Development and characterization of microsatellite markers of the fungal plant pathogen Sclerotinia trifoliorum

Genome ◽  
2010 ◽  
Vol 53 (6) ◽  
pp. 494-500 ◽  
Author(s):  
Evans Nyaga Njambere ◽  
George Vandemark ◽  
Weidong Chen
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Biology ◽  
Grain Legumes ◽  
Enriched Library ◽  
Mixed Mating ◽  
Sclerotinia Homoeocarpa ◽  
Sclerotinia Trifoliorum ◽  
Significant Linkage

Sclerotinia trifoliorum is an important pathogen of forage legumes and some grain legumes. Attempts to study its population biology using microsatellite markers developed for Sclerotinia sclerotiorum and Sclerotinia subarctica resulted in no amplification or low levels of polymorphism. This study reports the development and characterization of 33 microsatellite loci developed from a microsatellite-enriched library of S. trifoliorum. Based on a population of 42 isolates of S. trifoliorum, these microsatellite markers are highly polymorphic, with a mean of 6.5 alleles per locus (range 3–12) and a mean expected heterozygosity of 0.63 (range 0.26–0.9). Based on locations of these marker sequences in the S. sclerotiorum genome, these microsatellite loci are dispersed throughout the genome. However, 50% (265 of 528) of pairwise comparisons of the 33 microsatellite loci had significant linkage disequilibrium, which could be explained by the mixed mating systems (homothallism and heterothallism) and clonal reproduction of S. trifoliorum. Thirty of the 33 loci were successfully applied to S. sclerotiorum, and 28 loci were polymorphic. However, only 10 loci are applicable to Sclerotinia minor and 1 locus to Sclerotinia homoeocarpa . These markers are therefore useful for population structure assessment, QTL mapping, and ecological analyses in S. trifoliorum and potentially in other Sclerotinia species.

scholarly journals Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2936 ◽  
Author(s):  
Caroline E. Dubé ◽  
Serge Planes ◽  
Yuxiang Zhou ◽  
Véronique Berteaux-Lecellier ◽  
Emilie Boissin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
454 Sequencing ◽  
Genetic Distances ◽  
Null Alleles ◽  
Future Research ◽  
Significant Linkage ◽  
Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

scholarly journals Isolation and Characterization of Microsatellite Loci for the Ornamental Plant Primula obconica Hance (Primulaceae)

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 314-315 ◽  
Author(s):  
Hai-fei Yan ◽  
Xue-jun Ge ◽  
Chi-ming Hu ◽  
Gang Hao
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Ornamental Plant ◽  
Microsatellite Variation ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Fiasco Protocol

Nine microsatellite loci were isolated from Primula obconica using the FIASCO protocol. We used 30 individuals from three populations for the assessment of microsatellite variation. Seven loci were detected with microsatellite polymorphism. The number of alleles per locus ranged from three to seven. The average observed heterozygosity and expected heterozygosity ranged from 0.167 to 0.6 and from 0.409 to 0.653, respectively. These microsatellite markers will be useful to assess the genetic variation and genetic structure of P. obconica.

scholarly journals Genetic Characterization of the Central Javanese Duck using Microsatellite Markers

2021 ◽  
Vol 50 (1) ◽  
pp. 53-61
Author(s):  
Susanti R ◽  
Yuniastuti Ari ◽  
Dian Kartikasari Agustin
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Tandem Repeats ◽  
Species Conservation ◽  
Influenza Viruses ◽  
Conservation Strategy ◽  
Characteristic Analysis ◽  
Genetic Characteristics ◽  
Central Java

Duck conservation strategy based on genetic characteristics has been undertaken to preserve indigenous breeds and produce high quality offspring. In addition, the genetic characteristic analysis provides further information for studying avian influenza viruses. The aim of this research was to study the genetic characterisation of indigenous Central Javanese duck in Indonesia using microsatellite markers. Microsatellite or simple sequence repeats (SSR) or short tandem repeats (STR) of various breeds of Central Javanese duck were analysed on 35 local ducks which consisted of seven variants of Javanese ducks in Central Java. Ten pairs of duck microsatellite primers were used to amplify the DNA from feathers. Nine out of 10 microsatellite loci (90%) demonstrated polymorphic patterns containing 50 alleles. The number of alelles varied from two to 10 alleles at various polymorphic microsatellite loci with an average of 5.56 alelles per locus. From the study, CAUD013 locus was determined as the highest heterozygosity with 0.882 score while CAUD030 locus was the lowest one with 0.034 score.Similarly, CAUD030 locus had the lowest PIC score (0.30) whereas the CAUD013 locus had the highest PIC value (0.869). Hence, it was showed that microsatellite markers were highly polymorphic in several loci for the Central Javanese duck and may be useful for genetic description of other native duck in terms of species conservation.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

scholarly journals Short Note: Isolation and Characterization of 12 Polymorphic Microsatellite Markers in Engelhardia roxburghiana (Juglandaceae)

2014 ◽  
Vol 63 (1-6) ◽  
pp. 109-112 ◽  
Author(s):  
Dan-Dan Zhang ◽  
Pi Luo ◽  
Ying Chen ◽  
Zheng-Feng Wang ◽  
Wan-Hui Ye ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Short Note ◽  
Screening Method ◽  
Wide Distribution ◽  
Enriched Library ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
Polymorphic Microsatellite

Abstract Engelhardia roxburghiana is a common half evergreen tree with a wide distribution in southeast Asia. Despite its ecological and pharmaceutical values, its genetic diversity is poorly studied. Our objective was to develop nuclear microsatellite markers to investigate the level of genetic diversity within and among populations in the future. Using the microsatellite-enriched library and PCR-based screening method, 12 microsatellite markers were developed and showed polymorphism in a population. The number of alleles per locus for these 12 microsatellites ranged from four to 15. The observed and expected heterozygosities ranged from 0.358 to 0.897 and from 0.369 to 0.886, respectively. The developed microsatellites will be useful for studying genetic diversity and population structure in E. roxburghiana.

scholarly journals Genetic characterization of Albanian grapevine cultivars by microsatellite markers

OENO One ◽  
2005 ◽  
Vol 39 (3) ◽  
pp. 109
Author(s):  
Emmanuel D. Ladoukakis ◽  
François Lefort ◽  
Petraq Sotiri ◽  
Arjola Bacu ◽  
Efigjeni Kongjika ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Genetic Characterization ◽  
Allelic Profile ◽  
Genetic Profiling ◽  
Nuclear Microsatellite ◽  
Genetic Profiles

<p style="text-align: justify;">A recently restored ampelographic collection of Albanian grapevine accessions has been submitted to genetic profiling with eleven nuclear microsatellite markers, widely used in other studies. Microsatellite profiling resulted in 28 single profiles for 29 accessions. Two cultivars, Shesh I bardhë and Pucalla, were found to be synonyms. Genetic profiles of Albanian cultivars were compared at 8 microsatellite loci to 29 most commonly cultivated Greek cultivars. Albanian cultivars were found to be more closely related to Greek cultivars from Peloponnese. One Greek cultivar named Dempina was found to be genetically close to two Albanian cultivars Debina teki and Debina kala, which are homonyms Another cultivar, known as Toska or Sinambel displayed a tri-allelic profile at 5 loci over 10 analysed loci. Such a high number of tri-allelic loci found in one individual favours the hypothesis of triploidy but the chimerism hypothesis cannot be excluded without further work.</p>

scholarly journals Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species

2016 ◽  
Author(s):  
Wen Song ◽  
Dongmei Zhu ◽  
Yefeng Lv ◽  
Weimin Wang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Related Species ◽  
Polymorphic Information Content ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.

scholarly journals Characterization of Nuclear Microsatellite Markers for the Narrow Endemic Syringa josikaea Jacq. fil. ex Rchb.

2013 ◽  
Vol 41 (1) ◽  
pp. 301 ◽  
Author(s):  
Bertalan LENDVAY ◽  
Andrzej PEDRYC ◽  
Mária Höhn
Keyword(s):  
Microsatellite Markers ◽  
Ornamental Plants ◽  
Enriched Library ◽  
Microsatellite Primers ◽  
Genetic Lineages ◽  
Nuclear Microsatellite ◽  
Rare Endemic ◽  
Two Populations ◽  
Pcr Conditions

The species of the genus Syringa L. are among the most popular ornamental plants worldwide. One particular species, Syringa josikaea, a rare endemic of the Carpathian Mountains, is of great conservation interest. Although microsatellite markers may be useful for studying the genetic variability of varieties and populations, no microsatellites have previously been characterized for any species of the Syringa genus. Our aim was therefore to test the applicability of microsatellite primers developed for neighboring genera (Olea and Ligustrum) and to complement these with markers isolated and characterized for S. josikaea. Twelve primer pairs of Olea and Ligustrum were tested by optimizing PCR conditions and checking the variability in 40 samples of two populations of S. josikaea. Two of them proved to be easy to PCR amplify and variable at the same time. To develop new primers we constructed a microsatellite enriched library and sequenced 48 clones. 18 sequences contained microsatellite motifs, and three of the designed primer pairs presented high allele variability. The five primer pairs characterized for S. josikaea proved to be highly informative and sufficient to distinguish between individuals. These microsatellite primers are valuable tools to study genetic variation of native populations, genetic lineages of hybrids and cultivars of S. josikaea.

scholarly journals Isolation and Characterization of Twenty Polymorphic Microsatellite Loci for Moringa oleifera (Moringaceae)

HortScience ◽  
2010 ◽  
Vol 45 (4) ◽  
pp. 690-692 ◽  
Author(s):  
Jiang-Chong Wu ◽  
Jing Yang ◽  
Zhi-Jian Gu ◽  
Yan-Ping Zhang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
Moringa Oleifera ◽  
Microsatellite Primers ◽  
Genetic Studies ◽  
Isolation And Characterization ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite

By using a modified biotin-streptavidin capturing method, a total of 20 polymorphic microsatellite markers were developed from Moringa oleifera Lam. (Moringaceae), a useful multipurpose tree. Twenty-four domesticated individuals, with germplasms of India and Myanmar, were used to screen polymorphism of these 20 microsatellite markers. The number of alleles per locus ranged from two to six. The expected and observed heterozygosity varied from 0.3608 to 0.7606 and from 0.0000 to 0.8750, respectively. Seven loci were significantly deviated from Hardy-Weinberg equilibrium. The availability of these microsatellite primers would provide a powerful tool for aspects of detailed population genetic studies of M. oleifera.

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