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Mitochondrial D-Loop Variations for Discrimination of Commercial Korean Native Chicken Populations
Sultana, Hasina,Hoque, Md. Rashedul,Seo, Dong-Won,Kang, Bo-Seok,Heo, Kang-Nyeong,Jo, Cheorun,Lee, Jun-Heon The Korean Society of Poultry Science 2012 韓國家禽學會誌 Vol.39 No.4
The increasing demand for Korean native chicken meat indicates that the discovery of haplotypes is very important from both economic and conservation points of view. In this study, mtDNA D-loop sequences from two crossbred Korean native chicken populations of 138 individuals were investigated. Twenty six nucleotide substitutions were identified from sequence analysis and were classified into 12 haplotypes. The haplotype H_8 represents 73.47% of Woorimatdag (chicken population) sequences, which were identified in all five Woorimatdag chicken populations investigated. The H_7 haplotype (Dhap1) for D population covers 45% sequences, which indicate maternal inheritance from black Korean native chicken. On the other hand, Chap3 and Chap4 for C population are specific haplotypes, as H_5 and H_2, respectively. Based on the network profiles, six SNPs (C199T, A239G, G242A, A291G, T330C and C391A) of the D-loop region are effective markers for discrimination between Woorimatdag and Hanhyup chicken populations. Also, the phylogenetic analyses of Woorimatdag and Hanhyup chicken populations were used to identify the genetic relationships among the haplotypes. The results presented here can be used for developing molecular markers to discriminate between two commercial Korean native chickens.
Genetic Diversity Analyses of Asian Duck Populations using 24 Microsatellite Markers
Sultana, Hasina,Seo, Dongwon,Choi, Nu-Ri,Kim, Yeon-Su,Manjula, Prabuddha,Bhuiyan, Md. Shamsul Alam,Heo, Kang-Nyeong,Lee, Jun-Heon The Korean Society of Poultry Science 2017 韓國家禽學會誌 Vol.44 No.2
A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.
Genetic Diversity Analyses of Asian Duck Populations using 24 Microsatellite Markers
Hasina Sultana,Dongwon Seo,Nu-Ri Choi,Yeon-Su Kim,Prabuddha Manjula,Md. Shamsul Alam Bhuiyan,Kang-Nyeong Heo,Jun-Heon Lee 한국가금학회 2017 韓國家禽學會誌 Vol.44 No.2
A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.
Hasina Sultana,Dongwon Seo,Nu-Ri Choi,Md. Shamsul Alam Bhuiyan,이승환,Kang-Nyeong Heo,이준헌 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.2
Objective: The aim of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) of the melanogenesis associated transcription factor (MITF) and dopachrome tautomerase (DCT) genes on plumage coloration in Asian native duck breeds. MITF encodes a protein for microphthalmia-associated transcription factor, which regulates the development and function of melanocytes for pigmentation of skin, hair, and eyes. Among the tyrosinase-related family genes, DCT is a pigment cell-specific gene that plays important roles in the melanin synthesis pathway and the expression of skin, feather, and retina color. Methods: Five Asian duck varieties (black Korean native, white Korean native, commercial Peking, Nageswari, and Bangladeshi Deshi white ducks) were investigated to examine the polymorphisms associated with plumage colors. Among previously identified SNPs, three synonymous SNPs and one indel of MITF and nine SNPs in exon regions of DCT were genotyped. The allele frequencies for SNPs of the black and white plumage color populations were estimated and Fisher’s exact test was conducted to assess the association between the allele frequencies of these two populations. Results: Two synonymous SNPs (c.114T>G and c.147T>C) and a 14-bp indel (GCTGCAAAC AGATG) in intron 7 of MITF were significantly associated with the black- and white-colored breeds (p<0.001). One non-synonymous SNP [c.938A>G (p.His313Arg)] in DCT, was highly significantly associated (p<0.001) and a synonymous SNP (c.753A>G) was significantly associated (p<0.05) with black and white color plumage in the studied duck populations. Conclusion: The results of this study provide a basis for further investigations of the associations between polymorphisms and plumage color phenotypes in Asian duck breeds.
Identification of Polymorphisms in Plumage Color Related Genes in Korean Native Ducks
Sultana, Hasina,Seo, Dong-Won,Park, Hee-Bok,Cahyadi, Muhammad,Jin, Shil,Hoque, Md.-Rashedul,Kim, Yeon-Su,Heo, Kang-Nyeong,Jo, Cheorun,Gotoh, Takafumi FACULTY OF AGRIC PUBLICATIONS-KYUSHU UNIV 2015 Journal of the Faculty of Agriculture, Kyushu Univ Vol. No.
Identification of <i>MC1R </i>SNPs and their Association with Plumage Colors in Asian Duck
Sultana, Hasina,Seo, Dong-Won,Park, Hee-Bok,Choi, Nu-Ri,Hoque, Md. Rashedul,Bhuiyan, Md. Shamsul Alam,Heo, Kang-Nyeong,Lee, Seung-Hwan,Lee, Jun-Heon Japan Poultry Science Association 2017 Journal of Poultry Science Vol.54 No.2
Seo, Dongwon,Bhuiyan, Md. Shamsul Alam,Sultana, Hasina,Heo, Jung Min,Lee, Jun Heon Asian Australasian Association of Animal Productio 2016 Animal Bioscience Vol.29 No.4
Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.
한국 토종오리의 개체 식별 및 품종 구분을 위한 Microsatellite 마커 탐색
서동원(Dong Won Seo),술타나(Hasina Sultana),최누리(Nu Ri Choi),김연수(Yeon Su Kim),진실(Shil Jin),허강녕(Kang Nyeong Heo),진선덕(Seon Deok Jin),이준헌(Jun Heon Lee) 한국가금학회 2015 韓國家禽學會誌 Vol.42 No.1
& & 최근, 한국의 소비자들이 건강에 대한 관심이 증가하면서 단일불포화 지방산이 풍부해 건강에 긍정적인 영향을 줄 수 있는 오리고기의 수요가 급격하게 증가하고 있다. 하지만 대부분의 종 오리는 수입에 의존하고 있는 실정이기 때문에, 토종오리의 개발 및 보급이 필요한 실정이며, 이는 종자주권의 확립 및 농가 소득 증대에도 매우 필요한 일이라 할 수 있다. 따라서 본 연구에서는 24개의 microsatellite 마커를 확보하였으며, 이들 마커의 대립유전자수는 1~16개, 이형접합도는 0∼0.865, 다형성은 0∼0.841로 확인되었다. 이들 마커를 이용하여 임의 집단에서 동일개체 출현빈도를 계산한 결과는 임의 집단 1.64×10<SUP>-16</SUP>, 전형매 집단 2.60×10<SUP>-7</SUP>, 반형매 집단 1.30×10<SUP>-12</SUP>으로 높은 개체식별률과 친자확인도를 확인할 수 있었다. 하지만 이들 마커를 이용한 계통분석 결과, 토종오리와 실용오리 집단을 정확하게 구분하기에는 어려운 것으로 확인되었다. 따라서 추가연구를 통해 토종오리의 순종화 및 더 정확한 토종오리와 실용오리 집단 구분이 가능한 마커 개발이 필요할 것으로 사료된다. & & Recently, duck meat consumption has been rapidly increased because consumers recognized duck meat for healthy food. In relation to this, Korean duck industry need to develop Korean native duck (KND) breed for both conservation perspective and self-sufficient of the breeding stocks. In this study, 24 microsatellite (MS) markers were investigated for classification of KND and commercial duck (CD) breeds in the Korean market. Using these MS markers, the calculated number of alleles (K), expected heterozygosity (He) values and polymorphic information contents (PIC) were 1∼16, 0∼0.865 and 0∼0.841, respectively. Also, the expected probability of identical values in random individuals (PI), random sib (PIsib) and random half-sib (PIhalf-sib) were estimated as 1.64×10<SUP>-16</SUP>, 2.60×10<SUP>-7</SUP> and 1.30×10<SUP>-12</SUP>, respectively. The results indicated that the expected probabilities of identity powers were enough for the individual identification. However, KND and CD breeds were not fully discriminated well using the 24 MS markers, which may CD and KND has shared same origin or crossbred. Therefore, further studies will be ultimately needed for developing a genetically pure line of KND breed even though the DNA markers used. Finally, these results will provide useful information for individual traceability system in ducks.