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The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels) markers. Most of the indels loci were polymorphic (71% to 96%), and the genetic variability was similar in all populations. The average observed heterozygosities (HO) and expected heterozygosities (HE) ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst) for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088) than Myanmar (0.041) and Laotian (0.024) populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ) tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3) from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

Here, we studied the genetic diversity of native fowls in Laos by analyzing a mitochondrial DNA (mtDNA) sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced in 129 chickens from the areas of Vientiane, Luang Prabang and Pakse. In total, 29 haplotypes were identified and formed five clades. Haplotype diversity and nucleotide diversity of the native fowls in Laos were 0.85536±0.0172 and 0.010158±0.005555, respectively. Although the Laotian native fowls were distributed across five clades, most of them were clustered in two main clades (A and B), which were originated in China. The other haplotypes were contained in clades D, F, and I, which originated from continental southeast Asia. These results suggest that multiple maternal lineages were involved in the origin of domestic chicken in Laos. Moreover, there appear to be at least two maternal lineages, one from China and the other from the southeast Asian continent.

Pyropia is a genus comprising red algae of the Bangiaceae family that is commonly found in intertidal zones worldwide. However, understanding of Pyropia species that are prone to tropical regions remains limited despite recent breakthroughs in genomic research. Within the realm of Pyropia species thriving in tropical regions, P. vietnamensis stands out as a widely recognized species. In this study, we aimed to investigate Pyropia species in the southwest coast of Myanmar using physiological and molecular approaches, culture-based analyses, chloroplast rbcL and nuclear SSU gene sequencing, and whole chloroplast and mitochondrial genome sequencing. Physiological analysis showed that the Myanmar samples were more heat-tolerant than their Japanese counterparts, including those of subtropical origin. Additionally, molecular characterization revealed that the Myanmar samples were closely related to P. vietnamensis from India. This study is the first to sequence the chloroplast and mitochondrial genomes of Pyropia species from tropical regions. A unique deletion event was observed within a ribosomal RNA gene cluster in the chloroplast genome of the studied Pyropia species, which is a deviation from the usual characteristics of most Pyropia species. This study improves current understanding of the physiological and molecular characteristics of this comparatively understudied Pyropia species that grows in tropical regions., (© 2023. Springer Nature Limited.)

Myanmar indigenous chickens play important roles in food, entertainment, and farm business for the people of Myanmar. In this study, complete mitochondrial D-loop sequences (1232 bp) were analyzed using 176 chickens, including three indigenous breeds, two fighting cock populations, and three indigenous populations to elucidate genetic diversity and accomplish a phylogenetic analysis of Myanmar indigenous chickens. The average haplotype and nucleotide diversities were 0.948 ± 0.009 and 0.00814 ± 0.00024, respectively, exhibiting high genetic diversity of Myanmar indigenous chickens. Sixty-four haplotypes were classified as seven haplogroups, with the majority being haplogroup F. The breeds and populations except Inbinwa had multiple maternal haplogroups, suggesting that they experienced no recent purifying selection and bottleneck events. All breeds and populations examined shared haplogroup F. When 232 sequences belonging to haplogroup F (79 from Myanmar and 153 deposited sequences from other Asian countries/region) were analyzed together, the highest genetic diversity was observed in Myanmar indigenous chickens. Furthermore, Myanmar indigenous chickens and red junglefowls were observed in the center of the star-like median-joining network of 37 F-haplotypes, suggesting that Myanmar is one of the origins of haplogroup F. These findings revealed the unique genetic characteristic of Myanmar indigenous chickens as important genetic resources., (© 2021 Japanese Society of Animal Science.)

Defective appearances, including white spotting (WS), tongue defect (TD), and nipple defect (ND), in Japanese Black cattle potentially lead to economic losses to farmers in Japan. We estimated genetic parameters of defective appearances using 553,433 records of Japanese Black heifer calves housed in the Kagoshima Prefecture. Variance and covariance were estimated using the Gibbs sampling algorithm. The estimated heritability ranged from 0.29 for TD to 0.76 for WS. Percent breeding value (%BV) estimates indicated high variation in WS and ND among sires, reflecting higher heritability. Furthermore, there was a positive linear relationship between the %BV estimate of a sire and the mean incidence rate of each defect in his female offsprings. TD was positively associated with other defects. Therefore, genetic factors strongly affect the incidence of defective appearances in Japanese Black cattle., (© 2020 Japanese Society of Animal Science.)

Local cattle breeds are popular in Myanmar because they make excellent draught animals, so it is of fundamental importance that their genetic diversities and population structures are elucidated for breeding and conservation purposes. In this study, we characterized the genetic diversities and population structures of four popular Myanmar local cattle breeds and five native cattle populations from neighboring countries (Bangladesh, Laos, Cambodia, and Vietnam) using the GGP Bovine 50K array. The mean observed and expected heterozygosity estimates using pruned datasets ranged from 0.317 and 0.322, respectively, in Cambodia to 0.448 and 0.421, respectively, in Vietnam South. The four Myanmar local breeds exhibited similar levels of genetic diversity. However, AMOVA revealed significant genetic differentiation among the nine populations (p < 0.00001), and Neighbor-Net analysis showed that Shan Ngwar Pu was distinct from the other Myanmar local breeds. Furthermore, PCA and population structure analyses revealed that the native cattle from neighboring countries genetically influenced the Myanmar local breeds to some extent and that the genetic origins could also be observed in the local breeds. These findings highlight the importance of Myanmar local breeds as genetic resources and provide useful information for the future development of breeding strategies and conservation management plans., (© 2018 Japanese Society of Animal Science.)

Myanmar native horses are small horses used mainly for drafting carts or carriages in rural areas and packing loads in mountainy areas. In the present study, we investigated genotype distributions and allele frequencies of the LCORL/NCAPG, MSTN and DMRT3 genes, which are associated with body composition and locomotion traits of horses, in seven local populations of Myanmar native horses. The genotyping result of LCORL/NCAPG showed that allele frequencies of C allele associated with higher withers height ranged from 0.08 to 0.27, and 0.13 in average. For MSTN, allele frequencies of C allele associated with higher proportion of Type 2B muscular fiber ranged from 0.05 to 0.23, and 0.09 in average. For DMRT3, allele frequencies of A allele associated with ambling gait ranged from 0 to 0.04, and 0.01 in average. The presences of the minor alleles of these genes at low frequencies suggest a possibility that these horse populations have not been under strong selection pressure for particular locomotion traits and body composition. Our findings of the presence of these minor alleles in Southeast Asian native horses are also informative for considering the origins of these minor alleles associated with body composition and locomotion traits in horse populations., (© 2016 Japanese Society of Animal Science.)

This study aims to estimate the mitochondrial genetic diversity and structure of Japanese Polled and Kuchinoshima feral cattle, which are maintained in small populations. We determined the mitochondrial DMA (mtDNA) displacement loop (D-loop) sequences for both cattle populations and analyzed these in conjunction with previously published data from Northeast Asian cattle populations. Our findings showed that Japanese native cattle have a predominant, Asian-specific mtDNA haplogroup T4 with high frequencies (0.43-0.81). This excluded Kuchinoshima cattle (32 animals), which had only one mtDNA haplotype belonging to the haplogroup T3. Japanese Polled showed relatively lower mtDNA diversity in the average sequence divergence (0.0020) than other Wagyu breeds (0.0036-0.0047). Japanese Polled have been maintained in a limited area of Yamaguchi, and the population size is now less than 200. Therefore, low mtDNA diversity in the Japanese Polled could be explained by the decreasing population size in the last three decades. We found low mtDNA diversity in both Japanese Polled and Kuchinoshima cattle. The genetic information obtained in this study will be useful for maintaining these populations and for understanding the origin of Japanese native cattle., (© 2016 Japanese Society of Animal Science.)

Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis, which is the most common neoplastic disease of cattle. BLV infects cattle worldwide and affects both health status and productivity. However, no studies have examined the distribution of BLV in Myanmar, and the genetic characteristics of Myanmar BLV strains are unknown. Therefore, the aim of this study was to detect BLV infection in Myanmar and examine genetic variability. Blood samples were obtained from 66 cattle from different farms in four townships of the Nay Pyi Taw Union Territory of central Myanmar. BLV provirus was detected by nested PCR and real-time PCR targeting BLV long terminal repeats. Results were confirmed by nested PCR targeting the BLV env-gp51 gene and real-time PCR targeting the BLV tax gene. Out of 66 samples, six (9.1 %) were positive for BLV provirus. A phylogenetic tree, constructed using five distinct partial and complete env-gp51 sequences from BLV strains isolated from three different townships, indicated that Myanmar strains were genotype-10. A phylogenetic tree constructed from whole genome sequences obtained by sequencing cloned, overlapping PCR products from two Myanmar strains confirmed the existence of genotype-10 in Myanmar. Comparative analysis of complete genome sequences identified genotype-10-specific amino acid substitutions in both structural and non-structural genes, thereby distinguishing genotype-10 strains from other known genotypes. This study provides information regarding BLV infection levels in Myanmar and confirms that genotype-10 is circulating in Myanmar.

Chicken egg white ovotransferrin (OTF) has been reported to exist in three electrophoretic variants (OTF A , OTF B and OTF C ). In this report, we identified a causal polymorphism between the OTF B and OTF C variants in Japanese and Taiwanese native chickens and compared the antibacterial activity between these two variants. The cDNA sequence analyses from Satsumadori oviducts revealed that three non-synonymous SNPs T1809G (Ser52Ala), A2258G (Ile96Val) and G7823A (Asp500Asn) corresponded to the OTF electrophoretic phenotypes. Of the three SNPs, the G7823A mutation perfectly corresponded to the electrophoretic phenotypes OTF B (G/G, Asp500Asp), OTF B/C (G/A, Asp500Asn) and OTF C (A/A, Asn500Asn) in three chicken populations. The variants OTF B and OTF C exhibited similar antibacterial potency against Gram-positive and Gram-negative bacteria. This study provides, for the first time, molecular information on polymorphism of OTF B and OTF C variants of chicken ovotransferrin and its effect on the antimicrobial activity of the respective variants., (2016, Japan Poultry Science Association.)

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.

Cattle exhibit a range of carcass defects, including blood splash (BLS), intramuscular edema (INE), muscle steatosis (MUS), bruising (BR), trim loss (TRL) and others (OTH). These defects lower the carcass value and can result in significant economic loss to producers. We estimated the incidence, relationship with inbreeding coefficients and genetic parameters of carcass defects in Japanese Black cattle using 561 619 carcass records from Kagoshima, Japan during April 1988 through March 2011. The defect incidence ranged from 0.22% for TRL to 5.73% for BR. The incidence of MUS and BR increased from 1.21% to 6.57% and from 1.06% to 9.31%, respectively. The incidence of INE peaked at 7.44% in 1999 and decreased thereafter. We observed a positive linear relationship between the defect incidence and the inbreeding coefficients in MUS, BR and TRL (P < 0.01). The heritabilities estimated by univariate animal model with Gibbs sampling for BLS, INE, MUS, BR and TRL were 0.24, 0.06, 0.18, 0.05 and 0.02, respectively. The contribution of farm variance to phenotypic variance was negligible (0.01 to 0.04). Significant genetic correlations of TRL were estimated with MUS (0.63) and BR (0.63). Our results suggest that genetic factors contribute to the incidence of BLS and MUS., (© 2015 Japanese Society of Animal Science.)

The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels) markers. Most of the indels loci were polymorphic (71% to 96%), and the genetic variability was similar in all populations. The average observed heterozygosities (H O ) and expected heterozygosities (H E ) ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst) for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088) than Myanmar (0.041) and Laotian (0.024) populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ) tree, using Nei's genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3) from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

Here, we studied the genetic diversity of native fowls in Laos by analyzing a mitochondrial DNA (mtDNA) sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced in 129 chickens from the areas of Vientiane, Luang Prabang and Pakse. In total, 29 haplotypes were identified and formed five clades. Haplotype diversity and nucleotide diversity of the native fowls in Laos were 0.85536±0.0172 and 0.010158±0.005555, respectively. Although the Laotian native fowls were distributed across five clades, most of them were clustered in two main clades (A and B), which were originated in China. The other haplotypes were contained in clades D, F, and I, which originated from continental southeast Asia. These results suggest that multiple maternal lineages were involved in the origin of domestic chicken in Laos. Moreover, there appear to be at least two maternal lineages, one from China and the other from the southeast Asian continent.

1. The genetic architecture of the avian uncoupling protein (avUCP) was investigated and the relationship between avUCP gene expression and the amount of abdominal fat of Japanese quail was determined by quantitative real-time PCR. 2. The Japanese quail avUCP gene consists of six exons and five introns. Sequences of nucleotides and amino acids were 94·6% and 86·0% identical to those of the chicken avUCP gene, and phylogenetic analysis showed that the Japanese quail avUCP gene consists of the same clusters as the chicken and turkey avUCP. 3. Expression of the avUCP gene was significantly higher in the Pectoralis major (1·28 ± 0·24) than in the Biceps femoris (0·63 ± 0·14). 4. A positive correlation coefficient between the avUCP gene expression in the Pectoralis major and Biceps femoris was observed (r = 0·79, P = 0·02), whereas a negative correlation coefficient was observed between the abdominal fat percentage (AFP) and gene expression in both the Pectoralis major (r = -0·82, P = 0·01) and Biceps femoris (r = -0·61, P = 0·11). 5. The avUCP gene was associated with the accumulation of abdominal fat in Japanese quail and it was concluded that modulation of avUCP gene expression could be utilised to control abdominal fat accumulation in poultry.

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.

Lysozyme is one of the best characterized antimicrobial proteins in egg white. Three phenotypes of egg white lysozyme in Japanese quail, Coturnix japonica, (namely fast; slow; and the combination, FS) were observed by acid polyacrylamide gel electrophoresis. The fast phenotype showed faster mobility on Acid-PAGE than the slow phenotype. Comparison of the coding sequences for lysozyme derived from the slow and fast phenotypes revealed a nonsynonymous SNP at nucleotide position 115 from the translation initiation site, which alters AA sequence of lysozyme. This nonsynonymous SNP converted glutamine (Q) in the slow phenotype to lysine (K) in the fast phenotype at AA residue 21 of mature lysozyme (Q21K). Here, we investigated the effect of these phenotypes on muramidase activity, antibacterial activity, and hatchability. Muramidase activity toward isolated cell walls of Micrococcus lysodeikticus was in the order: fast allozyme > slow allozyme > chicken (Gallus gallus), but no significant difference was found among the 3 (P > 0.05). Antibacterial activity against live Staphylococcus aureus cells was significantly greater for the fast allozyme than the slow allozyme from 20 h after incubation (P < 0.05). For the antibacterial effects against live Escherichia coli cells, the activity of fast was significantly higher than that of slow at 16 h after incubation (P < 0.05). Hatchability was estimated for reciprocal crosses of Japanese quail with the FF (fast) and SS (slow) genotypes. Hatchability was 92.5% in FF male × SS female crosses and 87.2% in SS male × FF female crosses. A Cochran-Mantel-Haenszel test revealed a significant difference between the crosses (P < 0.05) and indicated that the female-derived slow phenotype led to improved rates of hatching. Our results suggest that the nonsynonymous SNP in Japanese quail lysozyme influences the electrophoretic migration, muramidase activity, and antibacterial activity of the protein, in addition to the hatchability of the eggs. These results demonstrate, for the first time, a significant difference in antibacterial activity and hatchability between 2 lysozyme phenotypes in Japanese quail.

Recently, single nucleotide polymorphisms (SNPs) have been used to identify genes or genomic regions responsible for economic traits, including genetic diseases in domestic animals, and to examine genetic diversity of populations. In this study, we genotyped 70 chicken autosomal SNPs using DigiTag2 assay to understand the genetic structure of the Japanese native chicken breeds Satsumadori and Ingie, and the relationship of these breeds with other established breeds, Rhode Island Red (RIR), commercial broiler and layer. Five breeds, each consisting of approximately 20 chickens, were subjected to the assay, revealing the following: Average expected heterozygosities of broiler, Satsumadori, RIR, layer and Ingie were 0.265, 0.254, 0.244, 0.179 and 0.176, respectively. Phylogenetic analysis using the concatenated 70 autosomal SNP genotypes distinguished all chickens and formed clusters of chickens belonging to the respective breeds. In addition, the 2-D scatter plot of the first two principal components was consistent with the phylogenic tree. Taken together with the pairwise F(st) distances, broiler and RIR were closely positioned near each other, while Ingie was positioned far from the other breeds. Structure analysis revealed that the probable number of genetic clusters (K) was six and four with maximum likelihood and ΔK values, respectively. The clustering with maximum likelihood revealed that, in addition to the clustering of the other five breeds, the Satsumadori was subdivided into two genetic clusters. The clustering with ΔK value indicated that the broiler and Rhode Island Red were assigned to the same genetic cluster., (© 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.)

Indonesian native chickens are considered an important genetic resource, particularly with respect to their excellent traits for meat and egg production. However, few molecular genetic studies of these native chickens have been conducted. We analyzed the genetic diversity and differentiation of 4 populations of Indonesian native chickens: Black Kedu (BK), Kedu (KD), Kampung (LOC), and Arab (AR). Blood samples from 188 individuals were collected in central and western Java. Genomic DNA was genotyped using 98 autosomal SNP markers, of which 87 were found to be polymorphic. The proportion of polymorphic loci and the average heterozygosity of each population were in the range of 0.765 to 0.878 and 0.224 to 0.263, respectively. The 4 populations of Indonesian chickens appeared to be derived from 3 genetic populations (K = 3): maximum likelihood clustering showed that the BK variety and AR breed were each assigned to a distinct cluster, whereas the LOC ecotype and KD variety were admixed populations with similar proportions of membership. Principal components analysis revealed that eigenvector 1 separated BK and AR from the other 2 populations. Neighbor-joining trees constructed from pairwise distance matrix (F(ST)) estimates, for individuals and between populations, corroborated that the LOC ecotype and KD variety were related closely, whereas the BK variety and AR breed diverged at greater distances. These results also confirmed the usefulness of SNP markers for the study of genetic diversity.

We used the IMNpRH2(12,000-rad) RH and IMpRH(7,000-rad) panels to integrate 2019 transcriptome (RNA-seq)-generated contigs with markers from the porcine genetic and radiation hybrid (RH) maps and bacterial artificial chromosome finger-printed contigs, into 1) parallel framework maps (LOD ≥ 10) on both panels for swine chromosome (SSC) 4, and 2) a high-resolution comparative map of SSC4, thus and human chromosomes (HSA) 1 and 8. A total of 573 loci were anchored and ordered on SSC4 closing gaps identified in the porcine sequence assembly Sscrofa9. Alignment of the SSC4 RH with the genetic map identified five microsatellites incorrectly mapped around the centromeric region in the genetic map. Further alignment of the RH and comparative maps with the genome sequence identified four additional regions of discrepancy that are also suggestive of errors in assembly, three of which were resolved through conserved synteny with blocks on HSA1 and HSA8., (© 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.)

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.

Six polymorphic sites of the bovine prion protein gene (PRNP) were genotyped in 569 animals of Asian native cattle, Japanese breeds, purebred mythun (Bos frontalis), and mythun x cattle composite animals. At the 23-bp indel site, a deletion (23-) allele was a major allele in all populations except mythun. At the 12-bp indel site, an insertion (12+) allele was a major allele in all populations. The 14-bp indel site was polymorphic in all Asian native cattle. In the octapeptide repeat region, a six-repeat allele was a major allele in all populations, and 5/5 and 4/6 genotypes were detected in Japanese Black and Mongolian cattle and in mythun, respectively. Two nonsynonymous single nucleotide polymorphisms (SNPs) (K3T and S154N) were detected in Asian native cattle and mythun. Haplotype analysis using the genotypes of the six sites estimated 33 different haplotypes. The haplotype 23- 12- K 6 S 14+ was found in all populations.

Genetic differences which exist in the prion protein gene (PRNP) have been reported to influence susceptibility of humans, sheep and goats to prion diseases. In cattle, however, none of the known coding polymorphisms has a direct effect on bovine spongiform encephalopathy (BSE). It has been reported that 23-bp insertion/deletion (indel) polymorphisms within the promoter region have a tentative association to BSE susceptibility in German cattle, and a lower number of 24-bp repeat units in the open reading frame (ORF) was reported to reduce BSE susceptibility in transgenic mice. In this study, because of the hypothesis that bovine PRNP promoter polymorphisms cause changes in PRNP expression, we genotyped PRNP polymorphisms in the promoter and intron 1 using 218 genomic DNA samples from two Japanese cattle breeds. We also analysed the expression levels of prion in 40 animals by quantification of real-time PCR using mRNAs extracted from the medulla oblongata to study the relationship between PRNP genotypes and PRNP expression. We found a significant correlation between promoter indel polymorphisms and PRNP-mRNA expression (P(0.0413)) and therefore hypothesize that differences in polymorphisms could be one of the causes of differences in PRNP expression levels. We also report a novel difference in PRNP expression (P < 0.0001) between Japanese Black and Japanese Brown cattle breeds. There was no significant difference based on age and sex of the animals.

Polymorphisms in the prion protein gene (PRNP) are known to be associated with transmissible spongiform encephalopathies in human, sheep and goats. There is tentative association between PRNP promoter polymorphism and bovine spongiform encephalopathy (BSE) susceptibility in cattle. In this study, we genotyped for six bovine PRNP polymorphic sites including a 23-bp indel in the promoter, a 12-bp indel in the intron 1, two nonsynonymous single nucleotide polymorphisms (SNPs), octapeptide repeats in the coding region and a 14-bp indel in the 3'-untranslated region in 178 animals representing Japanese Brown, Kuchinoshima feral, Mishima, Japanese Shorthorn and Holstein. In 64 Japanese Brown cattle, three indel sites were polymorphic. All of the six sites were monomorphic in Kuchinoshima. The 23-bp and 12-bp indel sites were polymorphic in Mishima cattle. The 23-bp and 14-bp indel sites were polymorphic in Japanese Shorthorn cattle. Both SNP sites were monomorphic in all cattle examined in this study. At the 23-bp indel site, the genotype frequencies of Japanese Brown and Holstein breeds were similar to that of BSE affected cattle. We estimated 12 different haplotypes from these genotypic data. A '23-12-K6S14+' haplotype was the major haplotype in all populations, whose frequencies ranged from 0.50 to 1.00.

To provide a gene-based comparative map and to examine a porcine genome assembly using bacterial artificial chromosome-based sequence, we have attempted to assign 128 genes localized on human chromosome 14q (HSA14q) to a porcine 7000-rad radiation hybrid (IMpRH) map. This study, together with earlier studies, has demonstrated the following. (i) 126 genes were incorporated into two SSC7 RH linkage groups by CarthaGene analysis. (ii) In the remaining two genes, TOX4 linked to TCRA located in SSC7 by two-point analysis, whereas SIP1 showed no significant linkage with any gene/marker registered in the IMpRH Web Server. (iii) In the two groups, the gene clusters located from 19.9 to 36.5 Mb on HSA14q11.2-q13.3 and from 64.0 to 104.3 Mb on HSA14q23-q32.33 respectively were assigned to SSC7q21-q26. (iv) Comparison of the gene order between the present RH map and the latest porcine sequence assembly revealed some inconsistencies, and a redundant arrangement of 16 genes in the sequence assembly.

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 an approximately 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.

A large number of significant QTL for economically important traits including average daily gain have been located on SSC1q, which, as shown by chromosome painting, corresponds to four human chromosomes (HSA9, 14, 15 and 18). To provide a comprehensive comparative map for efficient selection of candidate genes, 81 and 34 genes localized on HSA9 and HSA14 respectively were mapped to SSC1q using a porcine 7000-rad radiation hybrid panel (IMpRH). This study, together with the cytogenetic map (http://www2.toulouse.inra.fr/lgc/pig/cyto/genmar/htm/1GM.HTM), demonstrates that SSC1q2.1-q2.13 corresponds to the region ranging from 44.6 to 63.2 Mb on HSA14q21.1-q23.1, the region from 86.5 to 86.8 Mb on HSA15q24-q25, the region from 0.9 to 27.2 Mb on HSA9p24.3-p21, the region from 35.1 to 38.0 Mb on HSA9p13, the region from 70.3 to 79.3 Mb on HSA9q13-q21 and the region from 96.4 to 140.0 Mb on HSA9q22.3-q34. The conserved synteny between HSA9 and SSC1q is interrupted by at least six sites, and the synteny between HSA14 and SSC1q is interrupted by at least one site.

We are constructing high-resolution, chromosomal 'test' maps for the entire pig genome using a 12,000-rad WG-RH panel (IMNpRH2(12,000-rad))to provide a scaffold for the rapid assembly of the porcine genome sequence. Here we present an initial, comparative map of human chromosome (HSA) 11 with pig chromosomes (SSC) 2p and 9p. Two sets of RH mapping vectors were used to construct the RH framework (FW) maps for SSC2p and SSC9p. One set of 590 markers, including 131 microsatellites (MSs), 364 genes/ESTs, and 95 BAC end sequences (BESs) was typed on the IMNpRH2(12,000-rad) panel. A second set of 271 markers (28 MSs, 138 genes/ESTs, and 105 BESs) was typed on the IMpRH(7,000-rad) panel. The two data sets were merged into a single data-set of 655 markers of which 206 markers were typed on both panels. Two large linkage groups of 72 and 194 markers were assigned to SSC2p, and two linkage groups of 84 and 168 markers to SSC9p at a two-point LOD score of 10. A total of 126 and 114 FW markers were ordered with a likelihood ratio of 1000:1 to the SSC2p and SSC9p RH(12,000-rad) FW maps, respectively, with an accumulated map distance of 4046.5 cR(12,000 )and 1355.2 cR(7,000 )for SSC2p, and 4244.1 cR(12,000) and 1802.5 cR(7,000) for SSC9p. The kb/cR ratio in the IMNpRH2(12,000-rad) FW maps was 15.8 for SSC2p, and 15.4 for SSC9p, while the ratio in the IMpRH(7,000-rad) FW maps was 47.1 and 36.3, respectively, or an approximately 3.0-fold increase in map resolution in the IMNpRH(12,000-rad) panel over the IMpRH(7,000-rad) panel. The integrated IMNpRH(12,000-rad) andIMpRH(7,000-rad) maps as well as the genetic and BAC FPC maps provide an inclusive comparative map between SSC2p, SSC9p and HSA11 to close potential gaps between contigs prior to sequencing, and to identify regions where potential problems may arise in sequence assembly., (Copyright 2008 S. Karger AG, Basel.)

Insulin-like growth factor 1 receptor (IGF1R) is essential for the signalling of growth. In this study, we performed single nucleotide polymorphism (SNP) detection in the Japanese quail IGF1R coding region and an association study between SNPs and body weight in two lines (SS and LL) selected for large and small body weight. Of 21 SNPs obtained, a SNP at position AB292766:c.2293G>A led to the replacement of a valine with an isoleucine (V765I). The two lines were fixed for alternate alleles, with allele encoding valine fixed in the LL line. A significant effect of the SNP genotype was found on 10-week body weight (P < 0.01) and on 4- to 10-week and 6- to 10-week average daily gain (P < 0.05) in the F(2) family obtained from lines LL and SS. In six populations maintained in Japan or France, the frequency of allele encoding valine was higher than the allele encoding isoleucine.

Human cutaneous melanoma is a complex trait inherited in about 10% of cases. Although 2 high-risk genes, CDKN2A and CDK4, and 1 low risk gene, MC1R, have been identified, susceptibility genes remain to be discovered. Here, we attempted to determine new genomic regions linked to melanoma using the pig MeLiM strain, which develops hereditary cutaneous melanomas. We applied quantitative trait loci (QTL) mapping method to a significant genome-wide scan performed on 331 backcross pigs derived from this strain. QTLs were detected at chromosome-wide level for a melanoma synthetic trait corresponding to the development of melanoma. The peak positions on Sus scrofa chromosomes (SSC) were at 49.4 and 88.0 cM (SSC1), 56.0 cM (SSC13), 86.5 cM (SSC15) and 39.8 cM (SSC17), and, on SSC2, at 16.9 cM, in families derived from F1 males only (p < 0.05, except for SSC13, p < 0.01). Analysis of 7 precise specific traits revealed highly significant QTLs on SSC10 (ulceration), on SSC12 (presence of melanoma at birth), on SSC13 (lesion type), and on SSC16 and SSC17 (number of aggressive melanomas) at the respective positions 42.0, 95.6, 81.0, 45.3 and 44.8 cM (p < 0.001 and p < 0.05 respectively at the chromosome- and genome-wide levels). We also showed that MeLiM MC1R*2 allele, which determines black coat colour in pigs, predisposes significantly to melanoma. Interactions were observed between MC1R and markers located on SSC1 (p < 0.05). Taken together, these results indicate that MeLiM swine is a model for human multigenic diseases. Comparative mapping revealed human regions of interest to search for new melanoma susceptibility candidates., ((c) 2006 Wiley-Liss, Inc.)

Twenty-two and eight significant quantitative trait loci for economically important traits have been located on porcine chromosomes (SSC) 2q and SSC16 respectively, both of which have been shown to correspond to human chromosome 5 (HSA5) by chromosome painting. To provide a comprehensive comparative map for efficient selection of candidate genes, we assigned 117 genes from HSA5 using a porcine radiation hybrid (IMpRH) panel. Sixty-six genes were assigned to SSC2 and 48 to SSC16. One gene was suggested to link to SSC2 markers and another to SSC6. One gene did not link to any gene, expressed sequence tag or marker in the map, including those in the present investigation. This study demonstrated the following: (1) SSC2q21-q28 corresponds to the region ranging from 74.0 to 148.2 Mb on HSA5q13-q32 and the region from 176.0 to 179.3 Mb on HSA5q35; (2) SSC16 corresponds to the region from 1.4 to 68.7 Mb on HSA5p-q13 and to the region from 150.4 to 169.1 Mb on HSA5q32-q35 and (3) the conserved synteny between HSA5 and SSC2q21-q28 is interrupted by at least two sites and the synteny between HSA5 and SSC16 is also interrupted by at least two sites.

Bi- and uni-directional chromosome painting (ZOO-FISH) and gene mapping have revealed correspondences between human chromosome (HSA) 17 and porcine chromosome (SSC) 12 harboring economically important quantitative trait loci. In the present study, we have assigned 204 genes localized on HSA17 to SSC12 to generate a comprehensive comparative map between HSA17 and SSC12. Two hundred fifty-five primer pairs were designed using porcine sequences orthologous with human genes. Of the 255 primer pairs, 208 (81.6%) were used to assign the corresponding genes to porcine chromosomes using the INRA-Minnesota 7000-rad porcine x Chinese hamster whole genome radiation hybrid (IMpRH) panel. Two hundred three genes were integrated into the SSC12 IMpRH linkage maps; and one gene, PPARBP, was found to link to THRA1 located in SSC12 but not incorporated into the linkage maps. Three genes (GIT1, SLC25A11, and HT008) were suggested to link to SSC12 markers, and the remaining gene (RPL26) did not link to any genes/expressed sequence tags/markers registered, including those in the present study. A comparison of the gene orders among SSC12, HSA17, and mouse chromosome 11 indicates that intra-chromosomal rearrangements occurred frequently in this ancestral mammalian chromosome during speciation., (Copyright 2006 S. Karger AG, Basel.)

Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering approximately 4836.9 cR12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is approximately 15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering approximately 2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.

A phylogenetic tree for fowl including chicken in the genus Gallus and based on mitochondrial D-loop analysis further supports the hypothesis developed from morphology and progeny production that red junglefowl (RJF) is the direct ancestor of the chicken. The phylogenetic positions of the chicken and the other fowl species in the genus Gallus are of great importance when considering maintenance and improvement of chicken breeds through introgression of genetic variation from wild-type genomes. However, because the phylogenetic analysis based on the DNA sequences is not sufficient to conclude the phylogenetic positions of the fowls in the genus, in the present study, we have determined sequences of whole mitochondrial DNA (mtDNA) and two segments of the nuclear genome (intron 9 of ornithine carbamoyltransferase, and four chicken repeat 1 elements) for the species in the genus Gallus. The phylogenetic analyses based on mtDNA sequences revealed that two grey junglefowls (GyJF) were clustered in a clade with RJFs and chicken, and that one GyJF was located in a remote position close to Ceylon junglefowl (CJF). The analyses based on the nuclear sequences revealed that alleles of GyJFs were alternatively clustered with those of CJF and with those of RJFs and chicken. Alternative clustering of RJF and chicken alleles were also observed. These findings taken together strongly indicate that inter-species hybridizations have occurred between GyJF and RJF/chicken and between GyJF and CJF.

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.

Pig testicular lactate dehydrogenase-C (LDHC) cDNA was cloned and sequenced. The deduced sequence of 332 amino acids from pig LDHC shows 73% and 67% identity with that of pig LDHA (muscle) and LDHB (heart) respectively, whereas pig LDHA and LDHB isozymes shows 74% sequence identity. Pig and mouse LDHC cDNAs were subcloned into bacterial expression vector, and the expressed pig LDHC isozyme was shown to be as thermally stable as mouse LDHC isozyme. Pig genomic DNAs from Chinese Meishan, English Yorkshire, Danish Landrace and American Duroc were shown to exhibit polymorphic sites for restriction enzymes EcoRI, BamHI and PstI.

Ornithine transcarbamylase (OTC) is one of the urea cycle enzymes. While the chicken is a uricotelic animal, it has measurable OTC activity in its kidney. OTC activity is highly variable within and between chicken breeds. Chicken OTC may have some physiological significance because of its significant activity in the kidney. We cloned the OTC cDNA from chicken kidney and found 77% homology between the deduced amino acid sequence of the mature protein and that of mammals. The chicken OTC gene spans 26 kb, consists of 10 exons and 9 introns, and utilizes the same exon-intron boundaries as the human gene. The 5'-flanking region contains a putative TATA box and two potential regulatory sites, but neither the 5'-flanking region nor the splice sites correlated with variation in OTC activity. In intron 3, two polymorphic sites were found: one comprising a deletion of 401 nucleotides; and the other was a length and sequence polymorphic region located 8 bases upstream from the deletion. The latter polymorphism provides an explanation for phenotypic variation in OTC. Linkage analysis has suggested reassignment of the chicken OTC gene from the suggested Z chromosome to chromosome 1q.