neves, Haroldo H. R. [1, 2] ; Schenkel, Flavio S. [3] ; Albuquerque, Lucia G. [1] ; Carvalheiro, Roberto [1]
Total Authors: 9
Affiliation:
[1] Univ Estadual Paulista, Fac Ciencias Agr & Vet, BR-14884900 Sao Paulo - Brazil
[2] GenSys Consultores Associados SC Ltda, BR-90680000 Porto Alegre, RS - Brazil
[3] Univ Guelph, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1 - Canada
Total Affiliations: 3
Document type: Journal article
Source: BMC GENETICS; v. 17, JUN 21 2016.
Web of Science Citations: 5
Abstract

Background: QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Results: Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. Conclusions: The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high. (AU)

FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
Grantee:Lucia Galvão de Albuquerque
Support type: Research Projects - Thematic Grants
FAPESP's process: 13/17396-4 - Genome wide association of reproductive traits in Nellore cattle, including phenotypic information from NON-GENOTYPED animals
Grantee:Thaise Pinto de Melo
Support type: Scholarships in Brazil - Master
FAPESP's process: 14/09603-2 - Importance of incorporating phenotypic information of NON-GENOTYPED animals in Genome-Wide Association Studies
Grantee:Thaise Pinto de Melo
Support type: Scholarships abroad - Research Internship - Master's degree