Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars
Öztürk, Süleyman Can ; Göktay, Mehmet ; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne - \ 2018
Plant Molecular Biology Reporter 36 (2018)5-6. - ISSN 0735-9640 - p. 800 - 811.
Barcode - Filbert genomic SSRs - Fingerprinting - Genetic diversity - Illumina sequencing - Microsatellites - Population structure
European hazelnut (Corylus avellana) is a diploid tree species and is widely used in confections. Hazelnuts are, to a large part, produced in Turkey with the cultivar “Tombul” widely grown in the Black Sea region. In this work, the “Tombul” genome was partially sequenced by next-generation sequencing technology yielding 29.2% (111.85 Mb) of the ~ 385 Mb (1C). This sequence information was used to develop genetic markers in order to enable differentiation of material before the long maturation process and to facilitate future breeding strategies. A total of 90,142 simple sequence repeats (SSRs) were identified in the contigs giving a frequency of 1 SSR per 1240 nt in the assembly. Mononucleotides were the most abundant SSR marker type (60.9%) followed by di- and trinucleotides. Primer pairs were designed for 75,139 (83.3%) of the SSRs. Fifty SSR primers were applied to 47 hazelnut accessions from nine countries to test their effectiveness and polymorphism. The markers amplified an average of 3.2 fragments. The highest polymorphism information content value was for cavSSR11062 (0.97) and the lowest (0.04) was for cavSSR13386. Two markers were monomorphic: cavSSR12855 and cavSSR13267. Single-copy SSR primers were also assessed for their ability to discriminate 19 Turkish cultivars, and it was found that seven primer pairs (Cav4217, Cav14875, Cav14418, Cav2704, Cav12862, Cav3909, Cav1361) were sufficient for this task. Thus, this study developed new SSR markers for use in hazelnut breeding and genetic studies and also provide a method to distinguish and identify true-type Turkish cultivars.
Developing forensic tools for an African timber : Regional origin is revealed by genetic characteristics, but not by isotopic signature
Vlam, Mart ; Groot, Arjen de; Boom, Arnoud ; Copini, Paul ; Laros, Ivo ; Veldhuijzen, Katrui ; Zakamdi, David ; Zuidema, Pieter A. - \ 2018
Biological Conservation 220 (2018). - ISSN 0006-3207 - p. 262 - 271.
DNA - Geographic origin - Microsatellites - Stable isotopes - Timber forensics - Tropical timber
Combatting illegal timber trade requires forensic tools that independently verify claimed geographic origin of timber. Chemical and genetic wood characteristics are potentially suitable tools, but their performance at small spatial scales is unknown. Here we test whether stable isotopes and microsatellites can differentiate Tali timber (Erythrophleum spp.) at the level of forest concessions. We collected 394 wood samples from 134 individuals in five concessions in Cameroon and Congo Republic. The nearest neighbour concessions were 14 km apart and the furthest pair 836 km apart. We constructed genetic profiles using eight nuclear microsatellite markers and measured concentrations of δ18O, δ15N and δ13C. We differentiated provenances using PCA (microsatellites), ANOVA and kernel discriminant analysis (isotopes). Next, we performed assignment tests using blind samples (n = 12, microsatellites) and leave one out cross validation (LOOCV, isotopes). Isotopic composition varied strongly within concessions and only δ13C differed significantly between two concessions. As a result, LOOCV performed only marginally better than random. Genetic differentiation among provenances was also relatively low, but private alleles were commonly found. Bayesian clustering analysis correctly assigned 92% of the blind samples, including those of nearby concessions. Thus, Tali timber can be successfully assigned to the concession of origin using genetic markers, but not using isotopic composition. Isotopic differentiation may be possible at larger spatial scales or with stronger climatic or topographic variation. Our study shows that genetic analyses can differentiate the geographic origin of tropical timber at the scale of forest concessions, demonstrating their potential as forensic tools to enforce timber trade legislation.
Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits
Lemoine, Mélissa ; Lucek, Kay ; Perrier, Charles ; Saladin, Verena ; Adriaensen, Frank ; Barba, Emilio ; Belda, Eduardo J. ; Charmantier, Anne ; Cichoń, Mariusz ; Eeva, Tapio ; Grégoire, Arnaud ; Hinde, Camilla A. ; Johnsen, Arild ; Komdeur, Jan ; Mänd, Raivo ; Matthysen, Erik ; Norte, Ana Cláudia ; Pitala, Natalia ; Sheldon, Ben C. ; Slagsvold, Tore ; Tinbergen, Joost M. ; Török, János ; Ubels, Richard ; Oers, Kees van; Visser, Marcel E. ; Doligez, Blandine ; Richner, Heinz - \ 2016
Biological Journal of the Linnean Society (2016). - ISSN 0024-4066 - p. 668 - 685.
F-statistics - Isolation-by-distance - Latitude - Microsatellites - Parus major - Population genetic structure - Winter severity
Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species - the great tit Parus major - at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (<50 km), using 22 microsatellite markers. Overall we found a low but significant genetic differentiation among sites (FST = 0.008). Genetic differentiation was higher, and genetic diversity lower, in south-western Europe. These regional differences were statistically best explained by winter temperature. Overall, our results suggest that great tits form a single patchy metapopulation across Europe, in which genetic differentiation is independent of geographical distance and gene flow may be regulated by environmental factors via movements related to winter severity. This might have important implications for the evolutionary trajectories of sub-populations, especially in the context of climate change, and calls for future investigations of local differences in costs and benefits of philopatry at large scales.
Isolation and validation of microsatellite markers from a depleted South African sciaenid species, the dusky kob (Argyrosomus japonicus), by means of the FIASCO/454 approach
Mirimin, L. ; Ruiz Guajardo, J.C. ; Vervalle, J. ; Bester-Van der Merwe, Aletta ; Kerwath, S. ; Macey, B. ; Bloomer, P. ; Roodt-Wilding, R. - \ 2013
Conservation Genetics Resources 5 (2013)3. - ISSN 1877-7252 - p. 841 - 844.
454 GS-FLX - Argyrosomus spp - FIASCO - Microsatellites - Sciaenid
The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild population structure, assist the effectiveness of broodstock and breeding programmes, and ensure monitoring of potential interactions between wild and farmed fish. The present study uses a recently tested approach that combines the FIASCO enrichment protocol with 454 GS-FLX Next Generation Sequencing, to identify large numbers of microsatellite-containing sequences at a low cost and high discovery rate from the dusky kob genome. Following the FIASCO enrichment (targeting specifically tetranucleotide repeats), 2,355 potential tetranucleotide microsatellites (perfect repeat motifs including eight or more repeat units flanked by regions for primer design) were identified from 1/5th of a single 454 lane. From these sequences, a test panel of 60 potential markers was selected for validation. A total of eight (13 %) markers were successfully amplified from a test sample of wild dusky kob individuals and showed high levels of polymorphism (observed heterozygosity per locus ranging between 0.375 and 0.905). Cross-species amplification of seven of these markers was also successfully carried out in another closely related and commercially important South African sciaenid species, the silver kob (A. inodorus). The microsatellite markers developed in the present study are readily available tools suitable to address genetic variability of Argyrosomus species of southern Africa.
Isolation and characterization of microsatellites in Sparganium emersum and cross-species amplification in the related species S. erectum
Pollux, B.J.A. ; Ouborg, N.J. - \ 2006
Molecular Ecology Notes 6 (2006)2. - ISSN 1471-8278 - p. 530 - 532.
Dispersal - Gene flow - Microsatellites - Null alleles - Population genetics
We developed seven novel polymorphic microsatellite loci for the aquatic macrophyte Sparganium emersum (Sparganiaceae). These were characterized on 62 individuals collected from nine different populations. In this set of individuals, seven to 20 alleles per locus were detected and observed heterozygosity ranged between 0.16 and 0.95. Cross-species amplification was tested in the related species Sparganium erectum, and was successful for five of the seven microsatellite loci.