R van't Slot | PubMed Health

PubMed2004

Chicken single nucleotide polymorphism identification and selection for genetic mapping.

Single nucleotide polymorphisms (SNP) are the ideal markers for high-density genome wide mapping. A total of 327,000 expressed sequence tag (EST) sequences, obtained from the ChickEST project, were examined for the presence of SNP. A total of 32,268 potential chicken SNP were identified and stored in a customized Microsoft Access database and evaluated in silico for their usability for a high-density genetic map. Based on a minimum of 3 for the minor allele occurrence and a minimum of 30% for the minor allele frequency, 5,332 reliable SNP were selected, of which both SNP alleles were present in the database at a high frequency. To test the usefulness of the in silico SNP identification, 24 SNP affecting a BglII site were used for a genotyping study. A functional PCR assay could be designed for 21 of the 24 SNP. It was possible to validate 90% of this marker subset (21 SNP) by BglII restriction analysis. The high percentage of validated markers demonstrates the reliability of the 5,332 chicken SNP markers. Furthermore, the limited number of genomic DNA samples necessary to validate 90% of the SNP markers confirmed the prediction of the high frequency at which both alleles of the selected SNP were present in the tested chicken populations.

Animals↗

PubMed2000

The cps locus of Streptococcus suis serotype 2: genetic determinant for the synthesis of sialic acid.

The capsule of S. suis serotype 2 is composed of glucose, galatose, N-acetylglucosamine, rhamnose and sialic acid. Recently, we described a major part of the cps2 locus of S. suis serotype 2. Based on sequence homology genes encoding potential glucosyl-, galactosyl-, N-acetylglucosaminyl- and rhamnosyltransferase activities could be identified. However, we did not find genes involved in the synthesis of sialic acid. Here, we describe the cloning and characterization of a remaining part of the cps2 locus. Based on the establish sequence 11 potential genes, designated orf2L, orf2M, orf2N, cps2O to cps2T, orf2U and orf2V were identified. A gene homologous to genes involved in the polymerization of the repeating oligosaccharide unit (cps2O) as well as genes involved in the synthesis of sialic acid (cps2P to cps2T) were identified. Moreover, hybridizing experiments showed that the genes involved in the sialic acid synthesis are present in S. suis serotype 1, 2, 14, 27 and 1/2. The orf2M and orf2N regions showed similarity to proteins involved in the polysaccharide biosynthesis of other Gram-positive bacteria. However, these regions seemed to be truncated or were non-functional as the result of frame-shift or point mutations. At its 3;-end the cps2 locus contained two insertional elements (orf2U and orf2V), both of which seemed to be non-functional.

Bacterial Capsules↗