Characteristics of Seven Japanese Native Chicken Breeds Based on Egg White Protein Polymorphisms

Myint, Si Lhyam,Shimogiri, Takeshi,Kawabe, Kotaro,Hashiguchi, Tsutomu,Maeda, Yoshizane,Okamoto, Shin Asian Australasian Association of Animal Productio 2010 Animal Bioscience Vol.23 No.9

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) and of commercial breeds ($G_{ST}$ = 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.

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

Maw, Aye Aye,Shimogiri, Takeshi,Riztyan, Riztyan,Kawabe, Kotaro,Kawamoto, Yasuhiro,Okamoto, Shin Asian Australasian Association of Animal Productio 2012 Animal Bioscience Vol.25 No.7

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.

Gene Constitution of Egg White Proteins of Native Chicken in Asian Countries

Kinoshita, K.,Okamoto, S.,Shimogiri, T.,Kawabe, K.,Nishida, T.,Kakizawa, R.,Yamamoto, Y.,Maeda, Y. Asian Australasian Association of Animal Productio 2002 Animal Bioscience Vol.15 No.2

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 (Ov, $G_3$, $G_2$, $G_1$ and $Tf_{EW}$) were found to be polymorphic in Asian native chicken populations. The proportion of polymorphic loci ($P_{poly}$) and average heterozygosity ($\bar{H}$) 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 ($G_{ST}$) 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.

Sire-maternal Grandsire Model and Sire Model in Estimation of Genetic Parameters for Average Daily Gain and Carcass Traits of Japanese Black Cattle

Kim, Jong-Bok,Lee, Chaeyoung,Tsuyuki, Tsutomu,Shimogiri, Takeshi,Okamoto, Shin,Maeda, Yoshizane Asian Australasian Association of Animal Productio 2006 Animal Bioscience Vol.19 No.12

The objectives of this study were to estimate genetic parameters and sire breeding values for average daily gain (ADG) and carcass traits using sire-maternal grandsire model with REML approach, sire model with REML approach, sire model without relationships among sires and with REML and ANOVA approach, and to investigate advantages and disadvantages of these methods. Data were collected from 42,325 Japanese Black steers and heifers finished and slaughtered from 1991 to 2004. Traits analyzed in this study were average daily gain (ADG) during the fattening period, live weight at slaughter (LW), cold carcass weight (CW), estimated lean yield percentage (LYE), longissimus muscle area (LMA), subcutaneous fat thickness (SFT), rib thickness (RT), and marbling score (BMS). Bivariate analyses were also performed to obtain genetic and phenotypic correlation coefficients among traits. Estimated breeding values were obtained from each model, and simple and rank correlations among breeding values from each model were calculated. Estimates of heritability using the four models ranged from 0.25 to 0.31 in ADG, from 0.21 to 0.24 in LW, from 0.23 to 0.27 in CW, from 0.10 to 0.17 in DP, from 0.40 to 0.42 in LYE, from 0.19 to 0.31 in LMA, from 0.31 to 0.34 in SFT, from 0.26 to 0.33 in RT, and from 0.18 to 0.44 in BMS. The differences in heritability estimates using the four models seemed to be feasible in ADG, CW, DP, LMA, RT, and BMS. Genetic correlation coefficients of ADG with CW, SFT, RT and BMS were moderate to high and positive while the genetic correlation coefficients between ADG and LYE was low and negative. Correlation coefficients of BMS with SFT were negligible for both genetic and phenotypic correlations. The correlations of estimates evaluated from sire models with those from sire-maternal grandsire model were not large enough to convincing that breeding values using a sire model were corresponding to those using a sire-maternal grand sire model. If information of maternal grand sires are not available, the sire model with incomplete pedigree information included only sire of sire (Model 2) is optimal among the sire models evaluated in this study.

Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

A.A. Maw,K. Kawabe,T. Shimogiri,W. Rerkamnuaychoke,Y. Kawamoto,S. Masuda,S. Okamoto 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.1

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.

Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

Maw, A.A.,Kawabe, Kotaro,Shimogiri, T.,Rerkamnuaychoke, W.,Kawamoto, Y.,Masuda, S.,Okamoto, S. Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.1

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.

Genetic Diversity of mtDNA D-loop Polymorphisms in Laotian Native Fowl Populations

Kawabe, K.,Worawut, R.,Taura, S.,Shimogiri, T.,Nishida, T.,Okamoto, S. Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.1

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 $0.85536{\pm}0.0172$ and $0.010158{\pm}0.005555$, 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.