A. Millie Burrell

Genetic analyses of nickel tolerance in a North American serpentine endemic plant, Caulanthus amplexicaulis var. barbarae (Brassicaceae)

PREMISE OF THE STUDY The evolution of metal tolerance in plants is an important model for studies of adaptation to environment, population genetics, and speciation. Here, we investigated nickel tolerance in the North American serpentine endemic Caulanthus amplexicaulis var. barbarae in comparison with its nonserpentine sister taxon C. amplexicaulis var. amplexicaulis. We hypothesized that the serpentine endemic would have a heritable growth advantage on nickel-containing substrates. METHODS We employed an artificial growth assay to quantify biomass accumulation. Study plants were crossed to create an F(2:3) population that was used to determine the heritability of nickel tolerance and to map quantitative trait loci (QTL). Nickel accumulation in both laboratory populations and native specimens was examined using energy-dispersive x-ray fluorescence (EDXRF). KEY RESULTS The serpentine endemic had a dramatic growth advantage at concentrations of nickel >30 µmol/L. Caulanthus amplexicaulis var. barbarae and its nonserpentine sister taxon both accumulated nickel to substantial levels. Nickel tolerance was highly heritable (h(2) = 0.59) and not associated with accumulation. The QTL analyses identified two major loci for nickel tolerance, on linkage group 2 (LG2) and linkage group 9 (LG9). CONCLUSIONS In our study, nickel tolerance was determined by two major loci with large effects. At both loci, alleles from the serpentine parent conferred positive effects on nickel tolerance, suggesting that they are adaptive in the natural serpentine environment. The mechanism of nickel tolerance in the serpentine plant was not exclusion of nickel. Nickel tolerance may have an inducible component in C. amplexicaulis var. barbarae.

A comparative genomic map for Caulanthus amplexicaulis and related species (Brassicaceae)

Adaptation to environment is the cornerstone of ecological genetics. The subject of this study is a wild relative of the sequenced and annotated model plant species, Arabidopsis thaliana. Caulanthus amplexicaulis var. barbarae lives on serpentine soils, known for high concentrations of heavy metals and low concentrations of essential plant macronutrients, and provides a compelling example of an organism’s adaptation to environment. We constructed an F2 linkage map, using a cross to the nonserpentine sister taxon, C. amplexicaulis var. amplexicaulis. C. amplexicaulis is a member of a highly diverse set of taxa (within the tribe Thelypodieae), described here as the ‘Streptanthoid Complex’ that are adapted to a broad range of environments, yet share a common n = 14 chromosome number and likely arose by a recent radiation. The linkage map consists of 97 polymorphic microsatellite markers, and 40 exon‐primed intron‐crossing markers based on A. thaliana exon sequences and Brassica ESTs. The map covers 14 linkage groups and has a total length of 1513 cM. Both the patterns of marker segregation and the comparative map indicate that C. amplexicaulis is a diploid organism with a compact genome. All exon‐primed intron‐crossing markers, and an unexpectedly large number of microsatellite markers (83%), had significant similarity to the A. thaliana genome, facilitating the development of a comparative genome map. As a proof of principle, we used the comparative map to identify candidate genes underlying differences in sepal colour between the two parent taxa. We demonstrate that the genomic tools developed here will be portable throughout the Streptanthoid Complex.

Exploring origins, invasion history and genetic diversity of Imperata cylindrica (L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing

Imperata cylindrica (Cogongrass, Speargrass) is a diploid C4 grass that is a noxious weed in 73 countries and constitutes a significant threat to global biodiversity and sustainable agriculture. We used a cost‐effective genotyping‐by‐sequencing (GBS) approach to identify the reproductive system, genetic diversity and geographic origins of invasions in the south‐eastern United States. In this work, we demonstrated the advantage of employing the closely related, fully sequenced crop species Sorghum bicolor (L.) Moench as a proxy reference genome to identify a set of 2320 informative single nucleotide and insertion–deletion polymorphisms. Genetic analyses identified four clonal lineages of cogongrass and one clonal lineage of Imperata brasiliensis Trin. in the United States. Each lineage was highly homogeneous, and we found no evidence of hybridization among the different lineages, despite geographical overlap. We found evidence that at least three of these lineages showed clonal reproduction prior to introduction to the United States. These results indicate that cogongrass has limited evolutionary potential to adapt to novel environments and further suggest that upon arrival to its invaded range, this species did not require local adaptation through hybridization/introgression or selection of favourable alleles from a broad genetic base. Thus, cogongrass presents a clear case of broad invasive success, across a diversity of environments, in a clonal organism with limited genetic diversity.

Discovery of nuclear and plastid microsatellites, and other key genomic information, in the rare endemic plant ( Caulanthus amplexicaulis var. barbarae ) using minimal 454 pyrosequencing

Next-generation Roche 454 pyrosequencing was used to rapidly identify 149 novel nuclear microsatellite loci and five plastid microsatellites from non-enriched genomic DNA of the rare endemic Santa Barbara Jewelflower (Caulanthus amplexicaulis var. barbarae). Analysis of this dataset showed a high level of orthology to annotated genes of the model plant Arabidopsis thaliana, as well as low levels of repetitive DNA sequences (particularly transposon-like elements). Thus, a modest sequencing effort using the 454 (or equivalent long-read platform) is a cost-effective and highly informative first step in the development of molecular-genetic resources for a non-model organism.

Allelic variants in the PRR37 gene and the human-mediated dispersal and diversification of sorghum

Key messageAllele phylogenetic analysis of the sorghum flowering-time genePRR37provided new insight into the human-mediated selection of a key adaptive gene that occurred during sorghum’s diversification and worldwide dispersal.AbstractThe domestication and spread of the tropical cereal sorghum is associated with the historic movement of humans. We show that an allelic series at PRR37 (pseudo-response regulator 37), a circadian clock-associated transcription factor, was selected in long-day ecosystems worldwide to permit floral initiation and grain production. We identified a series of loss-of-function (photoperiod-insensitive) alleles encoding truncated PRR37 proteins, alleles with key amino acid substitutions in the pseudo-receiver domain, and a novel splice variant in which the pseudo-receiver domain is truncated. Each PRR37 allelic variant was traced to a specific geographic location or specialized agronomic type. We present a graphical model that shows evidence of human selection and gene flow of the PRR37 allelic variants during the global dispersal and agronomic diversification of sorghum. With the recent identification of the Ghd7 gene as an important regulator of flowering date in sorghum, we briefly examine whether loss-of-function Ghd7 allelic variants were selected prior to the human-mediated movement of sorghum from its equatorial center of origin to temperate climates worldwide.

Potential Biological Control Agents for Management of Cogongrass (Cyperales: Poaceae) in the Southeastern USA

Abstract Cogongrass, Imperata cylindrica (L.) Palisot de Beauvois (Cyperales: Poaceae), is a serious invasive weed in the southeastern USA. Surveys for potential biological control agents of cogongrass were conducted in Asia and East Africa from 2013 to 2016. Several insect herbivores were found that may have restricted host ranges based on field collection data and life histories. Stemborers in the genus Acrapex (Lepidoptera: Noctuidae) were collected from cogongrass in Tanzania, Uganda, and Japan. In the Philippines, larvae of Emmalocera sp. (Lepidoptera: Pyralidae) and Chilo sp. (Lepidoptera: Crambidae) were found boring in cogongrass. Cecidomyiid midges were found in both Japan and Indonesia. A Japanese midge identified as a Contarinia sp. (Diptera: Cecidomyiidae) caused deformation of the stem, whereas the Indonesian midge Orseolia javanica Kieffer & van Leeuwen-Reijinvaan (Diptera: Cecidomyiidae) induced the formation of a basal stem gall. Previous research suggested that the host range of O. javanica was restricted to cogongrass.

Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

Abstract Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.