Results of a whole‐genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four‐way cross

Harmegnies, Natacha; Davin, Fabienne; Smet, Stefaan De; Buys, Nadine; Georges, Michel; Coppieters, Wouter

doi:10.1111/j.1365-2052.2006.01523.x

Cited by 51 publications

(39 citation statements)

References 67 publications

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“…Our most prominent SNPs associated with meat colour a* and colour b* were on SSC4 und SSC14, respectively, where QTL were previously shown 22-23, 27-29. Further, Duthie and colleagues 21 detected a QTL for the pH of ham 24 hours post-mortem surrounding the same region of SSC14, which was also found in our study.…”

Section: Discussionsupporting

confidence: 87%

Discovery of Candidate Genes for Muscle Traits Based on GWAS Supported by eQTL-analysis

et al. 2014

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Biochemical and biophysical processes that take place in muscle under relaxed and stressed conditions depend on the abundance and activity of gene products of metabolic and structural pathways. In livestock at post-mortem, these muscle properties determine aspects of meat quality and are measurable. The conversion of muscle to meat mimics pathological processes associated with muscle ischemia, injury or damage in humans and it is an economic factor in pork production. Linkage, association, and expression analyses independently contributed to the identification of trait-associated molecular pathways and genes. We aim at providing multiple evidences for the role of specific genes in meat quality by integrating a genome-wide association study (GWAS) for meat quality traits and the detection of eQTL based on trait-correlated expressed genes and trait-associated markers. The GWAS revealed 51 and 200 SNPs significantly associated with meat quality in a crossbred Pietrain×(German Landrace×Large White) (Pi×(GL×LW)) and a purebred German Landrace (GL) population, respectively. Most significant SNPs in Pi×(GL×LW) were located on chromosomes (SSC) 4 and 6. The data of 47,836 eQTLs at a significance level of p<10-5 were used to scale down the number candidate genes located in these regions. These SNPs on SSC4 showed association with expression levels of ZNF704, IMPA1, and OXSR1; SSC6 SNPs were associated with expression of SIGLEC10 and PIH1D1. Most significant SNPs in GL were located on SSC6 and associated with expression levels of PIH1D1, SIGLEC10, TBCB, LOC100518735, KIF1B, LOC100514845, and two unknown genes. The abundance of transcripts of these genes in muscle, in turn, is significantly correlated with meat quality traits. We identified several genes with evidence for their candidacy for meat quality arising from the integrative approach of a genome-wide association study and eQTL analysis.

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Section: Discussionsupporting

confidence: 87%

Discovery of Candidate Genes for Muscle Traits Based on GWAS Supported by eQTL-analysis

et al. 2014

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“…Whereas pigs used to be bred for high fat deposition, in modern pig production systems lean meat is desired. AZGP1 also overlaps with a 16 Mb QTL for ear size, area and weight [38] and a 8.5 Mb QTL for vertebra number [39]. Ear morphology traits have been traditionally used to define breed standards.…”

Section: Discussionmentioning

confidence: 99%

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

et al. 2014

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BackgroundA major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds.ResultsOur results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response – e.g. IL12RB2 and STAB1–, probably as a result of strong artificial in the intensive production systems in pig.ConclusionsThe high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-601) contains supplementary material, which is available to authorized users.

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“…Samples for this study originated from the progeny of 5 boars and 180 sows (Rattlerow Seghers hybrid lines crossed for the purpose of a QTL-search experiment (Harmegnies et al, 2006). Female and castrate male piglets (n = 1671) were all fattened on the same diet, and were slaughtered at a live weight of approximately 110 kg.…”

Section: Experimental Designmentioning

confidence: 99%

Effect of sire and sex on the intramuscular fatty acid profile and indices for enzyme activities in pigs

2009

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Results of a whole‐genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four‐way cross

Cited by 51 publications

References 67 publications

Discovery of Candidate Genes for Muscle Traits Based on GWAS Supported by eQTL-analysis

Discovery of Candidate Genes for Muscle Traits Based on GWAS Supported by eQTL-analysis

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

Effect of sire and sex on the intramuscular fatty acid profile and indices for enzyme activities in pigs

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