Development and characterization of microsatellite markers for Vriesea simplex (Bromeliaceae) and cross-amplification in other species of Bromeliaceae

Ten polymorphic microsatellite loci were isolated and characterized for Vriesea simplex epiphytic and endemic species from the Brazilian Atlantic Rainforest. The number of alleles per locus ranged from 2 to 16. The observed and expected heterozygosity ranged from 0.000 to 0.414 and 0.068 to 0.795, respectively. All loci departed significantly from Hardy–Weinberg equilibrium. Linkage disequilibrium was not detected in any pair of loci. Transferability of 10 loci was positive across ten other Bromeliaceae species. The loci will be used for studying population genetic structure, mating system variation, and the origin and maintenance of reproductive barriers to gene exchange among sympatric Vriesea species.     

Development of novel chloroplast microsatellite markers for Miscanthus species (Poaceae)

? Premise of the study: A set of novel chloroplast microsatellite markers (cpSSRs) was developed for the bioenergy crop Miscanthus, and their utility in cross-species amplification was evaluated. ? Methods and Results: Twenty-eight novel primers flanking cpSSR loci were designed from a complete chloroplast genome sequence of Saccharum officinarum, a species closely related to Miscanthus. These primers were then tested on eight Miscanthus species, among which 16 cpSSR loci were found to be polymorphic. The number of alleles per polymorphic locus ranged from two to seven, with an average 3.94 alleles. ? Conclusions: These cpSSR markers can be applied to all Miscanthus species and will be useful for studying Miscanthus population structure, diversity, and phylogeography.     

Microsatellite loci for Paspalum atratum (Poaceae) and cross-amplification in other species

? Premise of the study: Paspalum atratum is a perennial, cespitose, tropical grass native to Central and South America. This species belongs to a polyploid complex (Plicatula group) little known at the genetic level. The characterized microsatellite markers provide new informative tools for further studies of the hybridization, mating systems, and structure of the population. ? Methods and Results: Using the microsatellite-enriched library method, we isolated and characterized 19 microsatellite markers from P. atratum. Eleven of them were polymorphic, showing a variable degree of variation, while eight were monomorphic in the samples analyzed. Additionally, the transferability of these microsatellite markers was tested in other species. ? Conclusions: These results suggest that the characterized markers have enough discriminatory potential to be used in genetic characterizations of Paspalum taxa, which are based on an understanding of their mating systems and genetic structure, as well as in understanding the evolutionary processes involved in the evolution of groups of Paspalum.     

Development and characterization of microsatellite markers for Echinopsis rhodotricha and cross-amplification in other species of Cactaceae

Located in central South America, the Chaco is a large subtropical dry forest characterized by plants with xeromorphic features, including numerous cacti. In the Brazilian Chaco at the northeasternmost part of the Chaquenian region, Echinopsis rhodotricha (Cactaceae, Trichocereeae) is one of the species threatened by intense deforestation caused by expanding pastureland. This study characterizes the microsatellite loci isolated from E. rhodotricha and cross-amplification in thirteen other cactus species. Twelve microsatellite loci were developed from an enriched genomic library. Eight of these were polymorphic and characterized in 48 individuals from three E. rhodotricha populations. The loci showed a mean of 3.2 alleles per locus and overall levels of expected and observed heterozygosities ranging from 0.00 to 0.83 and 0.00 to 0.66, respectively. Five loci showed significant departures from the Hardy–Weinberg equilibrium and also exhibited signs of null alleles. Cross-amplification in other Cactaceae species was successful, ranging from one (Ferocactus latispinus, Cacteae and Harrisia adscendens, Trichocereeae) to twelve loci (Echinopsis calochlora, Trichocereeae). The development of these microsatellite markers will contribute to investigations of population structure, genetic diversity, and gene flow in E. rhodotricha populations, as well as in other cactus species, providing information useful for the creation and delimitation of conservation areas in the Brazilian Chaco region.     

Development of microsatellite markers for the dwarf bamboo species Sasa cernua and Sasa kurilensis (Poaceae) in northern Japan

Ten polymorphic microsatellite markers were isolated from the dwarf bamboo species Sasa cernua and Sasa kurilensis. The applicability of these markers was confirmed by genotyping of open‐pollinated seeds and leaf samples from natural populations. Genotypes of seeds from each culm shared at least one allele from the maternal parent without contradiction. All 10 loci were polymorphic in S. cernua with 2–15 alleles (average H_E = 0.532). Eight loci were polymorphic in S. kurilensis with 2–10 alleles (average H_E = 0.532). These markers will be useful in detailing the extent of clonal and sexual reproduction in these species.     

Development of microsatellite loci for Pelophylax plancyi and cross-amplification in other ranid species

Thirteen polymorphic microsatellite loci were obtained from the gold-striped pond frog, Pelophylax plancyi. The number of alleles per locus ranged from 5 to 13 with an average of 8.38. The observed and expected heterozygosities (H _O and H _E) ranged from 0.533 to 0.890 and from 0.620 to 0.897, with averages of 0.686 and 0.751, respectively. In order to assess interspecific amplification, all primer pairs were tested with the same PCR conditions on three other Pelophylax species: Pelophylax hubeiensis, Pelophylax fukienensis, Pelophylax nigromaculata and two species from the genus Hylarana and Hoplobatrachus, respectively. All of these loci can be amplified successfully in the Pelophylax species, with eight loci amplified in all species tested.     

New microsatellite loci for Narcissus papyraceus (Amarillydaceae) and cross-amplification in other congeneric species

? Premise of the study: Microsatellite loci from a genomic library of the species Narcissus papyraceus were optimized and characterized for studies of population genetics. ? Methods and Results: Eleven markers that were successfully amplified showed polymorphism when tested on 50 individuals from two populations in southern Spain and northern Morocco. Overall, the number of alleles per locus ranged between 4 and 15. Between 8 and 11 loci successfully amplified in other eight Narcissus species. ? Conclusions: These markers will enable genetic diversity studies of N. papyraceus across its distribution range and conduct paternity analyses among individuals differing in flower morphology.     

Eight microsatellite loci in Phaedranassa schizantha Baker (Amaryllidaceae) and cross-amplification in other Phaedranassa species

Phaedranassa schizantha is a species endemic to Ecuador from which eight polymorphic microsatellite loci were isolated from an enriched genomic library. A total of 31 alleles with an average of four alleles per locus were detected across 29 individuals from a single natural population of P. schizantha. Observed heterozygosity ranged from 0.05 to 0.68. Most of the eight loci were successfully amplified in six Phaedranassa species. Five of those species are either “Vulnerable” or “Endangered” under IUCN criteria. These loci will be used to investigate patterns of inter- and intraspecific variation of Phaedranassa species, which will contribute data relevant to their conservation status.     

Development and characterization of microsatellite markers for endangered species Stipa pennata (Poaceae) and their usefulness in intraspecific delimitation

Molecular Biology Reports - Stipa pennata (Poaceae), has become a rare and endangered species in Central Europe due habitat loss and fragmentation. This species is characterized by high...     

A set of polymorphic dinucleotide and tetranucleotide microsatellite markers for the Indo-Pacific humpback dolphin (Sousa chinensis) and cross-amplification in other cetacean species

Eleven dinucleotide and five tetranucleotide polymorphic microsatellite loci were presented for the Indo-Pacific humpback dolphin Sousa chinensis, a species categorized as ‘data deficiency’ in the IUCN Red List. These markers were developed to allow future population studies, such as characterization of population structure and genetic diversity that are important for the species’ conservation. The number of alleles ranged from 2 to 9 with observed heterozygosity ranging from 0.167 to 0.917, and expected heterozygosity ranging from 0.159 to 0.913. Test of these loci in five additional cetacean species found that 10–13 loci have successful cross-amplifications.     

Polymorphic microsatellite loci for the genetic analysis of Lycoris radiata (Amaryllidaceae) and cross-amplification in other congeneric species

Lycoris radiata is a perennial herb that has been used in traditional Chinese medicine for a long time and has two main medicinal components in its bulb, lycorine and galanthamine. However, the original microsatellite loci have not been developed for any species of Lycoris. Total genomic DNA was extracted from fresh bulbs using a modified CTAB protocol. We isolated 10 microsatellite loci from 21 L. radiata individuals of a natural population from Yellow Mountain in Anhui Province, China. The number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.238 to 0.952 and from 0.455 to 0.784, respectively. One locus significantly deviated from Hardy-Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification of these microsatellite loci was characterized in additional five species (L. sprengeri, L. anhuiensis, L. albiflora, L. longituba, and L. chinensis) of Lycoris. The results suggest that these microsatellite markers would contribute to the population genetic studies of L. radiata and other related species.     

Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera

We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape level study of gene flow from transgenic glyphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of transgenic pollen both within the Agrostis complex and the related genera Polypogon.     

Aulonemia fulgor (Poaceae: Bambusoideae), a new species from Mexico

Aulonemia fulgor shares with most species of this primarily South American genus a paniculate inflorescence, unbranched spikelets (i.e., not pseudospikelets), and weak or scandent culms that bear a single branch at the node. It is unusual in its amphipodial rhizomes and distinctive leaf anatomy in which, unlike most bamboos, the more complex epidermis is the adaxial.     

Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology

? Premise of the study: The aim of this study was to assess the feasibility of developing chromosome-arm-specific microsatellite markers in wheat on a large scale based on chromosome survey sequences obtained with next-generation sequencing (NGS) technology. ? Methods and Results: The Illumina Hi Seq2000 sequencing platform was used to sequence DNA of isolated wheat chromosome-arm 7DL. The data were assembled and microsatellite loci were identified computationally. In total, 16315 microsatellites were identified from 161061 assembled contigs. Thirty-three markers were randomly selected for validation across 20 diverse wheat cultivars. Two nulli-tetrasomic stocks were also screened to validate the specificity of the newly developed markers. ? Conclusions: This is the first study on identification of chromosome-arm-specific microsatellite markers using NGS technology. These new chromosome-arm-specific markers will facilitate saturation of the 7DL genetic map, and their availability will support genetic mapping and positional cloning in wheat.     

Development of microsatellite markers in Lupinus luteus (Fabaceae) and cross-species amplification in other lupine species

? Premise of the study: Microsatellite primers were developed in Lupinus luteus L., an emerging temperate protein crop, to investigate genetic diversity, population structure, and to facilitate the generation of better yellow lupine varieties. ? Methods and Results: Thirteen polymorphic primer sets were evaluated in a European and Eastern European accession collection of L. luteus. The primers amplified di-, tri-, and tetranucleotide repeats with 2-4 alleles per locus. These revealed a moderate to low level of genetic variation, as indicated by an average observed heterozygosity of 0.0126. Select loci also amplified successfully in the closely related species L. hispanicus Boiss. & Reut. and in the New World species L. mutabilis Sweet. ? Conclusions: These results indicate the utility of primers for the study of genetic diversity across L. luteus populations and related lupine species. The use of these microsatellite markers will facilitate the implementation of several molecular breeding strategies in yellow lupine.