Microsatellite genotyping of carnation varieties

Microsatellite based DNA fingerprinting and assessment of genetic diversity in bougainvillea cultivars

Novel microsatellite markers were developed to investigate the genetic diversity and DNA fingerprinting of bougainvillea cultivars. Total of 175 SSRs were designed from over 50,000 SSRs identified in the whole genome sequence data, 33 highly polymorphic markers were identified. These selected SSRs produced a total of 165 alleles with 2 (BOUG-3 and BOUG-50) to 9 (BOUG-69) alleles per loci with an average of 5 alleles per locus. The overall size of the amplified products ranged from 90 bp (BOUG-51 and BOUG-81) to 320 bp (BOUG-162). The gene diversity per locus ranged from 0.13 to 0.91 with a mean of 0.71. Primer BOUG-73 and BOUG-124 exhibited highest gene diversity with greater number of alleles. The mean Nei's genetic diversity index was 0.678 with range of 0.134 (BOUG-77) to 0.958 (BOUG-69). The UPGMA based dendrogram divided the cultivars into seven major clusters. Clustering pattern was more distinct for bract types and variegated cultivars which were also confirmed by PCA scatter plot diagram. The pair-wise genetic distance estimates ranged from 0.089 to 0.86 with an average of 0.56. Each of the 125 cultivar profiled had unique marker profile indicating that the SSR markers identified are useful for identification and differentiation of bougainvillea cultivars. These informative markers identified from the study will be of great utility to assess the genetic diversity, understanding the population structure and in marker assisted breeding for improvement of bougainvillea.

Effect of rotational shepherding on demographic and genetic connectivity of calcareous grassland plants

Response to habitat fragmentation may not be generalized among species, in particular for plant communities with a variety of dispersal traits. Calcareous grasslands are one of the most species-rich habitats in Central Europe, but abandonment of traditional management has caused a dramatic decline of calcareous grassland species. In the Southern Franconian Alb in Germany, reintroduction of rotational shepherding in previously abandoned grasslands has restored species diversity, and it has been suggested that sheep support seed dispersal among grasslands. We tested the effect of rotational shepherding on demographic and genetic connectivity of calcareous grassland specialist plants and whether the response of plant populations to shepherding was limited to species dispersed by animals (zoochory). Specifically, we tested competing dispersal models and source and focal patch properties to explain landscape connectivity with patch-occupancy data of 31 species. We fitted the same connectivity models to patch occupancy and nuclear microsatellite data for the herb Dianthus carthusianorum (Carthusian pink). For 27 species, patch connectivity was explained by dispersal by rotational shepherding regardless of adaptations to zoochory, whereas population size (16% species) and patch area (0% species) of source patches were not important predictors of patch occupancy in most species. [Correction made after online publication, February 25, 2014: Population size and patch area percentages were mistakenly inverted, and have now been fixed.] Microsite diversity of focal patches significantly increased the model variance explained by patch occupancy in 90% of the species. For D. carthusianorum, patch connectivity through rotational shepherding explained both patch occupancy and population genetic diversity. Our results suggest shepherding provides dispersal for multiple plant species regardless of their dispersal adaptations and thus offers a useful approach to restore plant diversity in fragmented calcareous grasslands.

Directed dispersal by rotational shepherding supports landscape genetic connectivity in a calcareous grassland plant

Directed dispersal by animal vectors has been found to have large effects on the structure and dynamics of plant populations adapted to frugivory. Yet, empirical data are lacking on the potential of directed dispersal by rotational grazing of domestic animals to mediate gene flow across the landscape. Here, we investigated the potential effect of large-flock shepherding on landscape-scale genetic structure in the calcareous grassland plant Dianthus carthusianorum, whose seeds lack morphological adaptations to dispersal to animals or wind. We found a significant pattern of genetic structure differentiating population within grazed patches of three nonoverlapping shepherding systems and populations of ungrazed patches. Among ungrazed patches, we found a strong and significant effect of isolation by distance (r = 0.56). In contrast, genetic distance between grazed patches within the same herding system was unrelated to geographical distance but significantly related to distance along shepherding routes (r = 0.44). This latter effect of connectivity along shepherding routes suggests that gene flow is spatially restricted occurring mostly between adjacent populations. While this study used nuclear markers that integrate gene flow by pollen and seed, the significant difference in the genetic structure between ungrazed patches and patches connected by large-flock shepherding indicates the potential of directed seed dispersal by sheep across the landscape.

Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.)

Background

Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F₂ populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research.

Results

We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data.

Conclusions

The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.

Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology

Background

Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology.

Results

We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway.

Conclusions

We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

Strawberry cultivar identification based on hypervariable SSR markers

We genotyped strawberry cultivars by two newly selected and two previously reported SSR markers. All four markers produced interpretable electropherograms from 75 accessions consisting of 72 Fragaria × ananassa cultivars or lines and three octoploid Fragaria species accessions. These SSR markers were highly polymorphic; in particular, one of the newly developed markers, FxaHGA02P13, was capable of distinguishing all of the accessions except for a mutant strain that was derived from another accession in the set. When two markers were combined, all 48 full-sib individuals could be distinguished. Fingerprinting patterns were reproducible between multiple samples, including the leaves, sepals, and fruit flesh of the same accession. Principal-coordinate analysis of the 75 accessions detected several groups, which reflect taxon and breeding site. Together with other available markers, these SSR markers will contribute to the management of strawberry genetic resources and the protection of breeders' rights.