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

Autor(es)

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]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: BMC GENETICS; v. 17, JUN 21 2016.
• Citações Web of Science: 4

Resumo

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)

• Processo FAPESP: 09/16118-5 - Ferramentas genômicas no melhoramento genético de características de importância econômica direta em bovinos da raça Nelore
• Beneficiário: Lucia Galvão de Albuquerque
• Linha de fomento: Auxílio à Pesquisa - Temático
• Processo FAPESP: 13/17396-4 - Associação genômica ampla de características reprodutivas em bovinos da raça Nelore, incluindo informação fenotípica de animais não genotipados
• Beneficiário: Thaise Pinto de Melo
• Linha de fomento: Bolsas no Brasil - Mestrado
• Processo FAPESP: 14/09603-2 - Importância da incorporação de informações fenotípicas de animais não genotipados em estudos de associação genômica ampla
• Beneficiário: Thaise Pinto de Melo
• Linha de fomento: Bolsas no Exterior - Estágio de Pesquisa - Mestrado