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45 results for “SSR markers”
Data from: Altitude difference might contribute to the genetic divergence of giant panda' staple food Bamboo (Fargesia spathacea complex) based on 14 SSR markers
<p>The taxonomy in woody bamboo faces a lot of difficulties due to its long blooming intervals and complicated morphological variation. Whether the current taxonomy would reflect the genuine species divergence within woody bamboo is an intriguing question. <i>Fargesia spathacea</i> complex comprises fifteen closely related species with sympatric distribution in China. Their classification has long been controversy because of only a handful of vegetative traits available, thus providing a good opportunity to explore the evolutionary relationship and genetic differentiation in woody bamboo. Here we presented a study with 750 individuals from 39 representative populations in <i>Fargesia spathacea</i> complex using 14 SSR markers. We found varying degrees of genetic diversity across populations of the <i>Fargesia spathacea</i> complex (<i>He</i>=0.07-0.81) and largely negative <i>F</i> values at the population level, implying an excess of heterozygotes in the populations. Phylogenetic analyses revealed that all populations were divided into two major groups (cluster A and B), with the majority of fifteen species representing distinct genetic lineages. Based on the population genetic analysis along with morphological evidence, we confirmed the identity of three species (<i>F. decurvata</i>, <i>F. spathacea</i> and <i>F. murielae</i>) and suggested invalidation of four other species (<i>scabrida</i>, <i>F. robusta</i>, <i>F. denudata</i> and <i>F. nitida</i>). The delimitation of the rest eight species was yet to be explored. The ecological factor and spatial autocorrelation analysis supported that altitude difference might account for the distinct genetic divergence between two major groups.</p>
Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
<p>Pea (<em>Pisum</em> <em>sativum</em> L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (<em>Pisum</em> sp.) are remaining controversial. To characterize patterns of genetic and morphological variation and investigate the classification of <em>Pisum</em>, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea representing three species of <em>Pisum</em> utilizing 34 morphological traits and 87 polymorphic SSR markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of <em>Pisum fulvum</em>, <em>Pisum</em> <em>abyssinicum</em> and some wild <em>P. sativum</em> accessions, whereas groups II and III consisted of the two genetic groups under <em>P. sativum </em>representing different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of <em>Pisum</em>, <em>P. fulvum</em> and <em>P. abyssinicum</em> possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of <em>P. sativum</em> described by some authors were not supported in this study, with the exception of several genotypes of <em>P. sativum</em> subsp. <em>elatius</em> that were clustered with <em>P. fulvum</em> and <em>P. abyssinicum</em>. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.</p>
Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
<p>Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread <i>Elymus</i> species. <i>Elymus excelsus</i> Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of <i>E. excelsus</i> germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of <i>E. excelsus</i> from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei's genetic diversity (H) and Shannon's diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of <i>E. excelsus</i> germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (<i>F</i><sub><i>st</i></sub> = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (<i>H</i><sub><i>e</i></sub> = 0.197) was greater than that of the GSC (<i>H</i><sub><i>e</i></sub> = 0.176) and XJC (<i>H</i><sub><i>e</i></sub> = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that <i>E. excelsus</i> accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable <i>E. excelsus</i> germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.</p>
Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
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Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers
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Data from: Altitude difference might contribute to the genetic divergence of giant panda' staple food Bamboo (Fargesia spathacea complex) based on 14 SSR markers
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Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers
In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found.
Data from: SSR Markers for Filago subgen. Filago (Gnaphalieae: Asteraceae) and cross-amplification in three other subgenera
• Premise of the study: Microsatellite primers were developed for the first time in the genus Filago (Gnaphalieae: Asteraceae). These markers will facilitate low-scale phylogenetic, phylogeographic and population genetics studies within the genus Filago. • Methods and Results: Nine pairs of microsatellite primers were identified and optimized on two species of Filago using a microsatellite-enrichment library method and 454 GS-FLX technique. The set of primers amplified tri- to hexanucleotide repeats, and showed one to six alleles per locus for both species: F. gaditana and F. carpetana. Transferability was performed in 29 samples corresponding to nine representative species of Filago. • Conclusions: The results indicate the utility of the newly developed markers, which will be useful to go deeper into the phylogenetic relationships among the taxa within Filago. These microsatellites will enable phylogeographic, reproductive and genetic variation studies.
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Data from: Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes
During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms with one of the most complex reproductive strategies. We evaluated the utility of SSRs and SNPs for inferring the neutral genetic structure of Armillaria cepistipes (basidiomycetes) at different spatial scales. For that, 407 samples were collected across a small (150 km2) area in the Ukrainian Carpathians and a large (41 000 km2) area in the Swiss Alps. All isolates were analyzed at 17 SSR loci distributed throughout the whole genome and at 24 SNP loci located in different single-copy conserved genes. The two markers showed different patterns of structure within the two spatial scales studied. The multi-allelic SSR markers seemed to be best suited for detecting genetic structure in indigenous fungal populations at a rather small spatial scale (radius of ~50-100 km). The pattern observed at SNP markers rather reflected ancient divergence of distant (~1000 km) populations that in addition are separated by mountain ranges. Despite these differences, both marker types were suitable for detecting the weak genetic structure of the two A. cepistipes populations investigated.
Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea
Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages RepARK and RepeatMasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Ephydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra, and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabeled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labeled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.
Data from: Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers
Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity management units and genetic structure. Here we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait South China Sea and Northwest Pacific Ocean). In R. stylosa the genetic break was located more eastward between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves especially relating to replanting efforts and the definition of ESUs in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species determine their respective genetic structure and avoid artificially promoting hybridization in mangrove restoration programmes.
Fig. 5 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India
Fig. 5. Variation in percentage distribution of CRA (a) in different parts of L. speciosa (b) in all 12 populations of L. speciosa collected across a north–south geographical gradient in the Southern Western Ghats region of peninsular India.
Fig. 3 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India
Fig. 3. Principal Component Analysis performed on (a) SSR data obtained from 12 natural populations of L. speciosa (b) estimate of corosolic acid content across these populations. The percentage of variance explained by each axis is indicated in parenthesis.
Fig. 2 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India
Fig. 2. UPGMA cluster analysis of SSR data for 12 wild populations of L. speciosa across the Southern Western Ghats depicting pattern of grouping among populations.
Fig. 6 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India
Fig. 6. Map showing geographical location of collection sites of all 12 populations of L. speciosa in the Southern Western Ghats.
SSR and cpDNA marker dataset genetic integrity of M.sylvestris in Saxony, Germany
<p><i>Malus sylvestris</i> (Mill.) is the only indigenous wild apple species in Central Europe. Agriculture, forestry and urbanization increasingly endanger <i>Malus sylvestris </i>natural habitats. In addition, the risks of cross-hybridization associated with increase in the cultivation of the domesticated apple <i>Malus ×domestica</i> (Borkh.), threatens the genetic integrity of <i>M. sylvestris</i>.</p> <p>The present study investigated the number of hybrids, genetic diversity and genetic structure of 292 putative <i>M. sylvestris</i> that originate from five different natural <i>M. sylvestris</i> populations in Saxony, Germany. All samples were genetically analyzed using nine nuclear microsatellite markers (ncSSR) and four maternally inherited chloroplast markers (cpDNA) along with 56 apple cultivars commonly cultivated in Saxony.</p> <p>Eighty-seven percent of the wild apple accessions were identified as pure <i>M. sylvestris</i>. The cpDNA analysis showed six private haplotypes for <i>M. sylvestris,</i> whereas three haplotypes were present in <i>M. sylvestris </i>and<i> M. ×domestica.</i> The analysis of molecular variance (AMOVA) resulted in a moderate (ncSSR) and great (cpDNA) variation among pure <i>M. sylvestris</i> and <i>M. ×domestica </i>individuals indicating a low gene flow between both species. The genetic diversity within the pure <i>M. sylvestris</i> populations was high with a weak genetic structure between the <i>M. sylvestris</i> populations indicating an unrestricted genetic exchange between these <i>M. sylvestris</i> populations.</p> <p>The clear distinguishing of <i>M. sylvestris</i> and <i>M. ×domestica</i> confirms our expectation of the existence of pure <i>M. sylvestris </i>accessions<i> </i>in this area and supports the argument for the implementation of preservation measures to protect the <i>M. sylvestris </i>populations in<i> </i>Saxony. </p>
Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers
<p><span>Water yam</span><span> (<em>Dioscorea alata</em></span><span> L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about <em>Dioscorea</em> species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 <em>D. alata</em> accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.17 to 0.74, with a mean of 0.49, which suggests moderate genetic diversity of <em>D. alata</em> accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 91% of the variation was attributed to within-population while among-population contributed 9% of the total variation. The highest Nei's genetic distance (0.65) was for accessions sampled from Arusha and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped <em>D. alata</em> accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of <em>D. alata</em> accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of <em>D. alata</em> accessions for breeding programs in Tanzania.</span></p>
SSR results of 13 markers of 609 Pyricularia oryzae isolates in Vietnam
<p>Dataset represents values of SSR markers, in column, of 609 <em>Pyricularia</em> <em>oryzae</em> isolates, in row. "NA" means the data was missed. Those isolates that are name coded in VNN were collected from North Vietnam; the other, coded VNC, was collected in Central Vietnam. </p>
Data from: Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers
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