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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.

BACKGROUND The presence of residual left atrial low-voltage areas (LVA) has been shown to be strongly associated with atrial fibrillation (AF) recurrence after pulmonary vein isolation. A preliminary study showed that concomitant chronic kidney disease (CKD) increased the rate of AF recurrence. The association between CKD and LVA, however, has not been elucidated. In the present study, we investigated the association between CKD severity and LVA prevalence. Methods and Results: In total, 183 consecutive AF patients who underwent initial ablation for AF were enrolled in this retrospective observational study. Serum cystatin C before ablation was measured, and the estimated glomerular filtration rate (eGFR) was calculated. LVA were defined as sites of left atrial electrogram amplitude

Noi chicken is one of the most popular native breeds in the South of Vietnam because their good meat quality and disease resistance. Therefore, although price of their products (eggs and meat) is always high, they are always preferred. However, there have not been many studies on the morphology of this breed yet. In the current study, a total of 355 Noi chickens (164 males and 191 females) at 28 days old were selected and randomly allotted to individual cages until they reached the market weight at 84 days old. During the experiment, Noi broilers were fed ad libitum a diet with 17% crude protein and 3.000 kcal/kg ME produced by GreenFeed Vietnam Joint Stock Company. Average daily gain, feed conversion ratio and some morphological dimensions were recorded at two different stages of age (28-56 and 56-84 days old). Results were demonstrated that (i) significant differences in feed intake (P=0.006), body weight (P=0.019), beak length (P=0.014), thigh length (P=0.004), shank length (P=0.003), breast diameter (P=0.000), and thigh diameter (P=0.001) were found between males and females as well as between different stages; and (ii) body weight and some dimensions will increase rapidly at the first stage. An understanding on these economic traits helps researchers and producers have a more detailed glance on developing of each part of Noi chicken at different stages of age which they are the basic scientific foundation for further studies on this breed.

The aim of this study is to characterize some quantitative traits of Noi chicken, one of the Vietnamese famous native breeds for meat quality and fighting, at the stage of 0-28 days old. Therefore, 742 chicks were used to measure, record, analyze and evaluate on these traits. As results, there was significant difference in observation traits among stages of age (P=0.000). Interesting, the wings (+64.88%) and keel lengths (+58.83%) rapidly developed within the first week of life, followed by the most of other dimensions, especially breast diameter (+31.85%), thigh diameter (+71.17%) in the second week of age. An increase in the size of the measurements was due to development of the skeleton at observing time points along the experiment. However, there was strong development of muscle tissue in the second week of life as rate of the breast and thigh diameter was greatest. Noi chicks consumed amount of feed of 16.54 g/bird/day and gained a weight of 6.98 g/bird/day. Thus, their feed conversion ratio was 2.37 at the stage of 0-28 days old. Perhaps a direct positive relationship between observed traits and age were randomly established according biological characteristics of animal. This work provided initial benchmarks of Noi chicks for further studies.

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.

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.

Chicken egg white ovotransferrin (OTF) has been reported to exist in three electrophoretic variants (OTFA, OTFB and OTFC). In this report, we identified a causal polymorphism between the OTFB and OTFC 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 OTFB (G/G, Asp500Asp), OTFB/C (G/A, Asp500Asn) and OTFC (A/A, Asn500Asn) in three chicken populations. The variants OTFB and OTFC exhibited similar antibacterial potency against Gram-positive and Gram-negative bacteria. This study provides, for the first time, molecular information on polymorphism of OTFB and OTFC variants of chicken ovotransferrin and its effect on the antimicrobial activity of the respective variants.

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.

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.

The aim of this study was to determine the site of enzyme release from the acrosome and the fate of the acrosomal cap during the process of acrosome reaction (AR) in fowl sperm. Gelatin substrate coverslips with halos were subjected to scanning electron microscopy to determine the site from which acrosomal proteolytic enzyme was released to form a halo around the acrosome of individual sperm. Aliquots of sperm treated with solubilized inner perivitelline layer (IPL) containing 5 mmol CaCl2 were simultaneously subjected to fluorescent staining with fluorescein isothiocyanate-labeled peanut agglutinin and scanning electron microscopy to evaluate AR of sperm and to examine the status of the acrosomal region, respectively. Inside the halos, a gelatin-free (proteolyzed gelatin) layer was found extending some distance around the acrosome of sperm. All of the sperm showing the formation of halos on gelatin had a single circular opening around their subacrosomal rod at the base of the acrosomal cap. Interaction of sperm with solubilized IPL in the presence of 5 mmol CaCl2 resulted in 41.4 ± 1.8% of the sperm to undergo AR, as evaluated by fluorescein isothiocyanate-labeled peanut agglutinin. Similarly, as observed using scanning electron microscopy, 38.2 ± 2.3% of the sperm treated with solubilized IPL plus 5 mmol CaCl2 had exposed subacrosomal rod. In all sperm examined, no sign of disruption of the acrosomal membrane was found in the apical region of the acrosome. Rather, the acrosomal caps were found intact detached from the acrosomal region of the sperm, indicating that AR of fowl sperm resulted in the intact removal of the acrosomal cap. Based on these experimental observations, we suggest that the process of AR in fowl sperm is unique; the release of the acrosomal proteolytic enzyme may occur through a single circular opening formed at the base of the acrosomal cap and the acrosomal cap is detached in intact form from the posterior acrosomal region of the sperm.

1 Science of Bioresource Production, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima city, Kagoshima 890-0065, Japan 2 Faculty of Agriculture, University of the Ryukyus, Nishihara-cho, Okinawa 903-0213, Japan 3 Faculty of Medicine, University of the Ryukyus, Nishihara-cho, Okinawa 903-0213, Japan 4 Faculty of Agriculture, Kagoshima University, Kagoshima city, Kagoshima 890-0065, Japan 5 Professor Emeritus, Faculty of Agriculture, University of the Ryukyus, Nishihara-cho, Okinawa 903-0213, Japan

Japanese quail egg white lysozyme possesses two alleles (S and F). In our previous study, the F phenotype was more effective against bacteria than the S phenotype, whereas the female-derived S phenotype led to improved hatchability. In this study, we analyzed gene frequency of egg white lysozyme using Acid-PAGE and mismatch PCR-RFLP in 22 Japanese quail populations in Japan and compared with five populations in INRA, France. Genotyping of the lysozyme locus in 22 Japanese quail populations in Japan revealed that this locus is polymorphic in all populations except Nagoya University and Kagoshima University (LL and SS) populations. The S allele was a major allele with frequency from 0.69 to 1.00. In five French populations, it was polymorphic in all populations except AA population. The S allele was a major allele with frequency from 0.69 to 1.00. From these results, the lysozyme locus was polymorphic in the Japanese quails and the S allele was a major allele. The S allele was fixed in several populations which have been maintained as closed and small population.

In this study, we attempted to use amplified fragment length polymorphism (AFLP) in combination with selective genotyping to detect loci that affected shank length and body weight at 10 weeks of age in Japanese quail (Coturnix japonica). A total of 88 primer pairs were used in AFLP analyses of 10 and 13 males with the longest and shortest shank lengths, respectively, from an F2 intercross population derived from lines differentiated by large and small body size (LL and SS, respectively). Ten AFLP bands differed strikingly in frequency between the two groups (P 0.05), but did show a significant association with female body weight (P

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 (FST) 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.

The objective of this study was to examine whether domestic fowl (Gallus domesticus) sperm undergo maturation in their capacity for survival and fertilization in the male reproductive tract. Sperm collected from the testis, epididymis and the proximal, middle and distal vas deferens were simultaneously stored in vitro in minimum essential medium (MEM) at 39°C for 0, 3 and 6h, and at 4°C for 24 and 48h. Sperm membrane integrity was measured using the dual fluorescent stain SYBR-14/propidium iodide (PI). Aliquots of sperm from the various sites were subjected to artificial insemination (AI) into the uteri of hens to assess the duration of sperm survival in the oviduct and to determine the fertility status of the sperm. Testicular sperm exhibited a very low capacity to survive under in vitro liquid storage conditions, irrespective of the storage temperature used, and in the oviduct, and they had a low ability to fertilize the ovum. On the contrary, sperm from the distal vas deferens had a higher survival rate during in vitro storage periods, a longer life span in the oviduct, and high fertility. Survival and fertilizing capacity of the sperm recovered from the testes increased gradually (P

The objective of this study was to examine the binding potential of sperm to the epithelium of the sperm storage tubules (SST) in vitro and in vivo to assess the functional maturation of fowl sperm. Sperm from the testis, epididymis, as well as the proximal, middle and distal vas deferens were incubated in vitro with either the uterovaginal junction (UVJ)- or infundibular tissue containing SST at 39°C for 30 min. Aliquots of sperm were also artificially inseminated into the uteri of hens, and the UVJ and infundibulum were collected 24 h post artificial insemination (AI). After incubation and AI, tissues were washed to remove loosely adhered sperm and subjected to fluorescence staining with 4', 6-diamidino-2-phenylindole, dihydrochloride (DAPI) for counting the number of bound sperm per 0.25 mm 2 of surface area. Sperm from the testis, epididymis, and the three segments of the vas deferens exhibited their differential (p

Summary 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 Fst 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.

Analysis of SNPs on the Z sex chromosome is thought to be a useful approach to estimate genetic diversity and genetic relationships in chicken populations. The objective of this research was to analyze the genetic diversity and genetic relationship of Indonesian native chicken populations. Here, we genotyped six unlinked SNP loci on the Z chromosome of 103 hens and 85 cocks from the four populations of Indonesian native chickens: Black Kedu (BK), Kedu (KD), Kampung (LOC), and Arab (AR). Genetic diversity and matrix pairwise distance FST were computed for 23 BK, 116 LOC, 20 AR, and 29 KD chickens. Average expected heterozygosity was greater in LOC and KD than BK and AR. The lowest pairwise FST value was estimated at 0.028 (P

【In this study, to examine genetic variability within a breed and genetic relationships between populations/breeds, we genotyped 606 birds from seven Japanese native chicken breeds at seven polymorphic loci of egg white proteins and compared those with Asian native chicken populations and commercial breeds. Genotyping of the Japanese native breeds showed that ovalbumin, two ovoglobulins and ovotransferrin were polymorphic, but ovomacroglobulin, ovoflavoprotein and lysozyme were monomorphic. The proportion of polymorphic loci ( $P_{poly}$ ) and average heterozygosity ( $\bar{H}$ ) within a population ranged from 0.286 to 0.429 and from 0.085 to 0.158, respectively. The coefficient of gene differentiation ( $G_{ST}$ ) was 0.250 in the Japanese native chicken breeds. This estimate was higher than that of Asian native chicken populations ( $G_{ST}$ = 0.083) 0.083) and of commercial breeds ( $G_{ST}$ = 0.169) 0.169). Dendrogram and PCA plot showed that Satsuma-dori, Jitokko, Amakusa-daio and Hinai-dori were closely related to each other and grouped into Asian native chickens and that Tsushima-jidori, Nagoya and Chan (Utaichan) were ramified far from other Japanese native chicken breeds. The egg white protein polymorphisms demonstrated that the population differentiation of the seven Japanese native chicken breeds was relatively large.】

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.

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.

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×AC crossing. The rankings of each genotype with respect to BW, ADG and growth rate were AA>AC>CC, and statistical significance (P AA>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.

A single amino acid substitution between Asn and Ser at position 631 in the chicken Mx protein has been reported to determine resistant and sensitive antiviral activity. In this study, we investigate whether various kinds of chicken breeds and jungle fowls carry the resistant or sensitive Mx allelic gene by using the mismatched PCR-restriction fragment length polymorphism (RFLP) technique. In total, 271 samples from 36 strains of 17 chicken breeds and from 3 kinds of jungle fowls were examined. The rates of the resistant Mx gene and sensitive gene were 59.2% and 40.8%, respectively. Only a Red jungle fowl captured in Laos carried the resistant Mx gene, and the other three Red jungle fowls from Indonesia and Gray and Green jungle fowls all had the sensitive Mx gene. These results were confirmed by the determination of amino acid sequences in the GTPase effector domain of jungle fowls.

The gene constitution of polymorphisms of the four calpain genes (µ-calpain, m-calpain, p94, and µ/m-calpain) were analyzed in South-East Asian native chickens, White Leghorn and Broiler commercial chickens, and Red and Green jungle fowl. Polymorphisms were detected at all loci in chickens and Red jungle fowl, but only for CAPN1 (µ-calpain gene) in Green jungle fowl. CAPN2 and CAPN1.5 are linked on chicken chromosome 3, and the genotype for these loci were treated as haplotype. Some combinations of calpain loci were tested using principal component analysis, and the best combination (CAPN1, CAPN3, and CAPN1.5) was determined. The proportion of polymorphic loci (Ppoly) and heterozygosity ( ) were 1.00 and 0.316‐0.465 in domestic chickens and red jungle fowl, and 0.33 and 0.137 in Green jungle fowl, respectively. GST values suggested that the degree of subdivision among native chickens was relatively low except for Thailand, which was highest. Pair-wise FST testing, dendrogram and principal component analysis from the results of calpain loci showed that the four South-East Asian native and commercial chicken populations were close genetically.

Calpains are intracellular Ca2+-dependent proteases and enzymes that contribute to growth and meat quality. In the present study, we identified polymorphisms in four calpain genes (CAPN1, CAPN2, CAPN3, and CAPN1.5) expressed ubiquitously in chicken using polymerase chain reaction-restriction fragment length polymorphism, and mapped them using two backcross families (East Lansing (EL) and Kobe University (KU)). CAPN2 and CAPN1.5 mapped to two locations on chromosome 3 about 30 cM apart, while CAPN3 mapped to chromosome 5. CAPN1 was linked to a previously unlinked microsatellite marker LEI0140 to form a new linkage group called E66. CAPN2 and CAPN3 extend the amount of conserved synteny between chicken chromosome 3 and human chromosome 1, and between chicken chromosome 5 and human chromosome 15, respectively. Although CAPN2, CAPN3, and CAPN1.5 were found in the University of California Santa Cruz chicken genome browser gateway, CAPN1 and LEI0140 were not in specific genomic positions.

We performed exon trapping in order to locate functional genes on chicken chromosomes (GGA) and to identify functional gene sequences from chicken cosmids. Sequence analysis of 100 clones revealed 17 putative exons, five of which were identified with known sequences in a gene database search: thymopoietin beta (TMPO), U5 snRNP-specific 40 kDa protein (HPRP8BP), dihydropyridine receptor alpha 1 subunit (CACNL1A3), cystein string protein (CPS) and C15orf4. We attempted to map the genes to chicken chromosomes by using FISH and linkage analysis. The chromosomal localizations were GGA1 (TMPO), GGA10 (C15orf4), GGA23 (HPRP8BP) and GGA28 (CPS) by FISH and linkage analysis, while that of CACNL1A3 was predicted to be on a microchromosome by FISH but not by linkage analysis. Comparative mapping analyses between chickens and humans for the genes revealed both known and new synteny. The syntenic conservation between GGA1 and human chromosome (HSA) 12q23 (TMPO) and between GGA10 and HSA15q25 (C15orf4), were consistent with a recent publication, while two new syntenies were observed between GGA28 and HSA20q13.3 in CPS and between GGA23 and HSA1p34-35 in HPRP8BP. The information of presently mapped genes can contribute as anchor markers based on functional genes and the construction of a comparative map.

Blood samples were collected from four native breeds (Chahua chicken, Xishuangbanna Game chicken, Wuding chicken, and Yangbi Huang chicken) in the Yunnan province of China, and their protein polymorphisms were analyzed by using electrophoresies. Out of 16 loci examined, polymorphisms were found in the following eight loci: plasma esterase, plasma amylase, plasma alkaline phosphatase, plasma albumin, plasma transferrin, plasma postalbumin, and hemoglobin. The other eight loci, erythrocyte lactate dehydrogenase, erythrocyte 6-phosphogluconate dehydrogenase, erythrocyte phosphoglucomutase, erythrocyte phosphohexose isomerase, erythrocyte tetrazolium oxidase, erythrocyte malate dehydrogenase, erythrocyte esterase and hemoglobin, were monomorphic. The proportion of the polymorphic loci and the expected average heterozygosity were estimated as 0.438–0.500 and 0.141–0.174, respectively. A dendrogram was drawn according to the genetic distance, which was calculated by the Nei's genetic distance matrix, among four Chinese native breeds. The results indicated that Chahua, Wuding and Yangbi Huang chickens were genetically remote from Xishuangbanna Game chicken. Moreover, the genetic distance was calculated among the Sri Lankan, Bangladeshi and Nepalese native fowl populations, and another dendrogram was constructed. In the latter dendrogram, Chahua, Wuding and Yangbi Huang chickens were genetically closer to Sri Lankan and Bangladeshi native fowls than Xishuangbanna Game chicken.

Three electrophoretic variations (AA, BB and AB) of ovalbumin controlled by codominant alleles OvA and OvB have been observed in various chicken populations. We compared nucleotide sequences of the open reading frame between two alleles of ovalbumin gene. The difference between the two alleles was found as a non-synonymous substitution of asparagine to aspartic acid as a result of AAT to GAT point mutation at position 8032–8034 in exon 8. We developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol in combination with Mbo I restriction endnuclease mapping for the detection of this substitution. By the PCR-RFLP the allelic frequency of the OvB was estimated to be within the range of 0.000–0.150 in 11 Asian indigenous chicken populations and 0.000 in four improved breeds used in the present study. Gene frequency, estimated by PCR-RFLP in the present study, paralleled that obtained by protein polymorphisms of egg white. Thus, this study provides, for the first time, information of the occurrence of ovalbumin allele OvA and OvB in Asian indigenous chicken populations.

Genetic variations of seven egg white protein loci in 1,112 samples from eight Asian countries (Yunnan province of China, Mongolia, Nepal, Vietnam, Laos, Thailand, Myanmar, Indonesia) and 360 samples from two improved breeds (Isa Brown, Boris Brown) were investigated by using starch gel and polyacrylamide gel electrophoresis. Five egg white protein loci (Oν, G 3 , G 2 , G 1 and Tf E W ) were found to be polymorphic in Asian native chicken populations. The proportion of polymorphic loci (P p o l y ) and average heterozygosity (H) of Asian native populations varied from 0.143 to 0.714 and 0.014 to 0.225, respectively, and were higher than those of improved breeds. The subdivision index (G S T ) value among 18 native chicken populations in Asia is lower (0.0827) than among improved chicken populations (0.1693). This value means that the degree of subdivision among Asian native populations is lower than among improved breeds and gene constitutions among populations in Asia are similar.

The morphological identification and ecological studies on the 3 subspecies of red jungle fowls were carried out in Thailand, Laos and Vietnam from 1994 to 1998. A total of 59 red jungle fowls and 47 hybrids with native chicken were collected and applied to the detailed morphological examination. For the ecological investigation, the hearing survey was performed at 55 localities. Fifty nine red jungle fowls were identified to 3 subspecies groups, Gallus gallus gallus with white earlobes, and G. g. spadiceus and G. g. jabouillei with red earlobes. The earlobe color was used as the most important index for the subspecies identification. Collecting places of individuals were also used as an effective index from the result of zoogeographical survey. There is an extensive zone of intergradation among the habitats of these 3 subspecies. The G. g. gallus inhabiting the continental Thailand, Cambodia, Laos and Vietnam expresses pure white earlobes covered completely with white patch, and the G. g. gallus inhabiting deep south Thailand expresses incomplete white earlobes.Therefore, the names of G. g. gallus type C (Continental) and G. g. gallus type I (insular) are reasonable to these zoogeographically differentiated two groups of G. g. gallus.

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.

Egg white samples from native chicken were collected in 12 local populations in Indonesia. Polymorphisms of egg white protein were analyzed by using starch and polyacrylamide gel electrophoresis. 1) Polymorphism was found at 5 loci (Ov, G3, G2, TfEW and G1). 2) The variant of lysozyme was detected in only Ungaran population (qG1F=0.853, qG1S=0.147). 3) Average heterozygosities of each local population, subdivision index and genetic distance among local population were estimated as 0.028 to 0.141, 0.076 and 0.001 to 0.037 respectively. Genetic distances and degree of subdivision among local populations in Indonesia except Ungaran population were assumed as small.

The present study was done to evaluate and compare the genetic variability at initial generation in an experiment which was conducted to evaluate the heterosis effect in lines under different modes of selection for egg production using Jouy and Tours strains maintained in INRA. Genetic variability was analyzed for 6 lines (lines 1, 2, 3, 4, C and D) of the both strains by 10 protein loci (Hb-1, Alb, Tf, Es-D, Es-2, 6PGD, ADH, Acp, Prt and Amy). The values of Ppoly were calculated as 0.500-0.600 in Jouy strain and 0.70 in Tours strain. The values of H varied from 0.182 to 0.193 in Jouy strain and from 0.220 to 0.232 in Tours strain. Coefficients of gene differentiation (GST) among line was calculated as 0.019. This values suggests that genetic differentiation among the 6 lines is small. Based on genetic distance data, dendrograms were drawn by unweighted pair group method. Six lines were clustered in two groups. One group is composed of line 1, line 3 and line C, and the other group is composed of line 2, line 4 and line D. Based on 9 loci except Prt locus, genetic relationship among 6 lines in INRA and 6 laboratory populations in Japan was investigated. Genetic distances were calculated as 0.001-0.009 within INRA, 0.029-0.089 within Japanese stock and 0.081-0.184 between INRA stock and Japanese stock. GST calculated from gene frequency of 12 quail lines in INRA and Japan was estimated as 0.191 which is higher than the value among lines within INRA. This results suggest this genetic differentiation between INRA and Japan is larger than between lines in INRA stock and between laboratory lines in Japan. A dendrogram composed of the 12 quail lines showed two different clusters of six lines of INRA and 6 laboratory lines in Japan. These results suggest that gene constitution between quail lines in France and in Japan widely different.

In the present study, genomic DNA was prepared from dried chicken blood sample and subsequently used for analyzing DNA fingerprinting (DFP) of native and Red jungle fowl in the South Pacific Islands. These chicken genomic DNAs were sufficient in quantity and purity for multiple DFP analyses, and chicken blood could be stored for up to 3 months without physical degradation under dry condition.The DFP analyses were carried out by individual and population DFP. Similarities of DFP patterns and genetic distances among fowls in Fiji and Western Samoa were estimated using band sharing (BS) value and the mean number of nucleotide substitutions per nucleotide site, respectively. The results of population DFP were under the influence of data in individual DFP. From the BS values and genetic distances, the native fowls in five different islands of Fiji and Western Samoa could be distinguished in each island, and the difference was consistent with geographical distribution. Fijian and Western Samoan native fowls were found to form two separate groups. The Red jungle fowls in Fiji islands were closely related to each other, but were found to be related remotely to Red jungle fowls in Kagoshima University. Therefore, DFP analysis can be used to estimate relative genetic variability and to reconstruct the evolutionary relationships in small populations genetically isolated.

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 present study was conducted to clarify the changes of calpain and calpastatin activities in skeletal muscle as a function of growth rate at advancing age of commercial chickens, using male broiler and layer chickens of 2, 4, 6, and 8 weeks of age. The body weight of broilers were significantly greater than those of layers (P

電気泳動法および測光法によって判定される血液タンパク•非タンパク多型に基づき,Nepal在来羊種(Bhyanglung, Baruwal, Kagi, Lampuchhre)の8地方集団およびBangladesh在来羊の3地方集団との類縁関係を究明するため,雲南省中央部の祿豊および路南地域における在来緬羊集団を調査した.これらの雲南の地方集団において検索された20遺伝子座位のうち7座位,すなわち,Tf, Alp, Lap,Hb-β, X-p, CatおよびLy座位で遺伝子頻度に明らかな違いがみられた.しかしそれらの集団の平均ヘテロ接合体率(H)では差がなかった.この雲南集団はNepal-やBangladeshの全集団とTf, AlpおよびME座位において遺伝子頻度が著しく異なった.また,それらは,X-p座位でBhyanglung & Baruwalの全集団と,Ke座位ではKagi, BangladeshおよびLampuchhreの大部分の集団と類似していた.雲南の両集団のH値は池の地方集団(7-18%)に比べて高く(18-19%), Bangladeshの特にJessore-KhulnaやMymensingh集団(18-20%)の値に近かった.全検索座位および多型座位の遺伝子頻度から算出されたNEIの遺伝的距離および主成分分析では,この雲南集団はチベット系のBhyanglungやBaruwal集団ではなく,インド系のKagi, BangladeshおよびLampuchhre集団と密接な関係にあった.

Pathogenic races of wheat leaf rust fungus (Puccinia recondita f. sp. tritici) collected in Japan during 1990 to 1992 were identified using a Japanese race differential set, consisting of both international standards and Japanese additionals. Race 1B was common in Kanto, Chubu, Kinki and Chugoku districts. In Hokkaido, various races with wider virulence spectrum than that of race 1B were detected. Distribution of races was almost the same as that reported during the previous 60 years in Japan. Races which had never been detected earlier, such as race 8 and race 73, were identified from samples collected in Hokkaido. Reactions of 19 Thatcher-backcrossed near-isogenic lines with single leaf rust resistance gene were also examined. Eleven races identified by the Japanese differential set were divided into 27 virulence phenotypes by using the near-isogenic lines. Only one line with resistance gene Lr24 was resistant to all the cultures tested.