Real-Time and Conventional PCR Tools for Detection and Discrimination of Calonectria pseudonaviculata and C. henricotiae Causing Boxwood Blight.

Calonectria pseudonaviculata and C. henricotiae are the causal agents of boxwood blight, a devastating disease of boxwood that has caused significant economic impact on the nursery and landscape industries in the U.S. and in Europe. The two species are genetically distinct and are found in different geographic areas but are difficult to distinguish based on morphology and pathogenicity. Fast, accurate, and inexpensive methods to detect and differentiate these species is critical in stopping the spread of the disease. We designed primer pairs based on available sequences of four conserved regions-calmodulin, histone H3, internal transcribed spacer, and ß-tubulin-and tested their ability to differentiate the two Calonectria species. Here we report three primer pairs derived from sequence differences in the histone H3 region that can be used to specifically detect C. pseudonaviculata, C. henricotiae, or both species. Specificity of these primers was tested against nine isolates of C. pseudonaviculata, three isolates of C. henricotiae, 13 other Calonectria species, and five isolates from related genera using conventional and real-time PCR. These are the first primers available that can be used with either a multiplexed conventional PCR or SYBR-based real-time PCR to specifically detect and differentiate the two fungal species.

Using acetone for rapid PCR-amplifiable DNA extraction from recalcitrant woody plant taxa.

PREMISE: Quick and effective DNA extraction from plants for subsequent PCR amplification is sometimes challenging when working across diverse plant taxa that may contain a variety of inhibitory compounds. Time-consuming methods may be needed to overcome these inhibitory effects as well as the effects of various preservation and collection methods to extract DNA from leaf samples. Our objective was to develop a rapid DNA extraction protocol that could be used with diverse plant taxa to produce high-quality DNA suitable for downstream PCR applications. METHODS AND RESULTS: We tested the efficacy of acetone in extracting DNA from fresh, frozen, oven-dried, acetone-fixed, and herbarium leaf material of 22 species from 16 woody and herbaceous plant families. An improved simplified DNA extraction protocol was developed using acetone-fixed leaf material. The addition of 1% sodium dodecyl sulfate solution resulted in the optimal extraction from all tissue samples. The DNA resulting from the extraction protocol was readily amplified using real-time PCR assays. CONCLUSIONS: The protocol described here resulted in the extraction of DNA from recalcitrant plant species that was of sufficient quality and quantity for PCR amplification, as indicated by the low threshold cycle values from real-time assays. This method is simple, fast, and cost-effective, and is a reliable tool for extracting high-quality DNA from plant material containing PCR inhibitors.

Taxonomic similarity does not predict necessary sample size for ex situ conservation: a comparison among five genera.

Effectively conserving biodiversity with limited resources requires scientifically informed and efficient strategies. Guidance is particularly needed on how many living plants are necessary to conserve a threshold level of genetic diversity in ex situ collections. We investigated this question for 11 taxa across five genera. In this first study analysing and optimizing ex situ genetic diversity across multiple genera, we found that the percentage of extant genetic diversity currently conserved varies among taxa from 40% to 95%. Most taxa are well below genetic conservation targets. Resampling datasets showed that ideal collection sizes vary widely even within a genus: one taxon typically required at least 50% more individuals than another (though Quercus was an exception). Still, across taxa, the minimum collection size to achieve genetic conservation goals is within one order of magnitude. Current collections are also suboptimal: they could remain the same size yet capture twice the genetic diversity with an improved sampling design. We term this deficiency the 'genetic conservation gap'. Lastly, we show that minimum collection sizes are influenced by collection priorities regarding the genetic diversity target. In summary, current collections are insufficient (not reaching targets) and suboptimal (not efficiently designed), and we show how improvements can be made.

Use of Mycelium and Detached Leaves in Bioassays for Assessing Resistance to Boxwood Blight.

Boxwood blight caused by Calonectria pseudonaviculata is a newly emergent disease of boxwood (Buxus spp. L.) in the United States that causes leaf drop, stem lesions, and plant death. A rapid and reliable laboratory assay that enables screening hundreds of boxwood genotypes for resistance to boxwood blight is needed to enable breeding and selection of resistant cultivars. Using eight boxwood cultivars with differing susceptibilities, we examined parameters for a screening assay comparing whole plant inoculation with detached leaf inoculation, use of mycelium versus spores as the inoculum, comparison of times of the year for inoculation, and comparison of two leaf inoculation methods. Inoculation of detached leaves gave comparable results to inoculation of whole plants when compared across genotypes, although the detached leaf assay resulted in greater percentages of symptom expression. The time of year of plant inoculation (spring, summer, or winter) did not affect the relative expression of symptoms among the most resistant and susceptible genotypes. Inoculating plants with mycelium was as effective as spore inoculation for causing disease symptoms and allowed us to distinguish the more resistant genotypes, yet mycelium inoculation was much easier to prepare in large quantities for multiple assays.

Development of polymorphic genic-SSR markers by cDNA library sequencing in boxwood, Buxus spp. (Buxaceae).

PREMISE OF THE STUDY: Genic microsatellites or simple sequence repeat (genic-SSR) markers were developed in boxwood (Buxus taxa) for genetic diversity analysis, identification of taxa, and to facilitate breeding. • METHODS AND RESULTS: cDNA libraries were developed from mRNA extracted from leaves of Buxus sempervirens 'Vardar Valley' and sequenced using the Illumina MiSeq system. Approximately 11.9 million base pairs of sequence data were examined and 845 genic-SSRs were identified, including 469 dinucleotide, 360 trinucleotide, seven tetranucleotide, one pentanucleotide, and eight hexanucleotide repeats. Primer pairs were designed for 71 selectively chosen genic-SSRs containing trinucleotide repeat motifs and were used to amplify the corresponding loci in 18 diverse boxwood accessions. Twenty-three primer pairs amplified polymorphic loci, with two to 10 alleles per locus. • CONCLUSIONS: These novel polymorphic genic-SSR markers will aid in evaluating genetic diversity of boxwood germplasm and allow verification of hybrids and cultivars for breeding programs.