Fine mapping and single nucleotide polymorphism effects estimation on pig chromosomes 1, 4, 7, 8, 17 and X

Abstract

Fine mapping of quantitative trait loci (QTL) from previous linkage studies was performed on pig chromosomes 1, 4, 7, 8, 17, and X which were known to harbor QTL. Traits were divided into: growth performance, carcass, internal organs, cut yields, and meat quality. Fifty families were used of a F2 population produced by crossing local Brazilian Piau boars with commercial sows. The linkage map consisted of 237 SNP and 37 microsatellite markers covering 866 centimorgans. QTL were identified by regression interval mapping using GridQTL. Individual marker effects were estimated by Bayesian LASSO regression using R. In total, 32 QTL affecting the evaluated traits were detected along the chromosomes studied. Seven of the QTL were known from previous studies using our F2 population, and 25 novel QTL resulted from the increased marker coverage. Six of the seven QTL that were significant at the 5% genome-wide level had SNPs within their confidence interval whose effects were among the 5% largest effects. The combined use of microsatellites along with SNP markers increased the saturation of the genome map and led to smaller confidence intervals of the QTL. The results showed that the tested models yield similar improvements in QTL mapping accuracy.

Estimating additive and dominance variances for complex traits in pigs combining genomic and pedigree information

“…The low-density SNP chips were customized selecting markers (Illumina PorcineSNP60 BeadChip, San Diego, CA, USA; Ramos et al, 2009). These markers spanned the regions where quantitative trait loci (QTLs) had previously been detected in this population (Hidalgo et al, 2013). The SNPs were submitted to a quality control wherein 66 markers were discarded due to non-amplification and 81 were discarded due to a low Minor Allele Frequency (MAF < 0.05).…”

Quadrados mínimos parciais uni e multivariado aplicados na seleção genômica para características de carcaça em suínos

“…A genotipagem foi realizada via tecnologia Golden Gate/Vera Code R, no Laboratório de Genética Animal (LGA), Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, conforme descrito por HIDALGO et al (2011).…”

“…Esses marcadores foram obtidos apenas em regiões nas quais se observaram a presença QTL em estudos prévios (HIDALGO et al, 2011) nessa mesma população, caracterizando assim um mapeamento fi no apenas em regiões cromossômicas de interesse, o que explica o número reduzido de marcadores utilizados.…”

Genome association study through nonlinear mixed models revealed new candidate genes for pig growth curves

“…A threegeneration resource population was raised and managed as described by Hidalgo et al (2013) and Verardo et al (2015). Briefly, two naturalized Piau breed grandsires were crossed with 18 granddams from a commercial line composed of Large White, Landrace, and Pietrain breeds to produce the F1 generation, from which 11 F1 sires and 54 F1 dams were selected.…”

“…The low-density customized SNPChip with 384 markers was based on the Illumina Porcine SNP60 BeadChip (San Diego, CA, USA, Ramos et al, 2009). These SNPs were selected according to QTL positions that had been previously identified in this population by using meta-analyses (Silva et al, 2011) and fine mapping (Hidalgo et al, 2013;Verardo et al, 2015). Thus, although a small number of markers have been used, the customized SNPchip based on previously identified QTL positions ensures appropriate coverage of the relevant genome regions in this population.…”