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Arnica mallotopus is a perennial herb endemic to the snowy regions of Japan. At the southern edge of its distribution, in Kyoto Prefecture, overgrazing by sika deer and decreased snowfall have resulted in the rapid decline of A. mallotopus populations. Therefore, there is an urgent need for a conservation genetic analysis of the remaining local populations. In this study, we first developed 13 EST-SSR markers to evaluate genetic variation in A. mallotopus. The average number of alleles per locus was 5.33. Genetic analysis using these markers showed that the investigated samples were classified into two groups corresponding to landscape structure. One group isolated from a tributary of the Yura River showed a strong population bottleneck signal, likely resulting from founder effects and subsequent drifts. On the other hand, the genetic diversity of the second group in the main distribution along the Yura River was higher and less inbred. Overall, our assessment suggested recognizing the two genetic groups as management units in conservation programs for the threatened populations.

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

Premise of the study: Simple sequence repeat (SSR) markers were developed for Aster savatieri (Asteraceae) and the serpentine variety A. savatieri var. pygmaeus to re-evaluate their taxonomic status. Methods and Results: Using RNA-Seq data, 22 expressed sequence tag (EST)-SSR markers were developed. Polymorphisms were assessed in A. savatieri and in A. savatieri var. pygmaeus. The average number of alleles ranged from four to 15, and expected heterozygosity ranged from 0.417 to 0.870. Transferability was examined in six representative species of Japanese Aster and in Solidago virgaurea subsp. asiatica var. asiatica, a member of the tribe Astereae (Asteraceae); most of the loci were transferable to these examined species. Conclusions: These markers will be useful for genetic studies of variation in A. savatieri and other Aster species that occur in Japan.

Vrste roda Centaurium Hill često hibridizuju u prirodi. Brojni primeri ukazuju na značaj poliploidizacije i hibridizacije tokom specijacije u okviru ovog roda. Ukrštanjem Centaurium erythraea Rafn × C. littorale (Turner) Gilmour u uslovima in vitro, dobijeno je alotetraploidno potomstvo, što ide u prilog hipotezi postojanja nedovoljno efikasnih prereproduktivnih barijera, koje bi sprečavale hibridizaciju. Primenjene metode za detekciju hibridnih jedinki u uslovima in vitro su uspešno iskorišćene i u slučaju prirodnih populacija poreklom sa Subotičko-horgoške peščare. Novi takson, nazvan Centaurium pannonicum, je heksaploid nastao iz ukrštanja C. erythraea × C. littorale ssp. compressum (Hayne) Kischner, nakon fertilizacije, tj. spajanja diploidnog i tetraploidnog jedra. De novo razvijeni EST-SSR markeri ukazuju da C. pannonicum konvergira vrsti C. erythraea, dok je prema fitohemijskim markerima hibridni takson sličniji C. littorale ssp. compressum. Razvijeni setovi EST-SSR i fitohemijskih markera, su transferabilni i na druge vrste roda Centaurium, i mogu značajno doprineti daljim istraživanjima međuvrsne hibridizacije. C. pannonicum stabilno održava svoju heksaploidnu genetičku konstitutciju u prirodnim populacijama, umnogome zahvaljujući samooplodnji i/ili drugim vidovima ukrštanja u srodstvu.

Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species' unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (similar to 9.0 bp) were obtained, and 116,814 unigenes (>= 200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.

Vrste roda Centaurium Hill često hibridizuju u prirodi. Brojni primeri ukazuju na značaj poliploidizacije i hibridizacije tokom specijacije u okviru ovog roda. Ukrštanjem Centaurium erythraea Rafn × C. littorale (Turner) Gilmour u uslovima in vitro, dobijeno je alotetraploidno potomstvo, što ide u prilog hipotezi postojanja nedovoljno efikasnih prereproduktivnih barijera, koje bi sprečavale hibridizaciju. Primenjene metode za detekciju hibridnih jedinki u uslovima in vitro su uspešno iskorišćene i u slučaju prirodnih populacija poreklom sa Subotičko-horgoške peščare. Novi takson, nazvan Centaurium pannonicum, je heksaploid nastao iz ukrštanja C. erythraea × C. littorale ssp. compressum (Hayne) Kischner, nakon fertilizacije, tj. spajanja diploidnog i tetraploidnog jedra. De novo razvijeni EST-SSR markeri ukazuju da C. pannonicum konvergira vrsti C. erythraea, dok je prema fitohemijskim markerima hibridni takson sličniji C. littorale ssp. compressum. Razvijeni setovi EST-SSR i fitohemijskih markera, su transferabilni i na druge vrste roda Centaurium, i mogu značajno doprineti daljim istraživanjima međuvrsne hibridizacije. C. pannonicum stabilno održava svoju heksaploidnu genetičku konstitutciju u prirodnim populacijama, umnogome zahvaljujući samooplodnji i/ili drugim vidovima ukrštanja u srodstvu., Species of genus Centaurium Hill readily hybridize in natural habitats. Plenty of evidence reveal the importance of polyploidization and hybridization as evolutionary mechanisms responsible for speciation within this genus. Allotetraploids obtained from Centaurium erythraea Rafn × C. littorale (Turner) Gilmour cross under in vitro conditions supported hypothesis that pre-reproductive barriers existing in these species are poorly efficient in preventing hybridization. Implemented methodology for the detection of hybrid individuals were successfully applied in natural populations from Subotica-Horgoš sands. New taxon, named Centaurium pannonicum, is a hexaploid hybrid arisen from C. erythraea x C. littorale ssp. compressum (Hayne) Kischner cross, after fertilization, i.e. joining of diploid and tetraploid nuclei. De novo developed EST-SSR markers suggested that hybrid taxon converges to C. erythraea. As revealed by the selected set of phytochemical markers, C. pannonicum was more similar to C. littorale ssp. compressum. Developed sets of EST-SSR and phytochemical markers are transferable to other Centaurium species and could facilitate further investigation of interspecific hybridization within the genus. C. pannonicum maintains its hexaploidy in natural populations by self-fertilization and/or other forms of positive assortative crossing.

Premise of the study: Microsatellite markers were identified and characterized to study the genetic diversity and structure of Barringtonia racemosa (Lecythidaceae). Methods and Results: Based on the transcriptome data of B. racemosa, 30 primer pairs were initially designed and tested, of which 15 were successfully amplified and displayed clear polymorphisms across the 43 individuals from three distant populations tested in the study. The results showed that the number of alleles per locus ranged from two to seven and the expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.772 and from 0 to 0.933, respectively. Conclusions: The expressed sequence tag-simple sequence repeat (EST-SSR) markers described here will be useful for studying genetic diversity and structure of B. racemosa. Furthermore, all loci were successfully cross-amplified in B. asiatica and B. acutangula and will be of great value for genetic studies across this genus. © 2015 Xie et al.

Premise of the study: Microsatellite markers were identified and characterized to study the genetic diversity and structure of Barringtonia racemosa (Lecythidaceae). Methods and Results: Based on the transcriptome data of B. racemosa, 30 primer pairs were initially designed and tested, of which 15 were successfully amplified and displayed clear polymorphisms across the 43 individuals from three distant populations tested in the study. The results showed that the number of alleles per locus ranged from two to seven and the expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.772 and from 0 to 0.933, respectively. Conclusions: The expressed sequence tag-simple sequence repeat (EST-SSR) markers described here will be useful for studying genetic diversity and structure of B. racemosa. Furthermore, all loci were successfully cross-amplified in B. asiatica and B. acutangula and will be of great value for genetic studies across this genus. © 2015 Xie et al.

Premise of the study: Microsatellite markers were identified and characterized to study the genetic diversity and structure of Barringtonia racemosa (Lecythidaceae). Methods and Results: Based on the transcriptome data of B. racemosa, 30 primer pairs were initially designed and tested, of which 15 were successfully amplified and displayed clear polymorphisms across the 43 individuals from three distant populations tested in the study. The results showed that the number of alleles per locus ranged from two to seven and the expected heterozygosity and observed heterozygosity per locus varied from 0 to 0.772 and from 0 to 0.933, respectively. Conclusions: The expressed sequence tag-simple sequence repeat (EST-SSR) markers described here will be useful for studying genetic diversity and structure of B. racemosa. Furthermore, all loci were successfully cross-amplified in B. asiatica and B. acutangula and will be of great value for genetic studies across this genus. © 2015 Xie et al.

Primula sieboldii is a self-incompatible ornamental plant that has been cultivated for more than 300 years in Japan. In order to increase the available genomic resources for this species, 5651 expressed sequence tags (ESTs) were generated from seedling and winter bud cDNA libraries. After clustering and assembling ESTs, 2960 unigene elements that contain an homologous sequence to an S locus-linked gene of P. vulgaris were identified. In total, 127 simple sequence repeats (SSRs) were found. The most frequent di- and tri-SSR motifs were GA (78.6%) and ATT (12.9%), respectively. Twenty SSR and 40 single nucleotide polymorphism (SNP) markers were developed. These markers were evaluated for polymorphisms using 24 individuals (Y) from a population in Yatsugatake and 14 individuals (PS) from across the distributional range of P. sieboldii in Japan. The average level of expected heterozygosity within Y and PS was 0.39 and 0.48, respectively for EST-SSR markers and 0.26 and 0.29, respectively for SNP markers. The level of polymorphism for EST-SSR markers was lower than that for genomic SSR markers developed in a previous study. We also surveyed the genetic diversity of 56 cultivars, which had lower allelic richness than the Y and PS populations.

Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the ‘BAT93’ × ‘Jalo EEP558’ cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.

Microsatellites and gene-derived markers are still underrepresented in the core molecular linkage map of common bean compared to other types of markers. In order to increase the density of the core map, a set of new markers were developed and mapped onto the RIL population derived from the ‘BAT93’ × ‘Jalo EEP558’ cross. The EST-SSR markers were first characterized using a set of 24 bean inbred lines. On average, the polymorphism information content was 0.40 and the mean number of alleles per locus was 2.7. In addition, AFLP and RGA markers based on the NBS-profiling method were developed and a subset of the mapped RGA was sequenced. With the integration of 282 new markers into the common bean core map, we were able to place markers with putative known function in some existing gaps including regions with QTL for resistance to anthracnose and rust. The distribution of the markers over 11 linkage groups is discussed and a newer version of the common bean core linkage map is proposed.