scholarly journals Studies on Genetic Diversity of Selected Population of Hybrid Scallop Chlamys farreri（♀）× Patinopecten yessoensis（♂） by Microsatellites Markers

2015 ◽  
Vol 5 (1) ◽  
pp. 39 ◽  
Author(s):  
Biao Wu ◽  
Aiguo Yang ◽  
Ningning Cheng ◽  
Xiujun Sun ◽  
Zhihong Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Selective Breeding ◽  
Chlamys Farreri ◽  
Patinopecten Yessoensis ◽  
Microsatellites Markers ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Two Populations ◽  
Simple Sequence

<p class="1Body">The growth superiority of hybrid scallop <em>Chlamys farreri </em>(♀) × <em>Patinopecten yessoensis </em>(♂), as the following successive generation selection have been reported. However, the data about the genetic diversity in those population remains unexplored. In this study, the genetic structure analysis of F<sub>1</sub>, F<sub>2</sub> and F<sub>3 </sub>were conducted by PCR with 10 Simple Sequence Repeats (SSR) primers. It showed that a total of 68 alleles were detected, and the number of alleles per locus ranged from 3 to 11, Polymorphism Information Content<em> </em>(<em>PIC</em>) per locus ranged from 0.4729 to 0.8429. And, the average observed heterozygosity (<em>H<sub>o</sub></em>) of the three populations were 0.6100, 0.6975 and 0.7750, while the average expected heterozygosity (<em>H<sub>e</sub></em>) were 0.7607, 0.7751 and 0.7379 respectively. <em>F<sub>st </sub></em>values among the three populations were also low (<em>F<sub>st</sub></em>&lt;0.05) which suggested low genetic differentiation between each two populations. In all, those data indicated the genetic structure challenge caused by hybridization and selection, supplying a new angle to understand artificial selective breeding.</p>

scholarly journals Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

2022 ◽  
Author(s):  
Huiling Wang ◽  
Kuan Yang ◽  
Liwei Guo ◽  
Lifen Luo ◽  
Chi He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Yunnan Province ◽  
Polymorphic Information Content ◽  
Polyacrylamide Gel Electrophoresis ◽  
Panax Notoginseng ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

scholarly journals Genetic structure of nine horse populations

2008 ◽  
Vol 56 (2) ◽  
pp. 57-60
Author(s):  
Monika Burócziová ◽  
J. Říha ◽  
R. Židek ◽  
J. Trandžík ◽  
D. Jakabová
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Distance ◽  
International Society ◽  
Polymorphism Information Content ◽  
Slovak Republic ◽  
Microsatellites Markers ◽  
Expected Heterozygosity ◽  
History Of ◽  
Hardy Weinberg Equilibrium

In the present study was estimate the genetic diversity and relationships among nine horses breeds in Czech and Slovak Republic.In conclusion, the main objective of study was to show the level of genetic distance among the horse breeds with different history of breeding of each country. Furthermore, it should be clarified whether these populations and subpopulations are distinct enough from each other to justify defining separate breeds. This research concerns the variability of microsatellite markers in genotypes of horse. We compared the genetic diversity and distance among nine horse breeds Czech and Slovak Warmblood both of Czech origin, Slovak Warmblood of Slovak origin, Hucul, Hafling, Furioso, Noriker, Silesian Noriker and Bohemian-Moravian Belgian Horse.In total, 932 animals were genotyped for 17 microsatellites markers (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20, HTG6, HMS2, HTG7, ASB17, ASB23, CA425, HMS1, LEX3) recommended by the International Society of Animal Genetics.In the different population size, the allele frequencies, observed and expected heterozygosity, test for deviations from Hardy-Weinberg equilibrium and Polymorphism information content have been calculated for each breed. We analyzed genetic distance and diversity among them on the base of the dataset of highly polymorphic set of microsatellites representing all autozomes using set of PowerMar­ker v3.25 analysis tools and Structure 2.2. programme for results comparison.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

2014 ◽  
Vol 12 (3) ◽  
pp. 323-329 ◽  
Author(s):  
Guillermo Padilla ◽  
Rafel Socias i Company ◽  
Amando Ordás
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Average Value ◽  
La Palma ◽  
Expected Heterozygosity ◽  
Commercial Cultivars ◽  
Soft Shell ◽  
Genetic Profiles ◽  
Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

scholarly journals Genetic structure and diversity of a collection of Brassica rapa subsp. rapa L. revealed by simple sequence repeat markers

2011 ◽  
Vol 149 (5) ◽  
pp. 617-624 ◽  
Author(s):  
P. SOENGAS ◽  
M. E. CARTEA ◽  
M. FRANCISCO ◽  
M. LEMA ◽  
P. VELASCO
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Brassica Rapa ◽  
Genetic Relationships ◽  
Population Level ◽  
Research Centre ◽  
Breeding Programmes ◽  
Western Spain ◽  
Genetic Structure And Diversity ◽  
Simple Sequence

SUMMARYBrassica rapa subsp. rapa L. includes three different crops: turnips (roots), turnip greens (leaves) and turnip tops (inflorescences). A collection of B. rapa subsp. rapa from north-western Spain is currently kept at ‘Misión Biológica de Galicia’ (a research centre of the Consejo Superior de Investigaciones Científicas (CSIC), Spain). This collection has been characterized based on morphological and agronomical traits. A better understanding of the genetic diversity present in the collection is necessary in order to optimize its use and maintenance. The objectives of the present work were to assess the genetic diversity present in the B. rapa subsp. rapa collection, to establish genetic relationships among populations and to study the genetic structure of the collection. Eighty populations were analysed based on 18 simple sequence repeats (SSRs). Populations showed a broad range of genetic diversity, thus offering good potential for further genetic improvement. Most of the variability was found within the population level, probably due to high rates of allogamy, to migration and/or interchange of seed among local growers. Populations showed a low level of differentiation, grouping in just one cluster, and therefore they can be considered as samples of a highly variable metapopulation that can be used for B. rapa breeding programmes.

scholarly journals Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

2007 ◽  
Vol 132 (3) ◽  
pp. 357-367 ◽  
Author(s):  
P. Escribano ◽  
M.A. Viruel ◽  
J.I. Hormaza
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Group Method ◽  
Pair Group ◽  
Ssr Primers ◽  
Upgma Cluster Analysis ◽  
Ssr Loci ◽  
Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

scholarly journals Genetic diversity of walnut (Juglans regia L.) seedlings through SSR markers in north-western Himalayan region of Jammu

2020 ◽  
Vol 49 (4) ◽  
pp. 1003-1012
Author(s):  
Rafiq Ahmad Shah ◽  
Parshant Baksi ◽  
Amit Jasrotia ◽  
Deep JI Bhat ◽  
Rucku Gupta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Decision Making ◽  
Ssr Markers ◽  
Juglans Regia ◽  
Germplasm Management ◽  
Expected Heterozygosity ◽  
Western Himalayan Region ◽  
Ssr Primers ◽  
Genetic Dissimilarity ◽  
North Western

screening of 25 SSR markers, revealed 23 clear and consistent amplification profiles in the entire walnut germplasm set. A total of 54 alleles were amplified by SSR primers and the number of alleles range from 2 to 3. The PIC value ranged from 0.36 to 0.68. The dendrogram classified all genotypes into two main clusters with various degrees of subclustering. Estimated genetic dissimilarity coefficient ranged from 0.36 to 0.85. Through model-based cluster analysis all genotypes were grouped into 5 genetically distinct subpopulations. The expected heterozygosity at a given locus was found to range from 0.520 to 0.5477. Similarly, population differentiation measurements (Fst) ranged from 0.2286 to 0.2909. These findings would be helpful for decision making in future walnut breeding studies, germplasm management activities to maximize genetic diversity in walnut germplasm and may also prove useful in future for conducting association mapping in walnut for different traits.

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Rafael Oliveira Moreira ◽  
Eduardo de Andrade Bressan ◽  
Horst Bremer Neto ◽  
Angelo Pedro Jacomino ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Native Species ◽  
Genetic Parameters ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Paulo State ◽  
Allele Number ◽  
Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

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