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.

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock.Recently, linkage disequilibrium (LD) has received considerable attention as it may be exploited to more effectively map genes underlying both simple and complex (dichotomous and continuously distributed) traits (Terwilliger and Weiss 1998). The potential advantage of LD mapping over conventional linkage analysis performed within families lies in the use of "historical" recombinants, thereby increasing mapping resolution (e.g., Hästbacka et al. 1992;Talbot et al. 1999) and power. To be effective, however, LD-mapping requires a marker density compatible with the distances across which LD extends in the population of interest. Kruglyak (1999) estimated by simulation that useful levels of LD were unlikely to extend beyond an average distance of 3 kb in the human, thereby implying the need for a marker map comprising ∼500,000 SNPs Although experimental LD data are accumulating in the human (e.g., Laan and Pääbo 1997; Nickerson et al. 1998) and some primate species (Crouau-Roy et al. 1996), little is known about the extent of LD in most other mammals, including domestic species. In this paper, we have used genotypes obtained with a panel of 284 microsatellites to measure genome-wide LD in the dutch black-andwhite dairy cattle population. We make the remarkable observation that intrachromosomal LD extends over several tens of centimorgans, and that gametic phase disequilibrium is common between non syntenic loci.

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hIn broiler chickens, feed additives, including prebiotics, are widely used to improve gut health and to stimulate performance. Xylo-oligosaccharides (XOS) are hydrolytic degradation products of arabinoxylans that can be fermented by the gut microbiota. In the current study, we aimed to analyze the prebiotic properties of XOS when added to the broiler diet. Administration of XOS to chickens, in addition to a wheat-rye-based diet, significantly improved the feed conversion ratio. XOS significantly increased villus length in the ileum. It also significantly increased numbers of lactobacilli in the colon and Clostridium cluster XIVa in the ceca. Moreover, the number of gene copies encoding the key bacterial enzyme for butyrate production, butyryl-coenzyme A (butyryl-CoA):acetate CoA transferase, was significantly increased in the ceca of chickens administered XOS. In this group of chickens, at the species level, Lactobacillus crispatus and Anaerostipes butyraticus were significantly increased in abundance in the colon and cecum, respectively. In vitro fermentation of XOS revealed cross-feeding between L. crispatus and A. butyraticus. Lactate, produced by L. crispatus during XOS fermentation, was utilized by the butyrate-producing Anaerostipes species. These data show the beneficial effects of XOS on broiler performance when added to the feed, which potentially can be explained by stimulation of butyrate-producing bacteria through cross-feeding of lactate and subsequent effects of butyrate on gastrointestinal function. Cereal fibers are composed of carbohydrate polymers that are resistant to digestion in the small intestines of monogastric animals but are completely or partially fermented in the distal gut, and they are believed to stimulate gut health (1). The main components of the cereal fiber fraction are arabinoxylans (AX), pectins, resistant starch, cellulose, ␤-glucans, and lignin (2). Hydrolytic degradation of the heteropolymer AX results in a mixture of arabinose-substituted xylo-oligosaccharides (arabinoxylan-oligosaccharides) (AXOS) and nonsubstituted xylo-oligosaccharides (XOS) (3). XOS are oligomers consisting of xylose units linked through ␤-(1-4) linkages (4). Selective fermentation of XOS has been shown to induce changes in both the composition and activity of the gastrointestinal microbiota, improving the health and well-being of the host. This suggests that XOS could fulfill the definition of a prebiotic (5). The production of lactate and shortchain fatty acids (SCFA), including butyrate, upon fermentation of XOS, has been confirmed in several in vitro and in vivo studies (3, 6). Lactate can stimulate butyrate production due to crossfeeding between lactate-producing bacteria and lactate-utilizing butyrate-producing bacteria from Clostridium cluster XIVa (7). Butyrate has proven beneficial effects on gastrointestinal function, since it has anti-inflammatory properties, fuels epithelial cells, and increases the intestinal epithelial integrity. In addition, butyrate has been shown to improve growth pe...

Herve cheese is a Belgian soft cheese with a washed rind, and is made from raw or pasteurized milk. The specific microbiota of this cheese has never previously been fully explored and the use of raw or pasteurized milk in addition to starters is assumed to affect the microbiota of the rind and the heart. The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. Using classical microbiology, the total counts of bacteria were comparable for the 11 samples of tested raw and pasteurized milk cheeses, reaching almost 8 log cfu/g. Using the metagenomic approach, 207 different phylotypes were identified. The rind of both the raw and pasteurized milk cheeses was found to be highly diversified. However, 96.3 and 97.9% of the total microbiota of the raw milk and pasteurized cheese rind, respectively, were composed of species present in both types of cheese, such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens were present at low levels (0.5 and 1.6%, respectively) on the rind of both the raw and the pasteurized milk cheeses, even though this bacterium had been inoculated during the manufacturing process. Interestingly, Psychroflexus casei, also described as giving a red smear to Raclette-type cheese, was identified in small proportions in the composition of the rind of both the raw and pasteurized milk cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the common species of bacteria reached more than 99%. The main species identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum. Interestingly, 93 phylotypes were present only in the raw milk cheeses and 29 only in the pasteurized milk cheeses, showing the high diversity of the microbiota. Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer was present in the pasteurized milk cheeses. However, this specific microbiota represented a low proportion of the cheese microbiota. This study demonstrated that Herve cheese microbiota is rich and that pasteurized milk cheeses are microbiologically very close to raw milk cheeses, probably due to the similar manufacturing process. The characterization of the microbiota of this particular protected designation of origin cheese was useful in enabling us to gain a better knowledge of the bacteria responsible for the character of this cheese.