Set Of Microsatellite Markers Research Articles

Rapid Changes in the Genetic Composition of Stagonosporopsis tanaceti Population in Australian Pyrethrum Fields

A novel set of microsatellite markers were developed and employed for geographical and temporal population analyses of Stagonosporopsis tanaceti, the cause of ray blight of pyrethrum in Australia. Genotyping of 407 isolates, using 13 markers, suggested an asexual mode of reproduction with significant linkage disequilibrium and high levels of clonality. Low geographical differentiation and widespread distribution of a few multilocus genotypes (MLGs), in the absence of airborne ascospores, suggested the role of human-mediated movement of seed as a major means of long-distance pathogen dispersal. The genetic composition of S. tanaceti was stable for a decade then changed rapidly in only 2 years. Bayesian clustering analyses and minimum spanning networks determined only two major clonal lineages in and prior to 2010. However, in 2012, a previously unobserved cluster of MLGs was detected, which significantly increased in frequency and displaced the historically dominant MLGs by 2013. This rapid change in the genetic composition of S. tanaceti could indicate a second introduction then a selective sweep, or strong selection pressures from recently introduced fungicides or pyrethrum varieties. These results may have serious implications for durability of management strategies for this disease.

Development of Novel Microsatellite Markers in Jatropha curcas and Evaluation of Their Cross-Species Transferability

Jatropha curcas has been a species of interest all over the world due to its potential as a renewable biodiesel crop. In the present paper, a set of 40 novel genomic microsatellites from Jatropha developed through cloning and sequencing are reported. The microsatellite markers were evaluated at intra-specific, inter-specific and inter-generic levels. All forty markers successfully amplified fragments from J. curcas and J. integerrima showing their potential in linkage mapping using inter-specific breeding populations involving these species. The average number of alleles within 12 core accessions of J. curcas was 3.083. Polymorphic information content ranged from 0.15 to 0.80 within J. curcas accessions and from 0 to 0.37 among different genera. There was no significant deviation from Hardy–Weinberg equilibrium or linkage disequilibrium. Ten of these microsatellites showed polymorphism within Emblica officinalis while thirteen were polymorphic within Phyllanthus niruri and Ricinus communis accessions. These new set of microsatellite markers are expected to be especially useful in future for linkage mapping in J. curcas and for varietal identification and genetic diversity studies in other genera mentioned above.

Development of microsatellite loci from a reference genome for the Neotropical butterflyHeliconius numataand its close relatives

The Neotropical butterfly Heliconius numata (Lepidoptera: Nymphalidae: Heliconiinae) is known for its striking diversity of wing color patterns driven by the Müllerian mimicry of multiple local models and controlled by a single supergene locus. Such fine-scale variation of traits under strong selection offers a unique opportunity for the study of the ecology and genetics of adaptation. However, little is still known of the population processes driving geographical variation in wing-pattern phenotypes. We report the characterization of 26 microsatellite markers for the butterfly H. numata, including six located inside the wing color-pattern supergene region. All markers are polymorphic, with allele numbers ranging from 2 to 21 per locus, an observed heterozygosity of 0.111 to 0.848 and an expected heterozygosity of 0.126 to 0.942. A subset of 18 of these markers was tested on five closely related sympatric Heliconius species with an amplification success ranging from 88% to 94%. The obtained set of microsatellite markers provides a new and useful set of tools to investigate patterns of differentiation and selection in populations of mimetic Heliconius butterflies. Moreover, markers developed within the color-pattern supergene will facilitate characterization of the association between the genetic architecture and the functional diversity of wing patterns. Finally, the cross-species amplification success of the described markers extends their utility to also encompass comparative population genetic studies of closely related species within a clade of rapidly diversifying species.

Diversity in the breadfruit complex (Artocarpus, Moraceae): genetic characterization of critical germplasm

Breadfruit (Artocarpus altilis, Moraceae) is a traditional staple crop in Oceania and has been introduced throughout the tropics. This study examines important germplasm collections of breadfruit and its closest wild relatives and aims to (1) characterize genetic diversity, including identification of unknown and duplicate accessions, (2) evaluate genetic structure and hybridization within the breadfruit complex, and (3) compare utility of microsatellite markers to previously reported amplified fragment length polymorphism (AFLP) and isozyme markers in differentiating among cultivars. Data for 19 microsatellite loci were collected for 349 individuals (representing 255 accessions) including breadfruit (A. altilis), two wild relatives (Artocarpus camansi and Artocarpus mariannensis), and putative hybrids (A. altilis × A. mariannensis). Accessions were of mixed ploidy and regional origin, but predominantly from Oceania. Microsatellite loci collectively had a polymorphic information content (PIC) of 0.627 and distinguished 197 unique genotypes sorted into 129 different lineages, but a single genotype accounts for 49 % of all triploid breadfruit examined. Triploid hybrids and diploid A. altilis exhibited the highest levels of diversity as measured by allele number and gene diversity. Most accessions (75 %) of unknown origin matched either a known genotype or lineage group in the collection. Putative hybrids all had genetic contributions from A. mariannensis but ranged in the level of genetic contribution from A. altilis. Microsatellite markers were found to be more informative than isozyme markers and slightly less informative, with regard to accession discrimination, than AFLP markers. This set of microsatellite markers and the dataset presented here will be valuable for breadfruit germplasm management and conservation.

Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira.

The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America.

Isolation and characterization of microsatellite markers for Osmanthus fragrans (Oleaceae) using 454 sequencing technology.

Osmanthus fragrans (Oleaceae) is an evergreen shrub or small tree that grows in south China. In this study, Roche 454 FLX+ sequencing combined with the magnetic bead enrichment method was used to isolate microsatellite markers from the genome of O. fragrans. A total of 1471 microsatellites that contained enough flanking sequences for primer pair design were identified from 89,633 raw sequencing reads. One hundred primer pairs were randomly chosen to test primer amplification efficiency. Among these tested primer pairs, 20 yielded polymorphic amplification products across 16 individuals from the Albus, Luteus, and Aurantiacus groups. The number of alleles ranged from 2 to 6, with an average of 3.7. The observed heterozygosity ranged from 0 to 0.813, with an average of 0.460. Shannon's information index ranged from 0.463 to 1.707, with an average of 0.975. Six loci (Of 05, Of 06, Of 08, Of 12, Of 15, and Of 19) deviated significantly from Hardy-Weinberg equilibrium (P < 0.05), which was due to an excess of homozygotes or heterozygotes. Nine pairs of loci (Of 01 and Of 05; Of 04 and Of 05; Of 01 and Of 06; Of 04 and Of 12; Of 02 and Of 13; Of 04 and Of 13; Of 12 and Of 13; Of 04 and Of 19; Of 05 and Of 19) showed significant linkage disequilibrium, which indicated significant allelic association between the loci. This set of microsatellite markers will be valuable for molecular marker-assisted breeding in O. fragrans.

Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae).

• Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana.• Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci.• Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species.

Natural hybridization between Gossypium mustelinum and exotic allotetraploid cotton species.

Cotton has been collected in Brazil for decades for its conservation, evaluation, and the use of its genetic resources. Gossypium mustelinum is an allotetraploid cotton species that only occurs in Brazil, and little is known about its genetic potential for improvement. However, the species is threatened by habitat fragmentation and interspecific hybridization with exotic species of cotton. In this study, we investigated the rate of natural hybridization in two populations of G. mustelinum in Bahia, Brazil, with G. hirsutum and G. barbadense using a set of microsatellite markers.

Development of new set of microsatellite markers in cultivated tobacco and their transferability in other Nicotiana spp.

Scarcity of molecular markers in tobacco has been a limitation, hampering the acceleration of breeding efforts. Development of microsatellite markers is a prerequisite for mapping, tagging of many useful qualitative and quantitative traits and also for the generation of saturated linkage map. Use of microsatellite-enriched genomic libraries an efficient and rapid method for the identification of clones harboring microsatellite motifs leading to the development of microsatellite markers. In the present study, a total of 111 microsatellite motifs was identified from the enriched library, of which, 70 motifs (which includes perfect and imperfect repeat) were used for marker development. These newly developed markers could successfully differentiated different types of tobacco and diverse cultivars of Flue Cured Virginia (FCV) tobacco. The high rate of transferability (95-7% - 100%) of these microsatellite markers in a wide range of Nicotiana species indicated their potential as viable resources in the inter-specific gene transfer programme. The set of microsatellite markers developed in this study is a valuable addition to the already available DNA marker resources in tobacco.

Discovery and characterization of a first set of polymorphic microsatellite markers in Siganus oramin

Nine microsatellite DNA markers were developed and characterized for Siganus oramin by the 5'-anchored polymerase chain reaction technique. A total of 42 alleles were identified in 30 individuals, and the number of alleles per locus ranged from 3 to 7, with an average of 4.7. The observed and expected heterozygosity per locus ranged from 0.5333 to 1.0000 and from 0.5254 to 0.8474, respectively, with an average of 0.7422 and 0.6906, respectively. A significant deviation from the Hardy-Weinberg equilibrium was detected at one microsatellite locus after a Bonferroni's correction (P < 0.0056). No significant linkage disequilibrium was found between any of the pairs of the nine loci. The microsatellite loci developed in this study will improve our understanding of the genetic background of S. oramin.

Isolation and characterization of microsatellite markers for Axonopus compressus (Sw.) Beauv. (Poaceae) using 454 sequencing technology.

Axonopus compressus (Sw.) Beauv. is a perennial herb widely used as a garden lawn grass. In this study, we used Roche 454 pyrosequencing, combined with the magnetic bead enrichment method FIASCO, to isolate simple sequence repeat markers from the A. compressus genome. A total of 1942 microsatellite loci were identified, with 53,193 raw sequencing reads. One hundred micro-satellite loci were selected to test the primer amplification efficiency in 24 individuals; 14 primer pairs yielded polymorphic amplification products. The number of observed alleles ranged from two to six, with an average of 3.5. Shannon's Information index values ranged from 0.169 to 0.650, with an average of 0.393. Nei's genetic diversity values ranged from 0.108 to 0.457, with an average of 0.271. This first set of microsatellite markers developed for Axonopus will assist in the development of molecular marker-assisted breeding and the assessment of genetic diversity in A. compressus.

Isolation and Characterisation of a Dinucleotide Microsatellite Set for a Parentage and Biodiversity Study in Domestic Guinea Pig (Cavia Porcellus)

The domestic guinea pig is a valuable genetic resource because it is part of local folklore and food tradition in many South American countries. The economic importance of the guinea pig is due to its high feed efficiency and the quality of animal protein produced. For these reasons, our study is aimed to design a complete dinucleotide microsatellite marker set following international recommendation to assess the genetic diversity and genealogy management of guinea pigs. We selected a total of 20 microsatellites, looking for laboratory efficiency and good statistical parameters. The set was tested in 100 unrelated individuals of guinea pigs from Ecuador, Peru, Colombia, Bolivia and Spain. Our results show a high degree of polymorphisms with a total of 216 alleles and a mean number of 10.80±3.49 for markers with a combined exclusion probability of 0.99.

Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications.

BackgroundAnastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure.ResultsWe developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations.ConclusionsThis novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest.

Land use patterns skew sex ratios, decrease genetic diversity and trump the effects of recent climate change in an endangered turtle

AbstractAimChanges in both land use and climate can cause population declines and species extinctions, but the relative effects of these two stressors are often dependent on species‐specific life histories. Turtles are highly threatened as a taxonomic group and are particularly sensitive to environmental change due to their life history, habitat preferences and physiology. We used both sex data and genetic diversity across a landscape‐scale gradient in land use intensity and recent climate change to characterize the relative effects of these factors on three turtle species (including the endangered Blanding's turtle, Emydoidea blandingii) with different life histories and thus different vulnerabilities to environmental change.LocationWisconsin, USA.MethodsTurtles were captured and sampled for genetic analyses at 18 sites. Sampled individuals were genotyped for species‐specific sets of microsatellite markers, and population‐level genetic diversity was assessed using rarefied allelic richness and heterozygosity. The relative effects of road density, public land area and recent climate change on genetic diversity and sex ratio were evaluated using regression methods and model‐selection criteria.ResultsIncreased land use intensity was associated with male‐skewed sex ratios and decreased genetic diversity in E. blandingii but not co‐occurring species. Recent climate change did not explain variability in either sex ratio or genetic diversity for any of the three species examined.Main conclusionsChanging land use has multiple impacts on turtle populations that are modulated by species‐specific life history traits. Extensive terrestrial movements associated with nesting in E. blandingii increase female vulnerability to road mortality, which in turn has led to declines in genetic diversity. The predicted effects of recent climate change may have been dampened by behavioural plasticity. We suggest that the disproportionate effect of land use on E. blandingii warrants greater legal protection for this species.

HOW CAN WE EFFICIENTLY CHARACTERIZE GENES OF AGRONOMIC INTEREST IN OLIVE: TOWARDS THE GENETIC ASSOCIATION STUDIES?

Despite the socio-economic importance of olive oil and the need of olive breeding, genetic studies on agronomic traits are restricted to few biparental populations limiting the efficiency of QTL (Quantitative Trait Loci) mapping strategy. Association mapping based on a diversified collection of olive germplasm can be proposed as a complementary strategy to genetically map agronomic traits. Here, we aimed to develop tools for association mapping studies by defining a Mediterranean olive core collection and characterizing a massive set of microsatellite markers (SSRs). The worldwide olive germplasm bank of Marrakech, Morocco (561 accessions from 14 Mediterranean countries) was characterized using 17 nuclear SSRs and cpDNA markers and classified into east, centre and west Mediterranean gene pools. Combining two sampling methods maximizing the capture of diversity and genetic distance, we proposed two core collections of 50 and 94 accessions including all nuclear SSR alleles, cpDNA haplotypes and states of agro-morphology (from Olea databases) from the WOGB Marrakech. These core collections include cultivars considered as the most important in Mediterranean olive producing countries and display a limited genetic structure between east and west/center gene pools. Hence, they are efficient candidates for phenotyping agronomic trait and to explore the largest variability in distinct environmental conditions. Concurrently, we developed a set of genomic and Expressed Sequence Tag (EST)-derived SSRs that were used to complete the genetic map of ‘Oliviere’ × ‘Arbequina’ segregating population. Molecular markers will be used on the proposed core collections to assess the linkage disequilibrium decay according to the genetic distance and to further develop association mapping studies.

Development and characterization of nine polymorphic microsatellite markers for the blue sheep (Pseudois nayaur)

Pseudois nayaur is a major component of Caprini and a keystone species in Qinghai-Tibet Plateau ecosystems. Due to the excessive hunting and habitat loss, its numbers are being reduced drastically. We developed and characterized the first set of microsatellite markers in this species to investigate its population genetic diversity and structure. Nine polymorphic loci displayed an average of 5.73 alleles (range between 2 and 14) and the levels of expected heterozygosity ranged from 0.422 to 0.816. Cross-amplification within dwarf blue sheep was successful for the nine loci. The loci characterized here will be useful for detecting fine-scale spatial structuring and resolving the taxonomic status of divergent Pseudois populations.

Novel polymorphic EST-derived microsatellite markers for the red-listed five needle pine, Pinus dabeshanensis

Pinus dabeshanensis is an endangered five needle pine endemic to mid-South of China. This pine finds its very limited natural occurrence in the Dabie mountains area with altitudes ranging 900–1400 m. We identified 3,516 SSR loci from the transcriptome assembly of the congeneric species P. lambertiana, and evaluated 671 loci we found. Finally, 28 novel polymorphic microsatellite markers were developed for P. dabeshanensis. Markers were characterized using 36 individuals, representing all existing populations from across the species geographic range. Species level analysis of these 28 polymorphic markers revealed the mean number per locus was 2.786 (range 2–6) and mean observed and expected heterozygosities were 0.332 (range 0.000–1.000) and 0.316 (range 0.033–0.691), respectively. This study provides the first set of microsatellite markers for the conservation genetics which in turn will facilitate conservation management for this pine.

A set of novel microsatellite markers developed for a traditional Chinese medicinal plant, Sarcandra glabra (Chloranthaceae)

A set of novel microsatellite markers developed for a traditional Chinese medicinal plant, Sarcandra glabra (Chloranthaceae)

Microsatellite markers for the Arctic copepod Calanus glacialis and cross-amplification with C. finmarchicus

Calanus glacialis is a major component of Arctic zooplankton and a keystone species in Arctic marine ecosystems. Due to the observed climate warming, its numbers are being reduced to the advantage of a sibling Atlantic species Calanus finmarchicus. We developed and characterized the first set of microsatellite markers in this species to investigate its population genetic structure and dispersal capabilities. Nine polymorphic loci displayed an average of 7.3 alleles (range between 2 and 13) and the levels of expected heterozygosity ranged from 0.039 to 0.806. These provide a valuable tool to understand present connectivity patterns across Arctic regions, look for signatures of past climate effects and predict the response to future climate-driven environmental changes. Additionally, due to the cross-amplification with C. finmarchicus, the markers can be used to discriminate between these sibling species.

Establishment of a Microsatellite Marker set for Individual Identification in Goat

Establishment of a Microsatellite Marker set for Individual Identification in Goat