Genetic diversity in European and Chinese pig breeds – the PigBioDiv project

2004 ◽  
Vol 30 ◽  
pp. 321-323
Author(s):  
S. Blott ◽  
M. SanCristobal ◽  
C. Chevalet ◽  
C.S. Haley ◽  
G. Russell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Markers ◽  
Allele Frequencies ◽  
Second Phase ◽  
Diversity Analysis ◽  
Square Root ◽  
Neighbor Joining ◽  
Pig Breeds ◽  
Nj Tree ◽  
F Statistics

Characterisation of genetic diversity in a large number of European pig populations has been undertaken with EC support. The populations sampled included local (rare) breeds, national varieties of the major international breeds, commercial lines and the Chinese Meishan breed. A second phase of the project will sample a further 50 Chinese breeds. Neutral genetic markers (AFLP and microsatellites), with individual or bulk typing, were used and compared.DNA from 59 European pig populations was extracted on samples of about 50 individuals per population. Individuals were typed for 50 microsatellites and for 148 AFLP bands. A subset of 25 populations was typed for 20 microsatellites on pools of DNA. Allele frequencies were estimated by direct allele counting for the co-dominant markers. Frequencies of AFLP negative alleles (absent bands) were obtained by taking the square root of absent band frequencies. Within-breed variability was summarised using standard statistics: expected and observed heterozygosity, mean observed and effective numbers of alleles, and F statistics. Between-breed diversity analysis was based on a bootstrapped Neighbor-Joining (NJ) tree derived from Reynolds distances (DR). The standard distance of Nei (DS) was also calculated.

scholarly journals Variasi Genetik Itik Bayang Berbasis Marka Mikrosatelit Pada Lokus AY287 dan Lokus AY283

2017 ◽  
Vol 11 (2) ◽  
pp. 91 ◽  
Author(s):  
Rusfidra Rusfidra ◽  
Y. Heryandi ◽  
Jamsari Jamsari ◽  
E. Y. Rahman
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Key Words ◽  
Genetic Markers ◽  
Microsatellite Loci ◽  
Gel Electrophoresis ◽  
Genetic Resource ◽  
Allele Frequencies ◽  
Blood Samples

West Sumatera Province has poultry genetic resource of local duck that potential in supply<br />eggs and duck meat. Bayang duck was set by Indonesian Agricultural Ministry in 2012 as national livestock breeds in Indonesia. Microsatellite markers are widely used as a genetic identifier because of their abundant existence, co-dominant and high polymorphic. The purpose of this study was to determine the genetic diversity of Bayang ducks based on two microsatellite loci which include AY287 and AY283. DNA substances used in the study were blood samples from 24 Bayang duck in Pesisir Selatan Regency. The isolated DNA genom from 24 blood samples of Bayang duck could be detected by gel electrophoresis. Results showed that AY287 locus has 6 alleles; allele A (108 bp), allele B (142 bp), allele C (183 bp), allele D (227 bp), allele E (272 bp) and allele F (340 bp). Both allele E and F were specific genetic markers of Bayang duck. Alleles frequencies of the AY287 locus were as follow: allele C (26,93%), allele D (19,24%), allele A (15,38%), allele B (15,38%), allele E (15,38%) and allele F (7,69%). The AY283 locus has 6 alleles consisted of allele A (230 bp), allele B (320 bp), allele C (345 bp), allele D (390 bp), allele E (450 bp) and allele F (500 bp). Allele frequencies of this marker were allele B (20,51%), allele D (20,51%), allele E (20,51%), allele A (15,39%), allele C (15,39%), and allele F (7,69%), respectively. Our finding suggest that two microsatellite markers, AY287 and AY283, were polymorphic in Bayang duck population.<br />Key words: Bayang duck, microsatellite, AY283, AY287

scholarly journals Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

2016 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J Fuchs ◽  
Eduardo J Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50 Jatropha curcas Costa Rican samples using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was also evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable when compared to worldwide values for J. curcas. The PIC (PIC = 0.276) and inbreeding coefficient (f = -0.102) were both low. Clustering was not related to the geographical origin of accessions but Costa Rican J. curcas consistently clustered as a separate group. International accessions clustered independently of collection sites suggesting a lack of genetic structure, probably due to a wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of Jatropha curcas germplasm bank in Costa Rica.

AFLP markers for analysis of genetic diversity and structure of teak (Tectona grandis) in India

2015 ◽  
Vol 45 (3) ◽  
pp. 297-306 ◽  
Author(s):  
Vivek Vaishnaw ◽  
Naseer Mohammad ◽  
Syed Arif Wali ◽  
Randhir Kumar ◽  
Shashi Bhushan Tripathi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Central India ◽  
Tectona Grandis ◽  
Neighbor Joining ◽  
Peninsular India ◽  
Genetic Diversity And Structure ◽  
Superior Genotypes ◽  
Very High ◽  
Elite Trees ◽  
F Statistics

Five amplified fragment length polymorphism (AFLP) primer combinations (E-AAC × M-CAT, E-AAC × M-CTG, E-ACA × M-CTC, E-ACA × M-CTA, and E-ACC × M-CTA) were employed for analysis of genetic diversity, differentiation, and structure of 96 genotypes of teak (Tectona grandis L. f.) from 10 natural locations in India. The analysis of the AFLP marker data by both versions, i.e., GST and θ, of F statistics showed a similar trend due to the outcrossing nature of teak. The primer combination E-AAC × M-CAT detected maximum polymorphism in the teak genome. The analysis of molecular variance assigned a large proportion of the genetic diversity to within sampled locations and a very small proportion to among locations. The population genetic structure resolved by the neighbor joining tree, principal coordinate analysis, and no-admixture and admixture model Bayesian-based analyses irrefutably revealed two distinct centers of teak diversity, i.e., central India and peninsular India. Furthermore, the very high proportion of genetic diversity residing within locations encourages the intensive selection and (or) collection of diverse superior genotypes (elite trees) from each location for the conservation of germplasm and the genetic improvement of teak.

scholarly journals Variasi Genetik Itik Bayang Berbasis Marka Mikrosatelit Pada Lokus AY287 dan Lokus AY283

2017 ◽  
Vol 11 (2) ◽  
pp. 91
Author(s):  
Rusfidra Rusfidra ◽  
Y. Heryandi ◽  
Jamsari Jamsari ◽  
E. Y. Rahman
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Key Words ◽  
Genetic Markers ◽  
Microsatellite Loci ◽  
Gel Electrophoresis ◽  
Genetic Resource ◽  
Allele Frequencies ◽  
Blood Samples

West Sumatera Province has poultry genetic resource of local duck that potential in supply<br />eggs and duck meat. Bayang duck was set by Indonesian Agricultural Ministry in 2012 as national livestock breeds in Indonesia. Microsatellite markers are widely used as a genetic identifier because of their abundant existence, co-dominant and high polymorphic. The purpose of this study was to determine the genetic diversity of Bayang ducks based on two microsatellite loci which include AY287 and AY283. DNA substances used in the study were blood samples from 24 Bayang duck in Pesisir Selatan Regency. The isolated DNA genom from 24 blood samples of Bayang duck could be detected by gel electrophoresis. Results showed that AY287 locus has 6 alleles; allele A (108 bp), allele B (142 bp), allele C (183 bp), allele D (227 bp), allele E (272 bp) and allele F (340 bp). Both allele E and F were specific genetic markers of Bayang duck. Alleles frequencies of the AY287 locus were as follow: allele C (26,93%), allele D (19,24%), allele A (15,38%), allele B (15,38%), allele E (15,38%) and allele F (7,69%). The AY283 locus has 6 alleles consisted of allele A (230 bp), allele B (320 bp), allele C (345 bp), allele D (390 bp), allele E (450 bp) and allele F (500 bp). Allele frequencies of this marker were allele B (20,51%), allele D (20,51%), allele E (20,51%), allele A (15,39%), allele C (15,39%), and allele F (7,69%), respectively. Our finding suggest that two microsatellite markers, AY287 and AY283, were polymorphic in Bayang duck population.<br />Key words: Bayang duck, microsatellite, AY283, AY287

Allozyme variation in Piceamariana from Newfoundland: genetic diversity, population structure, and analysis of differentiation

1986 ◽  
Vol 16 (4) ◽  
pp. 713-720 ◽  
Author(s):  
Francis C. Yeh ◽  
M. A. K. Khalil ◽  
Yousry A. El-Kassaby ◽  
Diane C. Trust
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Complex Structure ◽  
Allozyme Variation ◽  
Allele Frequencies ◽  
Discriminant Functions ◽  
Migration Patterns ◽  
Forest Regions ◽  
F Statistics

Seeds from 21 populations of Piceamariana (Mill.) B.S.P. from five forest sections of the boreal forest regions in Newfoundland were analyzed for electrophoretically detectable variation in 15 proteins coded by 23 genetic loci. On the average, 38% of the loci per population were polymorphic, the number of alleles per locus was 1.44, and the expected and observed heterozygosities were 0.107 and 0.120, respectively. Contingency χ2 analysis for homogeneity of allele frequencies indicated differentiation (P < 0.05) among the 21 populations and among populations within regions. The spatial pattern of allele frequencies was correlated with geographic variables at six loci. Analysis of F-statistics showed a 6.9% excess of heterozygotes relative to Hardy–Weinberg expectations. Only 5.9% of the observed genetic variation appeared to be interpopulational, the remainder was due to differences among individuals within populations. Estimates of genetic distance among regions were only slightly larger on average (0.014) than among populations within regions (0.012). Two significant (P < 0.05) canonical discriminant functions accounted for 55% of the total variance in the 13 polymorphic loci. A complex structure of genetic variation associated with regional and altitudinal differentiation was evident, possibly the expression of underlying genetic processes such as natural selection and past migration patterns.

scholarly journals Molecular characterization and genetic diversity ofJatropha curcasL. in Costa Rica

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2931 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J. Fuchs ◽  
Eduardo J. Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50Jatropha curcassamples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values forJ. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f =  − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of theJatropha curcasgermplasm bank in Costa Rica.

scholarly journals Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

2017 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J Fuchs ◽  
Eduardo J Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50 Jatropha curcas Costa Rican samples using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was also evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable when compared to worldwide values for J. curcas. The PIC (PIC = 0.276) and inbreeding coefficient (f = -0.102) were both low. Clustering was not related to the geographical origin of accessions but Costa Rican J. curcas consistently clustered as a separate group. International accessions clustered independently of collection sites suggesting a lack of genetic structure, probably due to a wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of Jatropha curcas germplasm bank in Costa Rica.

scholarly journals Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica

2017 ◽  
Author(s):  
Marcela Vásquez-Mayorga ◽  
Eric J Fuchs ◽  
Eduardo J Hernández ◽  
Franklin Herrera ◽  
Jesús Hernández ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Costa Rica ◽  
Jatropha Curcas ◽  
Geographical Origin ◽  
Wide Distribution ◽  
Costa Rican ◽  
Nrdna Its ◽  
Neighbor Joining ◽  
Germplasm Bank ◽  
Nj Tree

We estimated the genetic diversity of 50 Jatropha curcas Costa Rican samples using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was also evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable when compared to worldwide values for J. curcas. The PIC (PIC = 0.276) and inbreeding coefficient (f = -0.102) were both low. Clustering was not related to the geographical origin of accessions but Costa Rican J. curcas consistently clustered as a separate group. International accessions clustered independently of collection sites suggesting a lack of genetic structure, probably due to a wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of Jatropha curcas germplasm bank in Costa Rica.

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