• Title, Summary, Keyword: Genetic Relationship

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Genetic Divergence and Relationship Among Four Abalone Species by Isozyme and AFLP analyses (Isozyme 및 AFLP분석에 의한 전복류 4종간의 유전적 차이 및 유연관계)

  • Park Choul-ji;Kijima Akihiro
    • Journal of Aquaculture
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    • v.18 no.4
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    • pp.252-259
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    • 2005
  • Isozyme and AFLP analyses were examined to estimate the utilities of them as a genetic marker. The utilities were evaluated by genetic divergence and relationships among the four distinct abalone species; Haliotis discus hannai collected from northeast coast of Japan and Yellow-Sea coast of China, H. rufescens collected from west coast of USA, H rubra collected from southeast coast of Australia and H midae collected from Cape Town of South Africa. Isozyme and AFLP analyses showed a clear genetic divergence between every pair of species. Genetic relationships among the low species estimated by isozyme and AFLP analyses reflected to geographical distribution and morphological characteristics. In conclusion, Isozyme and AFLP analyses are suitable genetic markers far estimates of genetic divergence and relationship among abalone species.

Analysis of Genetic Relationship of Native Iris species Plants using RAPD (RAPD를 이용한 자생 Iris속 식물의 유전적 유연관계 분석)

  • Ahn Young-Hee
    • Journal of Environmental Science International
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    • v.14 no.3
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    • pp.265-269
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    • 2005
  • This study was carried out to provide the basic data for an identifying system for Iris species distributed in Korean market from complete analysing of genetic relationship between three native Iris species and one cultivar bred from the native Iris plant. RAPD analysis of genetic relationship among 4 Irises was possible. According to the RAPD analysis, they were divided into two groups. Among 4 Irises used in this study, Iris laevigata 'Veriegata', Iris laevigata and Iris setosa were classified into the same group since they had many similarities even though the habitat of Iris laevigata in Korean peninsular is restricted mainly in the south and Iris setosa is naturally inhabited in the northern part of Kangwondo. The value for the dissimilarity index of Iris laevigata and Iris laevigata 'Veriegata' was 6.757. The value for the dissimilarity index of Iris laevigata and Iris dichotoma was 95.000, so that they were genetically the farthest among them since the genetic relationship between two species are separated far if the value of the dissimilarity index is close to 100.

Genetic variation and relationship of Artemisia capillaris Thunb.(Compositae) by RAPD analysis

  • Kim, Jung-Hyun;Kim, Dong-Kap;Kim, Joo-Hwan
    • Korean Journal of Plant Resources
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    • v.22 no.3
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    • pp.242-247
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    • 2009
  • Randomly Amplified Polymorphic DNA (RAPD) was performed to define the genetic variation and relationships of Artemisia capillaris. Fifteen populations by the distributions and habitat were collected to conduct RAPD analysis. RAPD markers were observed mainly between 300bp and 1600bp. Total 72 scorable markers from 7 primers were applied to generate the genetic matrix, and 69 bands were polymorphic and only 3 bands were monomorphic. The genetic dissimilarity matrix by Nei's genetic distance (1972) and UPGMA phenogram were produced from the data matrix. Populations of Artemisia capillaris were clustered with high genetic affinities and cluster patterns were correlated with distributional patterns. Two big groups were clustered as southern area group and middle area group. The closest OTUs were GW2 and GG1 in middle area group, and GB1 from southern area group was clustered with OTUs in middle area group. RAPD data was useful to define the genetic variations and relationships of A. capillaris.

Genetic Relationship in Chicken Breeds Using Molecular Co-ancestry Information

  • Ahlawat, S.P.S.;Vijh, R.K.;Mishra, Bina;Kumar, S.T. Bharani;Tantia, M.S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.1
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    • pp.6-10
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    • 2008
  • Five chicken populations viz. Chittagong, Ghagus, Kalasthi, Kadaknath, Tellichery were genotyped using 25 highly polymorphic microsatellite loci. White leg horn was taken as an outgroup. To reveal the relationship and distinctiveness among five indigenous breeds various genetic distances based on molecular co-ancestry were estimated and multidimensional scaling was performed. The Ghagus and Kalasthi breeds were closely related and their separation was recent, whereas Chittagong had a remote ancestry with other indigenous chicken populations.

Evaluation of Genetic Variation and Phylogenetic Relationship among North Indian Cattle Breeds

  • Sharma, Rekha;Pandey, A.K.;Singh, Y.;Prakash, B.;Mishra, B.P.;Kathiravan, P.;Singh, P.K.;Singh, G.
    • Asian-Australasian Journal of Animal Sciences
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    • v.22 no.1
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    • pp.13-19
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    • 2009
  • In the present study, genetic analyses of diversity and differentiation were performed on four breeds of Indian zebu cattle (Bos indicus). In total, 181 animals belonging to Ponwar, Kherigarh, Gangatiri and Kenkatha breeds were genotyped for 20 cattle specific microsatellite markers. Mean number of alleles observed per locus (MNA) varied between 5.75 (Kenkatha) to 6.05 (Kherigarh). The observed and expected heterozygosity for the breeds varied from 0.48 (Gangatiri) to 0.58 (Kherigarh) and 0.65 (Kenkatha) to 0.70 (Kherigarh), respectively. $F_{IS}$ estimates of all the breeds indicated significant deficit of heterozygotes being 28.8%, 25.9%, 17.7% and 17.7% for Gangatiri, Ponwar, Kherigarh and Kenkatha, respectively. The $F_{ST}$ estimates demonstrated that 10.6% was the average genetic differentiation among the breeds. Nei's genetic distance DA and Cavalli- Sforza and Edwards Chord distance ($D_C$) and the phylogenetic tree constructed from these reflected the close genetic relationship of Gangatiri and Kenkatha, whereas Ponwar appears to be more distant.

Assessment of genetic diversity and phylogenetic relationship of Limousin herds in Hungary using microsatellite markers

  • Szucs, Marton;Szabo, Ferenc;Ban, Beata;Jozsa, Csilla;Rozsa, Laszlo;Zsolnai, Attila;Anton, Istvan
    • Asian-Australasian Journal of Animal Sciences
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    • v.32 no.2
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    • pp.176-182
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    • 2019
  • Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

Microsatellite Polymorphism and Genetic Relationship in Dog Breeds in Korea

  • Cho, G.J.
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.8
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    • pp.1071-1074
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    • 2005
  • Microsatellite polymorphism and their genetic relationships were estimated using genotype information of 183 dogs from 11 microsatellite loci. The breeds include the indigenous Korean breeds Jindo dog (30), Poongsan dog (20) and Miryang dog (44) together with Chihauhau dog (31) and German Shepherd dog (58). Jindo dogs showed the highest expected heterozygosity (0.796${\pm}$0.030) and polymorphic information contents (0.755) in all populations. The phylogenetic analysis showed the existence of two distinct clusters supported by high bootstrap values: the Korean native dogs and other dogs. They clearly show that Poongsan dog and Miryang dog are closely related to each other when compared with Jindo dog. Microsatellite polymorphism data was shown to be useful for estimating the genetic relationship between Korean native dogs and other dog breeds, and also can be applied for parentage testing in those dog breeds.

Relationships between genetic polymorphisms and transcriptional profiles for outcome prediction in anticancer agent treatment

  • Paik, Hyo-Jung;Lee, Eun-Jung;Lee, Do-Heon
    • BMB Reports
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    • v.43 no.12
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    • pp.836-841
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    • 2010
  • In the era of personal genomics, predicting the individual response to drug-treatment is a challenge of biomedical research. The aim of this study was to validate whether interaction information between genetic and transcriptional signatures are promising features to predict a drug response. Because drug resistance/susceptibilities result from the complex associations of genetic and transcriptional activities, we predicted the inter-relationships between genetic and transcriptional signatures. With this concept, captured genetic polymorphisms and transcriptional profiles were prepared in cancer samples. By splitting ninety-nine samples into a trial set (n = 30) and a test set (n = 69), the outperformance of relationship-focused model (0.84 of area under the curve in trial set, P = $2.90{\times}10^{-4}$) was presented in the trial set and validated in the test set, respectively. The prediction results of modeling show that considering the relationships between genetic and transcriptional features is an effective approach to determine outcome predictions of drug-treatment.

Genetic Relationships among the Poplars of Section Leuce (Genus Populus) revealed by RAPD Marker Analysis (RAPD 표식자(標識者) 분석(分析)에 의한 사시나무속(屬) Leuce절(節) 포플러의 유연관계(類緣關係))

  • Hong, Kyung-Nak;Hyun, Jung Oh;Hong, Yong Pyo
    • Journal of Korean Society of Forest Science
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    • v.87 no.2
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    • pp.153-163
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    • 1998
  • Genetic relationships of some poplars in the section Leuce, including 5 species and 11 clones of Populus alba${\times}$glandulosa, were investigated on the basis of RAPD marker analysis. Twenty-two of the 88 arbitrary 10-mer primers, showed reproducible amplification in the preliminary experiment with 6 samples, were used for PCR and generated a total of 181 RAPD markers. Genetic relationships among the analyzed samples were tested by two phenetic methods of the UPGMA and the neighbor-joining, which revealed the close genetic relationship between P. glandulosa and P. alba. And the close genetic relationship between P. glandulosa and P. davidiana was ascertained by the principal component analysis. Based on the observation of the close genetic relationship between them, it was deduced that P. glandulosa might be originated by the saltational speciation caused by the hybridization between P. alba and P. davidiana in nature.

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The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study

  • Lee, Young-Sup;Kim, Hyeon-Jeong;Cho, Seoae;Kim, Heebal
    • Genomics & Informatics
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    • v.12 no.4
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    • pp.254-260
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    • 2014
  • Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.