Assignment of CPS1, OTC, CRYD2, ARG2 and ASS genes to the chicken RH map

An attempt was made to assign five genes, CPS1, OTC, ASS, CRYD2, and ARG2, to chicken chromosomes (GGA) by radiation-hybrid mapping. OTC was assigned to GGA1; ARG2 to GGA5; CPS1 to GGA7; and CRYD2 to GGA19. ASS was not, however, assigned to a specific chromosomal position

Evaluation of PRNP Expression Based on Genotypes and Alleles of Two Indel Loci in the Medulla Oblongata of Japanese Black and Japanese Brown Cattle

BACKGROUND: Prion protein (PrP) level plays the central role in bovine spongiform encephalopathy (BSE) susceptibility. Increasing the level of PrP decreases incubation period for this disease. Therefore, studying the expression of the cellular PrP or at least the messenger RNA might be used in selection for preventing the propagation of BSE and other prion diseases. Two insertion/deletion (indel) variations have been tentatively associated with susceptibility/resistance of cattle to classical BSE. METHODOLOGY/PRINCIPAL FINDINGS: We studied the expression of each genotype at the two indel sites in Japanese Black (JB) and Japanese Brown (JBr) cattle breeds by a standard curve method of real-time PCR. Five diplotypes subdivided into two categories were selected from each breed. The two cattle breeds were considered differently. Expression of PRNP was significantly (p<0.0001) greater in the homozygous deletion genotype at the 23-bp locus in JB breed. Compared to the homozygous genotypes, the expression of PRNP was significantly greater in the heterozygous genotype at the 12-bp locus in JB (p<0.0001) and in JBr (p = 0.0394) breeds. In addition, there was a statistical significance in the PRNP levels between the insertion and the deletion alleles of the 23-bp locus in JB (p = 0.0003) as well as in JBr (p = 0.0032). There was no significance in relation to sex, age, geographical location or due to their interactions (p>0.05). CONCLUSION: Our results suggest that the del/del genotype or at least its del allele may modulate the expression of PRNP at the 23-bp locus in the medulla oblongata of these cattle breeds

An integrated RH map of porcine chromosome 10

BACKGROUND: Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH2(12,000-rad )porcine WG-RH panel, integrated with the IMpRH(7000-rad )WG-RH, genetic and BAC fingerprinted contig (FPC) maps. RESULTS: Map vectors from the IMNpRH2(12,000-rad )and IMpRH(7,000-rad )panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR(7,000 )and 1814.5 cR(12,000), respectively. The second group covers SSC10q at map distances of 1336.9 cR(7,000 )and 3353.6 cR(12,000), yielding an overall average map resolution of 16.4 kb/cR(12,000 )or 393.5 kb per marker on SSC10. This represents a ~2.5-fold increase in map resolution over the IMpRH(7,000-rad )panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built. CONCLUSION: This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH2(12,000-rad )and IMpRH(7,000-rad), genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10

South-East Asia bovine populations and the Japanese cattle breeds do not harbour the E211K variant of the PRNP

An important outcome of intensive worldwide Bovine spongiform encephalopathy (BSE) obtained with the surveillance by The National Creutzfeldt-Jakob Disease Surveillance Unit (http://www.cjd.ed.ac.uk/figures. htm), has been the detection of atypical BSE in cattle. The discovery of a prion protein gene (PRNP) E211K variant in an atypical BSE case is particularly remarkable because it is analogous to the most common pathogenic mutation in humans (E200K), which causes hereditary Creutzfeldt-Jakob disease (CJD). Knowledge of the distribution and frequency of PRNP E211K variants in cattle populations is critical for understanding and managing atypical BSE. This study was carried out to investigate the prevalence of the E211K variant in the South-East Asia bovine populations and in the Japanese cattle breeds. It was discovered that E211K variant was monomorphic for a G allele and the GG genotype in the 745 animals analyzed in this study. Therefore, neither the Bos indicus nor the Bos taurus animals analyzed are presently known to harbor the 211K variant predicting that the number of carriers for this variant will also be vanishingly low

Genetic Diversity of Myanmar and Indonesia Native Chickens Together with Two Jungle Fowl Species by Using 102 Indels Polymorphisms

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island

Identification of TENP as the Gene Encoding Chicken Egg White Ovoglobulin G2 and Demonstration of Its High Genetic Variability in Chickens.

Ovoglobulin G2 (G2) has long been known as a major protein constituent of chicken egg white. However, little is known about the biochemical properties and biological functions of G2 because the gene encoding G2 has not been identified. Therefore, the identification of the gene encoding G2 and an analysis of its genetic variability is an important step toward the goal of understanding the biological functions of the G2 protein and its utility in poultry production. To identify and characterize the gene encoding G2, we separated G2 from egg white using electrophoresis on a non-denaturing polyacrylamide gel. Two polymorphic forms of G2 protein (G2A and G2B), with different mobilities (fast and slow respectively), were detected by staining. The protein band corresponding to G2B was electro-eluted from the native gel, re-electrophoresed under denaturing conditions and its N-terminal sequence was determined by Edman degradation following transfer onto a membrane. Sequencing of the 47 kDa G2B band revealed it to be identical to TENP (transiently expressed in neural precursors), also known as BPI fold-containing family B, member 2 (BPIFB2), a protein with strong homology to a bacterial permeability-increasing protein family (BPI) in mammals. Full-length chicken TENP cDNA sequences were determined for 78 individuals across 29 chicken breeds, lines, and populations, and consequently eleven non-synonymous substitutions were detected in the coding region. Of the eleven non-synonymous substitutions, A329G leading to Arg110Gln was completely associated with the noted differential electrophoretic mobility of G2. Specifically G2B, with a slower mobility is encoded by A329 (Arg110), whereas G2A, with a faster mobility, is encoded by G329 (Gln110). The sequence data, derived from the coding region, also revealed that the gene encoding G2 demonstrates significant genetic variability across different chicken breeds/lines/populations. These variants, and how they correlate with egg white properties, may allow us to understand further G2's functions

Genotypic Frequency in Asian Native Chicken Populations and Gene Expression Using Insulin-like Growth Factor 1 (IGF1) Gene Promoter Polymorphism

A single nucleotide polymorphism (SNP) site, alleles A and C, within promoter region of insulin-like growth factor 1 gene (IGF1) showed significant association with chicken growth, body composition and skeletal traits. In the present study, we performed genotyping of this SNP in Asian native chicken populations, layer and broiler populations using PCR-RFLP and comparison of gene expression level and growth traits among the SNP genotypes. By the PCR-RFLP, allele C frequency was estimated to be within the range of 0.64-1.00 in 12 Asian native chicken populations, 0.48-1.00 in eight layer stocks and 0.00-0.14 in two broiler stocks examined in this study. In all chicken populations, the observed number of each SNP genotype was in good agreement with the Hardy-Weinberg expectations. Body weight (BW), average daily gain (ADG), growth rate and IGF1 gene expression level in three-week liver were compared among three SNP genotypes obtained by AC&times;AC crossing. The rankings of each genotype with respect to BW, ADG and growth rate were AA&gt;AC&gt;CC, and statistical significance (P&lt;0.05) was found within AA and CC in BW and ADG. The rankings of each genotype with respect to the IGF1 gene expression level was AC&gt;AA&gt;CC. Although we could not find statistically significant difference among the genotypes in the growth rate and the gene expression level, the mean values of CC were lower than those of AA in all traits

Assignment of CPS1, OTC, CRYD2, ARG2 and ASS genes to the chicken RH map

An attempt was made to assign five genes, CPS1, OTC, ASS, CRYD2, and ARG2, to chicken chromosomes (GGA) by radiation-hybrid mapping. OTC was assigned to GGA1; ARG2 to GGA5; CPS1 to GGA7; and CRYD2 to GGA19. ASS was not, however, assigned to a specific chromosomal position