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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.

The electrophoretic variation in bovine hemoglobin-beta (HBB) is one of the most investigated genetic markers. The presence of a unique HBB variant, HBB(X), in Southeast Asian cattle has been reputed as a sign of gene-flow from wild bovine species. In this study, we analyzed the DNA sequences of HBB genes in domestic and wild bovine species to verify this belief. Isoelectric focusing of HBB chain revealed that the HBB(X) in domestic cattle had dimorphism and was separated into HBB(X1) and HBB(X2). The HBB(X1) had the same DNA sequence of the common HBB variant in gayal (Bos gaurus frontalis), while some of the HBB(X2) were identical with that of Cambodian banteng (Bos javanicus birmanicus). As a result, we confirmed that the bovine HBB variants can be a good indicator of introgression between wild and domestic cattle. The HBB(X1) was always predominant to HBB(X2) in the continental populations, suggesting that the gaur had contributed to the gene pool of domestic cattle in this region much more than the banteng. On the other hand, the mitochondrial DNA analysis could not detect gene-flow from wild species. Autosomal markers that can trace the phylogeny between alleles are suitable for the assessment of bovine interspecific introgression.

【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.

Summary Trends in heterozygosity in the process of producing inbred strains of Japanese quail were examined through the characterization of protein polymorphisms based on gene frequencies of 7 polymorphic loci. The average heterozygosity (Ho) at generation 1 was 0.472 and it decreased with increasing inbreeding coefficient (F) to 0.214 at generation 5 when F was 0.594. In all generations, the observed heterozygosities of the surviving families tended to be higher than those of the families that did not survive. The frequency of heterozygotes of the Es-4 locus in surviving families was higher than that of the extinct families in each generation and the difference became conspisuous in generation 4. These results suggests that a heterozygote advantage of Es-4 locus is revealed by inbreeding.

Summary The polymorphism of five enzyme loci (amylase, alkaline phosphatase, albumin, for 4-week body weight was compared to that of the unselected control line (C). for 4 week body weight was compared to that of the unselected control line (C). Three loci in the C line and two in the P line demonstrated polymorphism. Plasma amylase was separated into six bands and zymograms were classified on the basis of these bands into nine phenotypes. Three of the nine types were of relatively high activity and six were of relatively low activity. All nine types were found in the C line, whereas, all birds of the P line had only the most active type. Two alkaline phosphatase alleles (Akp-2B and Akp-2C) were segregating in the C line. Gene frequencies of alkaline phosphatase for the Akp-2B allele were 0.92 in the C line and 1.00 in the P line. Two albumin alleles (AlbQ1 and AlbQ2) were segregating in both populations. Gene frequencies for the AlbQ1 allele were 0.74 in the C line and 0.81 in the P line. Two red cell esterase-D alleles (Es-DF and Es-Ds) were segregating in both populations. The gene frequency for the Es-Ds allele (0.61) was higher than that of the Es-DF allele in the C line. In the P line the frequency of the Es-DF allele was higher than that of the Es-Ds allele. Heterozygosities of the C and P lines were estimated as 0.2258 and 0.1560 respectively. The relative inbreeding coefficient of the P line, calculated from heterozygosities was 0.31.

In this study, we analyzed DNA sequence of mitochondrial DNA (mtDNA) control regions on the 130 native domestic pigs and eight wild boars in the mainland South and South-east Asian countries including Bhutan, Cambodia, Laos, Myanmar, and Vietnam. Forty-four haplotypes were found in the 138 individuals, 41 were in the domestic and four were in wild boars. Only one haplotype was shared by domestic and wild population in Bhutan. In other cases, mtDNA of wild boars did not show close affinity to that of the domestic pigs in the same location, indicating that the native domestic pigs in these countries did not originate in the present habitat. Phylogenetic analyzes of mtDNA haplotypes recapitulated several major clusters identified in other studies, but 11 haplotypes were grouped in a new cluster we named MTSEA. In most cases, more than one lineage group were present in a sampling station, indicating that the present indigenous domestic pigs may have multiple origins. The MTSEA haplotypes were present in relatively high frequencies in domestic pigs in the mountainous area of mainland South-east Asia (Cambodia and Laos), with a few found in Myanmar and Bhutan. The distributions of MTSEA haplotypes are in great conformity with the distribution of present-day Mon-Khmer language and indicated the existence of yet another independent domestication. The D2 haplotypes that distribute high frequency (almost 100%) throughout the Chinese breeds were dominant in Bhutan, Myanmar, and Vietnam. These results suggest an existence of human-mediated dispersal of domestic pigs from north to the south during the historical expansion of Sino-Tibetan and Tai peoples. The D3 haplotypes previously reported in north India were found in sympatric domestic and wild pigs in Bhutan. The D3 haplotype is an important proof of independent domestication event and/or great gene flow between wild and domestic pigs in the foot of Himalaya.

The musk shrew (Suncus murinus) is an insectivore species that inhabits tropical and subtropical Asia widely. To clarify the genetic relationship among wild musk shrew populations, we examined the electrophoretic variants of biparentally inherited genetic markers at 10 loci coding for eight blood proteins/enzymes in a total of 639 animals and compared the results obtained from the mitochondrial DNA data. The principal-component analysis performed using the allele frequency data revealed that the 17 populations could be divided into two major groups, a South Asian group and a Southeast Asian group that includes several island populations bound by Myanmar. The degrees of genetic divergence among populations were higher within the Southeast Asian group than within the South Asian group. This finding was incongruent with the mtDNA diversity. Analysis conducted at the individual level showed that a shrew from the central region in Myanmar that carries a South Asian type of mtDNA showed the electrophoretic variants specific to the Southeast Asian group, suggesting that this region is a contact zone between the two major groups.

The beta 3-adrenergic receptor (ADRB3) is a G protein-coupled receptor that is involved in regulating energy homeostasis. We have studied DNA sequences of porcine ADRB3 to find candidate genetic polymorphisms for economically important growth and performance traits in pigs. Five novel haplotypes derived from the three In/dels and 44 SNPs were identified among domestic pigs and wild boars. Three of them encode non-synonymous amino acid sequences by five missense polymorphisms and a frameshift by a thymine insertion. The amino acid polymorphic sites were distributed as follows: one substitution was in extracellular loop 1, three substitutions were in intracellular loop3 and one substitution and the deletion of two amino acids were at the carboxyl-terminal. There was no polymorphism in the transmembrane domains. In addition, we surveyed the allelic frequency of the thymine insertion that cause frameshift in South-east Asian local pigs, including some commercial breeds and wild boars. This thymine insertion was distributed widely in the domestic pigs and wild boars. The frequencies of this allele were relatively low in Western improved breeds, while they were very common in Asian breeds and wild boars in Asia. This result indicates that this insertion originally occurred in ancient Asian wild boars and then circulated among Asian domestic pigs. This allele also spread over Western breeds, probably through the introgression of Asian pigs into European stocks during the 18th and 19th centuries.

Summary 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.

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.

In this study on Japanese quail, heterosis for weight, growth rate, and fitness traits were estimated and growth curves were fitted to traits and were compared. Crossing (SR) was performed between females of a very small line (SS) which was selected for low body weight at the age of six weeks and males of a randombred population (RR) from the same origin. Heterosis for female body weight was observed at 4 and 6 weeks of age, but it was not significant for adult size in males and females. The four growth curve models of Brody, Logistic, Gompertz and Bertalanffy were compared and the Gompertz model was the most suitable. Heterosis by the Gompertz model was negative for the age at the point of inflexion and the age at the 90% body weight of the asymptote in both sexes, but it was larger for the second trait. There was no heterosis for fertility and viability from 6 weeks up to 100 days of age in the female, but it was significant for hatchability and survival rate up to 6 weeks of age. Large heterosis was found for the age at first egg, the number of eggs and the total egg weight up to 100 days of age. However, the average egg weight of SR was lighter than that of RR, showing no heterosis.

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.

1. Four Japanese quail lines were developed using 13 generations of reciprocal recurrent (lines AA and BB) or within-line selection (lines DD and EE) for high egg number until 98 d of age. In these lines and their reciprocal crosses, egg production, egg weight and mortality were monitored for up to 21 months to evaluate the impact of selection method and line origin on long-term production and heterosis. 2. Both hen-housed total egg number (EN) and hen-day egg laying rate (ELR) were consistently lower in recurrent lines than in lines under within-line selection: after 13 months of test, the difference was -47.1 eggs for EN and -20% for ELR%, whereas mortality was similar at around 20%. 3. Line EE was the best pure line for early egg production (55.2 eggs at 98 d of age) and also gave eggs which were consistently about 2 g larger than those from line DD but it had the highest overall mortality (78.5%) of all lines. On average, line DD laid 399 eggs (EN) over the whole experiment, 84 more than Line EE. 4. Crossbreds from the 2 types of pure lines and line DD had similar patterns and rates of egg production during the whole experiment, as indicated by the similarity of the curves adjusted for those lines by using the monomolecular model for EN and the modified compartmental model for ELR. 5. However, heterosis was higher from recurrent selection lines and it increased more with time than did heterosis from within-line selection lines.

Introduction In much animal production, commercial animals are crossbreds from closed lines or breeds under long-term directional selection. Therefore it is desirable to be able to predict heterosis gains over the generations as it is done for genetic progress under within-line selection. However, heterosis is the phenotypic expression of a complex phenomenon which may involve several types of genetic effects like dominance and epistasis. In animal breeding, basic quantitative genetics theory indicates that heterosis should be proportional to (squared) differences in gene frequency between populations (e.g. F alconer and M acK ay 1996), and it has been found approximately correct, so it is commonly used for planning crosses. Under that type of heterosis, however, selection towards the same objective in two populations should bring gene frequencies closer, and therefore it should eventually decrease heterosis. On the other hand, reciprocal recurrent selection designed to increase genetic distance between lines should eventually achieve maximum heterosis (O llivier 1982). Some experiments reviewed by brun (1982) have already compared genetic progress under within-line and reciprocal recurrent selection, but they did not focus on comparing the trend of heterosis with generations between the two selection methods. Also, heterosis was monitored periodically in some selection experiments on poultry, and results were reviewed by F airfull (1990). They were somewhat contradictory, but they generally failed to relate genetic progress to loss of heterosis under within-line selection. Moreover, in commercial production, as purebreds and crossbreds are not contemporaries and are generally maintained under very different management systems, estimations of heterosis and of the evolution of crossbred advantage over the generations may be difficult to obtain. Using the Japanese quail as an experimental animal, the present work was initiated specifically to follow the changes in heterosis brought about by selection for a single heterotic trait, early egg production (M invielleet al. 1995). For that purpose, two selection methods expected to have opposite effects on heterosis, directional within-line (or individual) selection and reciprocal recurrent selection, were applied for 13 generations in four quail lines started from two different origins, and trends of heterosis in the selected character and in weight and egg traits were evaluated.

Apolipoprotein E (apoE) phenotypes were determined in 199 unrelated native sheep (Khalkhas line) of Central Mongolia, using a polyacrylamide gel isoelectric focusing-immunoblotting technique, and the plasma lipid levels in different phenotypes were assayed enzymatically. Twenty-eight phenotypes were identified in this sheep. In addition to all the previously detected seven apoE variants composing the phenotypes, four new variants were discovered, which were called E8, E9, E10, and E11. From the population data, these were found to be genetically controlled by four codominant alleles, designated APOE8, APOE9, APOE10, and APOE11, based on the same mode of inheritance as in the seven variants. These alleles were detected at a low frequency, in the range of 0.005 to 0.0126. The Khalkhas sheep differed most significantly from the Baruwal and Lampuchhre sheep of Nepal and the Vietnamese sheep with respect to the allele frequencies found in some Asian local sheep previously examined. Type 1/1 and/or 2/7 sheep had significantly higher plasma levels of total cholesterol and low-density lipoprotein cholesterol than type 7/7 sheep (P < 0.05 and/or P < 0.02).

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.

Most of the triacylglycerol hydrolase activity in the hen liver showed its maximum activity at pH 6.0 and at 40°C. The hydrolase activity was markedly inhibited by serum of the laying hen. At 145 and 167 days of age, the activity was markedly decreased to less than one half that in the young hen. The hydrolase activity in cockerel was monitored to compare with that of hen. In cockerels, the hydrolase activity tended to increase with age of days. On estrogenization of the male chicks, the hydrolase activity in the liver was significantly decreased in contrast to an increase in lipid content in the liver. These observations suggest that the degradation of triacylglycerol in the liver is regulated by estradiol with the increase in lipogenesis for egg production.

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

Oligonucleotide probes specific for simple tandem repeat sequences produce individual specific DNA fingerprints in man and animal species tested so far. In the present study, a polynucleotide (TG)n was used to investigate DNA fingerprint variability in three breeds (Thoroughbred, Tokara horse and Noma horse) in order to clarify the relationships among Japanese native horses by using DNA fingerprinting (DFP). Estimates of the probabilities of finding identical fingerprints in two unrelated individuals of different breeds were in the range from 2.1×10-1 to 3.6×10-5.Similarities in DFP patterns between individuals were estimated by using the band sharing (BS) value. From the BS values, individuals within breeds tended to be more similar to each other with regard to DFP pattern than to individuals of other breeds. Furthermore, the genetic distance among the horse breeds was estimated as the mean number of nucleotide substitutions per nucleotide site. All individuals of three different ferent breeds were distributed into particular clusters and the Tokara horse was far from other breeds. DFP analysis can therefore be effectively used to assess the genetic relationship among breeds of horses.

The present study was conducted to know the correlation between both the calpain and calpastatin activities in the skeletal muscle and fractional growth rate (FGR) in normal growth condition using male Satsuma native fowl. FGR was expressed as the ratio of daily gain calculated by the daily gain during 2-3 weeks of age to body weight at 2 weeks of age. The 14 experimental birds with same initial body weight at 2 weeks of age (110g/bird) were selected from 175 birds.The mean of body weight at 3 weeks of age (g) and FGR (%/day) were 207.5±11.9 and 12.66±1.54, respectively. Calpain activities in units/g muscle and units/mg extractable muscle protein were 1.023±0.093 and 0.024±0.004, respectively. The calpastatin activities in units/g muscle and units/mg extractable muscle protein were 0.287±0.027 and 0.013±0.003, respectively. The correlation coefficient between calpain activity in units/g muscle and FGR was -0.66. But, there was no significant correlation between either activities of calpain (units/mg extractable muscle protein) and calpastatin (units/g muscle and units/mg extractable muscle protein) and FGR.

The origin of the domestic fowl and its relationship to the jungle fowl is a continuing interest to the scientists working with poultry. The present study was conducted in order to clarify the relationships among the domestic and jungle fowls using DNA fingerprinting (DFP). These DFP analyses were carried out by mixing equal amounts of DNA from several individuals of a particular population, resulting in a DFP parttern characteristic of the population. Similarities of DFP pattern between breeds or species of fowl were estimated using band sharing (BS) value. From the BS values, the Japanese native stocks and Chinese native stocks were found to form two separate groups, respectively. BS values between Green Jungle Fowl and all other stocks were generally low. Genetic distance among the domestic and jungle fowls was estimated as the mean number of nucleotide substitutions per nucleotide site. The results indicated that Red Jungle Fowl was relatively close to the domestic fowls. On the other hand, Green Jungle Fowl was found to be related most remotely to the domestic fowls. Thus, DFP analysis with mixed DNA could be effectively used to assess the genetic relationship among the stocks of fowls.

The present study was conducted to analyze biochemical marker genes and to clarify genetic variation in 4 Mongolian gerbil (Meriones unguiculatus) strains (MGS/Sea, MON/Jms Gbs, Kwl: Mongolian Gerbil and Hos: Mongolian gerbil) maintained in Japan. Cellulose acetate, starch gel or agar gel electrophoresis was used. Of the 23 kinds of proteins detected, variation was found only in liver acid phosphatase (Acp2); no variation in other proteins was found within or among strains. The results suggest that these 4 Mongolian gerbil strains are genetically similar. A strain difference was found in the Acp2 locus of liver acid phosphatase. The Kwl: Mongolian Gerbil strain had a band of Acp2 locus, whereas MGS/Sea, MON/Jms and Hos: Mongolian gerbil strains did not.

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.

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 (p0.05). 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.

The mithun (Bos frontalis), synonymous with mithan and gayal, is considered to be a domesticated form of gaur (B. gaurus). However, there has been a controversy concerning its origin. In an effort to address this issue, the mitochondrial cytochrome b (cytb) genes of 20 mithun from Myanmar and 13 from Bhutan were sequenced to trace its maternal origin. Seven cytb haplotypes were found in the 33 mithun, and the phylogenetic tree for these haplotypes clearly showed three embranchments involving five gaur types, a B. indicus type, and a B. taurus type. Sixteen Myanmar and 12 Bhutan mithun had gaur haplotypes, while a B. indicus haplotype was found in three Myanmar and one Bhutan mithun. The B. taurus haplotype was detected in a single Myanmar animal. These results demonstrated that the principal maternal origin of mithun was gaur and suggested that it was directly domesticated from gaur. However, some introgression of domestic cattle existed in current mithun populations. The presence of cattle mtDNA raised the question of how many cattle nuclear genes might have been integrated into the gene pool of mithun.

The electrophoretic variation in bovine hemoglobin-beta (HBB) is one of the most investigated genetic markers. The presence of a unique HBB variant, HBB(X), in Southeast Asian cattle has been reputed as a sign of gene-flow from wild bovine species. In this study, we analyzed the DNA sequences of HBB genes in domestic and wild bovine species to verify this belief. Isoelectric focusing of HBB chain revealed that the HBB(X) in domestic cattle had dimorphism and was separated into HBB(X1) and HBB(X2). The HBB(X1) had the same DNA sequence of the common HBB variant in gayal (Bos gaurus frontalis), while some of the HBB(X2) were identical with that of Cambodian banteng (Bos javanicus birmanicus). As a result, we confirmed that the bovine HBB variants can be a good indicator of introgression between wild and domestic cattle. The HBB(X1) was always predominant to HBB(X2) in the continental populations, suggesting that the gaur had contributed to the gene pool of domestic cattle in this region much more than the banteng. On the other hand, the mitochondrial DNA analysis could not detect gene-flow from wild species. Autosomal markers that can trace the phylogeny between alleles are suitable for the assessment of bovine interspecific introgression.

Chymotrypsinogen is a principal precursor of pancreatic proteolytic enzymes. We previously isolated a cDNA clone for human prechymotrypsinogen from a human pancreatic cDNA library. In the present study, we used this cDNA sequences to isolate genomic DNA clones. Three overlapping cosmid clones spanning approximately 65-kb genomic sequences were isolated from a human cosmid library. The genomic DNA clones were characterized by restriction enzyme mapping and by hybridizing them to subfragments of the cDNA. The sequence tagged sites for human chymotrypsinogen gene were created by designing two oligonucleotides. Furthermore, the isolated genomic clones were confirmed to be localized on chromosome 16q23 by fluorescence in situ hybridization and G-banding analysis.

Calpain activity was determined by western blot analysis of steady-state concentrations of m-calpain (calpain requiring millimolar Ca2+ for activation) and also by northern blot analysis of steady-state concentrations of mRNA encoding m-calpain in three lines of quail: a random-bred control line (RR) and two lines selected for body weight, one for increased body weight (LL) and another for decreased body weight (SS). The m-calpain activities in skeletal muscle were higher in the SS line and lower in the LL line. From western blot analysis, enzyme levels of calpain were almost the same for all three lines. At the level of gene expression, the mRNA concentration encoding m-calpain was higher in the LL and lower in the SS line. These results suggest that the regulation of calpain activity in skeletal muscle is a three-step process, regulation at the transcription level, regulation at the enzyme level, and regulation of the activation of calpain.