Most traits and disorders have a multifactorial background indicating that they are controlled by environmental factors as well as an unknown number of quantitative trait loci (QTLs). The identification of mutations underlying QTLs is a challenge because each locus explains only a fraction of the phenotypic variation. A paternally expressed QTL affecting muscle growth, fat deposition and size of the heart in pigs maps to the IGF2 (insulin-like growth factor 2) region. Here we show that this QTL is caused by a nucleotide substitution in intron 3 of IGF2. The mutation occurs in an evolutionarily conserved CpG island that is hypomethylated in skeletal muscle. The mutation abrogates in vitro interaction with a nuclear factor, probably a repressor, and pigs inheriting the mutation from their sire have a threefold increase in IGF2 messenger RNA expression in postnatal muscle. Our study establishes a causal relationship between a single-base-pair substitution in a non-coding region and a QTL effect. The result supports the long-held view that regulatory mutations are important for controlling phenotypic variation.

Background: PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment. In PLINK, the-homozyg function is used to perform ROH analyses and relies on several input settings. These settings can have a large impact on the outcome and default values are not always appropriate for medium density SNP array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are lacking, albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different livestock and pet species are used to demonstrate the importance of PLINK input settings. Moreover, the effects of pruning SNPs for low minor allele frequencies and linkage disequilibrium on ROH detection are shown. Results: We introduce the genome coverage parameter to appropriately estimate F ROH and to check the validity of ROH analyses. The effect of pruning for linkage disequilibrium and low minor allele frequencies on ROH analyses is highly population dependent and such pruning may result in missed ROH. PLINK's minimal density requirement is crucial for medium density genotypes and if set too low, genome coverage of the ROH analysis is limited. Finally, we provide recommendations for the maximal gap, scanning window length and threshold settings. Conclusions: In this study, we present guidelines for an adequate and robust ROH analysis in PLINK on medium density SNP data. Furthermore, we advise to report parameter settings in publications, and to validate them prior to analysis. Moreover, we encourage authors to report genome coverage to reflect the ROH analysis' validity. Implementing these guidelines will substantially improve the overall quality and uniformity of ROH analyses.

Myostatin (MSTN), a transforming growth factor beta superfamily member, is an essential factor for the growth and development of muscle mass. The protein functions as a negative regulator of muscle growth and is related to the so-called double-muscling phenotype in cattle, where a series of mutations renders the gene inactive. One particular breed of pigs, the Belgian Piétrain, also shows a heavily muscled phenotype. The similarity of muscular phenotypes between the double-muscled cattle and Piétrain pigs indicated that MSTN may be a candidate gene for muscular hypertrophy in pigs. In this study, we sequenced and analysed the complete MSTN gene from 45 pigs of five different breeds, including the heavily muscled Piétrain breed at one extreme and the Meishan and Wild boar breeds at the other extreme. In total, 7626 bp of the porcine MSTN gene were sequenced, including the 5' and 3' UTR. Fifteen polymorphic loci were found, three of which were located in the promoter region, five in intron 1 and seven in intron 2. Most mutations were found when comparing the obtained MSTN sequence with porcine MSTN sequences already published. However, one polymorphism located at position 447 of the porcine MSTN promoter had a very high allele frequency in the Piétrain pig breed and disrupted a putative myocyte enhancer factor 3 binding site. Real-time PCR using Sybr Green showed that this mutation was associated with expression levels of the MSTN gene in m. longissimus dorsi at an age of 4 weeks.

Broiler chickens and laying hens are intensively selected for productive traits. The management of these highly productive animals must be optimal to allow their full genetic potential to be expressed. If this is not done, inefficient production and several metabolic diseases become apparent. The causes of the latter are multifactorial but diet and, particularly, interactions between diet, other environmental and genetic factors play an important role. An imbalance between oxygen supply and the oxygen required to sustain rapid growth rates and high food efficiencies causes ascites in broiler chickens. It is clear that several nutritional factors, the amount of food given, its physical form and the composition of the diet have a major impact on the occurrence of ascites and sudden death syndrome in broiler chickens. Furthermore, the possible involvement of structural endogenous factors such as proportional changes in the respiratory and cardiovascular systems, shifts in the glyco1ytic:oxidative muscle metabolism ratio, and structural changes within the lung capillary system cannot be excluded. In addition, functional causal factors, such as the hypothyroid state associated with decreased maintenance metabolism as a result of the selection for fast growth rate and improved food efficiency, are likely to be involved. Both structural and functional causal mechanisms may already be initiated during the embryonic stage.

1. Due to intensive selection, broiler chickens became the most efficient meat-producing animals because of their fast growth, supported by a virtually unlimited voluntary feed intake. These characteristics cause many problems in the management of broiler breeder hens because of the negative correlation between muscle growth and reproduction effectiveness. 2. This problem, namely the fast muscle growth versus reproduction health paradox, induces a second paradox, acceptable reproduction and health versus hunger stress and impaired welfare, because broiler breeder hens require dedicated programmes of feed restriction (1) to maximise egg and chick production and (2) to avoid metabolic disorders and mortality in broiler breeders. 3. Given that poultry selection is a global large-scale business and chickens are a prolific species, improvement in profit can only be obtained by selecting on feed conversion and/or for higher breast meat percentage, which will intensify the broiler-breeder paradox. 4. New feeding strategies are being studied, but it is questionable if the paradox can be solved by management tools alone. Because breeding and selection are long-term processes, involving animals, farmers, consumers, industry, environment etc., a more sustainable breeding goal needs to be determined by a multidisciplinary approach and an open debate between several actors in the discussion. 5. Using dwarf broiler breeder hens could be one alternative, because dwarf hens combine relatively good reproductive fitness with ad libitum feeding. Another possibility is to accept lower broiler productivity by assigning economic values to welfare and including integrity traits in an extended breeding goal.