Abstract
BackgroundThe traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses.ResultsThree generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes.ConclusionsThe use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation.
Highlights
The traditional strategy to map Quantitative trait loci (QTL) is to use linkage analysis employing a limited number of markers
The QTL scan has allowed to confirm QTL regions previously identified in the IBMAP population as well as identify new ones (Table 3) and many others at chromosome-wide significant level that are considered as suggestive (Additional file 1: Table S1)
Six of which were significant to the genome-wide level: three QTLs for BFT75 in SSC4, SSC11 and SSC17, two for SW in SSC1 and SSC4 and one for BLW in SSC4 (Table 3)
Summary
The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. The traditional strategy to map QTLs has been to use linkage analysis employing a limited number of microsatellite markers. These analyses usually mapped the QTLs to large intervals, 20 cM or more, which. Several candidate genes, such as LEPR, MTTP and FABP5, have been analyzed reporting some successful results [10,11,12,13,14,15,16]
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