Computational protocol: Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data

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Protocol publication

[…] Animals from an experimental cross of Iberian × Landrace pig lines, known as IBMAP material (Ovilo et al., , ), were used. Animal management and experimental assays were performed with standard procedures following internationally recognized guidelines and with the approval of the funding institutions ethics committee. The population was established from 3 F0 Iberian sires and 30 F0 Landrace dams and includes 70 F1, 403 F2, 56 F3, and 227 individuals from two backcrosses (79 from BC1 and 148 from BC2). Intramuscular fatty acid composition records were measured by gas chromatography in 200 g of longissimus dorsi samples taken from F3 and backcrosses animals (Table ). Indexes (UI, AC, DBI, PI, and C20:4/C18:2 ratio) were calculated as described in Pamplona et al. (). A total number of 416 animals, from 62 families, belonging to the F3 and backcross generations of the IBMAP experimental cross were genotyped with the PorcineSNP60 Genotyping Bead Chip (Illumina) using the Infinium HD Assay Ultra protocol (Illumina). Raw individual data had high-genotyping quality (call rate > 0.99). The SNPs with call rates less than 0.85, those with a minor allele frequency less than 0.15, those located in sex chromosomes or those not mapped in the Sscrofa10 assembly were removed. Genotype quality filtering was performed using GenomeStudio software and the SNPs selection, filtering by allele frequency and position was done using PLINK software (Purcell et al., ). [...] A sex-averaged SSC12 linkage map was constructed using the option Fixed of the updated CRI-MAP v2.502 (Green et al., ) as described in Muñoz et al. (). The order given to the SNPs within the chromosome followed the physical order of the Sscrofa10 assembly. QTL scanning was performed with the following models:where yi is the i-th individual record; batch is the slaughter batch (eight in total); βc is a covariate coefficient with ci being carcass weight; aQTL is the QTL additive effect; Pai is the additive coefficient calculated as Pai = Pr(QQ) − Pr(qq), the probability of the i-th individual being homozygous for alleles of Iberian origin minus the probability of being homozygous of alleles of Landrace origin; dQTL is the QTL dominant effect; Pdi is the additive dominant calculated as Pdi = Pr(Qq); ui is the infinitesimal genetic effect; and ei is the random residual. A similar model fitting two different QTL effects was used for performing complementary analyses to check the hypothesis of a second QTL mapping in the same chromosome:All the statistical analyses were performed using the Qxpak v.5.1 software (Perez-Enciso and Misztal, ). A total number of 374 markers were employed for calculating Pai and Pdi coefficients. Likelihood ratio tests (LRT) were calculated comparing the full model and a reduced model without the corresponding QTL effect. The nominal P-values were calculated assuming a χ2 distribution of the LRT with the degrees of freedom given by the difference between the number of estimated parameters in the reduced and full models. The procedure of Benjamini and Yekutieli () based on the P-values of the multiple tests was used for controlling the false discovery rate (FDR) at a desired level. As it is recommended for QTL analysis, the chromosome positions with FDR < 0.05 were considered harboring significant QTL and those with FDR < 0.10 would fit suggestive QTL. […]

Pipeline specifications

Software tools GenomeStudio, PLINK, QxPak
Applications WGS analysis, GWAS
Organisms Homo sapiens
Chemicals Acetyl Coenzyme A, Fatty Acids, Monounsaturated, Palmitic Acids