Using Common Gardens and AFLP Analyses to Identify Metapopulations of Indigenous Plant Materials for Rangeland Revegetation in Western USA

Past mismanagement, overgrazing, invasive weedy species, wildfires, marginal crop production, mineral and energy extraction, recreation and global climate change are challenges currently facing rangelands (Pierson et al. 2011). These disturbances may lead to long-term reductions in biodiversity, altered nutrient and water cycling, diminished forage production for livestock and wildlife, increased wildfire frequency and increased soil erosion and stream sedimentation (Sheley et al. 2008). Rangeland revegetation with desirable plant materials may be required to improve degraded conditions, speed recovery, and prevent further erosion and degradation. There is a critical need for plant materials to restore and revegetate rangeland ecosystems. Legumes indigenous to western North America are of particular interest for revegetation because they provide biologically fixed nitrogen, increase plant production, enhance forage quality and provide food sources for grazing animals and pollinators. Some land managers in the USA are concerned with the genetic identity of populations used for revegetation. To balance concerns of genetic identity, ecological adaptation, and economical seed production, we assessed genetic variation and its phenotypic expression in Astragalus filipes Torr. ex A. Gray (basalt milkvetch), Dalea ornata (Douglas) Eaton & Wright (western prairie clover) and D. searlsiae (A. Gray) Barneby (Searls’ prairie clover) using common-garden and AFLP (amplified fragment length polymorphism) techniques. These data were used to define population structures (genetically differentiated groups) within each species, which served as a basis for commercial release and rangeland revegetation (Johnson et al. 2012)

Genetic diversity of \u3ci\u3eDanthonia spicata\u3c/i\u3e (L.) Beauv. based on genomic simple sequence repeat markers

Danthonia spicata (L.) Beauv., commonly known as poverty oatgrass, is a perennial bunch-type grass native to North America. D. spicata is often found in low input turfgrass areas on the East Coast of the United States and has potential for development as a new native low input turfgrass species. Roche 454 sequenced randomly sheared genomic DNA reads of D. spicata were mined for SSR markers using the MIcroSAtellite identification tool. A total of 66,553 singlet sequences (approximately 37.5 Mbp) were examined, and 3454 SSR markers were identified. Trinucleotide motifs with greater than six repeats and possessing unique PCR priming sites within the genome, as determined by Primer-BLAST, were evaluated visually for heterozygosity and mutation consistent with stepwise evolution using CLC Genomics software. Sixty-three candidate markers were selected for testing from the trinucleotide SSR marker sites meeting these in silico criteria. Ten primer pairs that amplified polymorphic loci in preliminary experiments were used to screen 91 individual plants composed of at least 3–5 plants from each of 23 different locations. The primer pairs amplified 54 alleles ranging in size from 71 to 246 bp. Minimum and maximum numbers of alleles per locus were two and 12, respectively, with an average of 5.4. A dendrogram generated by unweighted pair group method with arithmetic mean cluster analysis using the Jaccard’s similarity coefficient was in agreement with the grouping obtained by Structure v2.3. The analyses were dominated by clonal groupings and lack evidence for gene flow with some alleles present in a single plant from a single location. Fourteen multilocus genotype groups were observed providing strong evidence for asexual reproduction in the studied D. spicata populations

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties

Genetic diversity of \u3ci\u3eDanthonia spicata\u3c/i\u3e (L.) Beauv. based on genomic simple sequence repeat markers

Danthonia spicata (L.) Beauv., commonly known as poverty oatgrass, is a perennial bunch-type grass native to North America. D. spicata is often found in low input turfgrass areas on the East Coast of the United States and has potential for development as a new native low input turfgrass species. Roche 454 sequenced randomly sheared genomic DNA reads of D. spicata were mined for SSR markers using the MIcroSAtellite identification tool. A total of 66,553 singlet sequences (approximately 37.5 Mbp) were examined, and 3454 SSR markers were identified. Trinucleotide motifs with greater than six repeats and possessing unique PCR priming sites within the genome, as determined by Primer-BLAST, were evaluated visually for heterozygosity and mutation consistent with stepwise evolution using CLC Genomics software. Sixty-three candidate markers were selected for testing from the trinucleotide SSR marker sites meeting these in silico criteria. Ten primer pairs that amplified polymorphic loci in preliminary experiments were used to screen 91 individual plants composed of at least 3–5 plants from each of 23 different locations. The primer pairs amplified 54 alleles ranging in size from 71 to 246 bp. Minimum and maximum numbers of alleles per locus were two and 12, respectively, with an average of 5.4. A dendrogram generated by unweighted pair group method with arithmetic mean cluster analysis using the Jaccard’s similarity coefficient was in agreement with the grouping obtained by Structure v2.3. The analyses were dominated by clonal groupings and lack evidence for gene flow with some alleles present in a single plant from a single location. Fourteen multilocus genotype groups were observed providing strong evidence for asexual reproduction in the studied D. spicata populations

Transcriptome profiling of Kentucky bluegrass (\u3ci\u3ePoa pratensis\u3c/i\u3e L.) accessions in response to salt stress

Background: Kentucky bluegrass (Poa pratensis L.) is a prominent turfgrass in the cool-season regions, but it is sensitive to salt stress. Previously, a relatively salt tolerant Kentucky bluegrass accession was identified that maintained green color under consistent salt applications. In this study, a transcriptome study between the tolerant (PI 372742) accession and a salt susceptible (PI 368233) accession was conducted, under control and salt treatments, and in shoot and root tissues. Results: Sample replicates grouped tightly by tissue and treatment, and fewer differentially expressed transcripts were detected in the tolerant PI 372742 samples compared to the susceptible PI 368233 samples, and in root tissues compared to shoot tissues. A de novo assembly resulted in 388,764 transcripts, with 36,587 detected as differentially expressed. Approximately 75 % of transcripts had homology based annotations, with several differences in GO terms enriched between the PI 368233 and PI 372742 samples. Gene expression profiling identified salt-responsive gene families that were consistently down-regulated in PI 372742 and unlikely to contribute to salt tolerance in Kentucky bluegrass. Gene expression profiling also identified sets of transcripts relating to transcription factors, ion and water transport genes, and oxidation-reduction process genes with likely roles in salt tolerance. Conclusions: The transcript assembly represents the first such assembly in the highly polyploidy, facultative apomictic Kentucky bluegrass. The transcripts identified provide genetic information on how this plant responds to and tolerates salt stress in both shoot and root tissues, and can be used for further genetic testing and introgression

Variation and Correlations among European and North American Orchardgrass Germplasm for Herbage Yield and Nutritive Value

Efforts to improve water-soluble carbohydrate (WSC) concentrations are common in perennial forage grass breeding. Perennial ryegrass (Lolium perenne) breeding has been very successful in developing new cultivars with high WSC and high agronomic performance. Breeding efforts are ongoing to improve the WSC of other perennial forage grasses, such as orchardgrass (Dactylis glomerata). The United States Department of Agriculture Forage and Range and Deutsche Saatveredelung orchardgrass breeding programs cooperated to characterize the expression and genotype by environment interaction (GEI) of water-soluble carbohydrates in a collection of orchardgrass populations from both breeding programs. Additionally, the effort characterized the relationship between water-soluble carbohydrates and other agronomic and nutritive value traits in these populations. Overall, the Deutsche Saatveredelung populations had higher herbage mass (15%), rust resistance (59%), and later maturity. The Forage and Range Research populations had higher water-soluble carbohydrates (4%), nutritive value, and earlier maturity. However, results were highly dependent on GEI. Differences were very pronounced at the French and German field locations, but less pronounced at the two US locations. Combining the germplasm from the Forage and Range Research and Deutsche Saatveredelung programs may be a way to develop an improved base germplasm source that could then be used separately in the EU and US for water-soluble carbohydrate and other trait improvement

Phenotypic and Genetic Characterization of Western Prairie Clover Collections From the Western United States

Few North American legumes are available for rangeland revegetation in the semiarid western United States. Western prairie clover (Dalea ornata [Douglas ex Hook.] Eaton J. Wright) is a perennial legume with desirable forage characteristics and is distributed in the northern Great Basin, Snake River Basin, and southern Columbia Plateau. Understanding the genetic and ecotypic variability of this species is a prerequisite for developing populations suitable for revegetation purposes. To address this need, we established two common-garden plots of western prairie clover from 22 sites in Idaho, Oregon, and Washington. Significant variation was detected among the collections for all traits measured. Among the measured traits, flowering date was correlated with collection-site temperature and elevation. Population structure estimates from 474 amplified-fragment length polymorphism markers resulted in two distinct, genetically differentiated groups and a third admixed group, and flowering date played a significant role in discriminating those genetic-based groupings of collections. Positive correlations were observed between phenotypic and genetic distance matrices (r = 0.33, P = 0.005), phenotypic and geographic distance matrices (r = 0.35, P = 0.002), and genetic and geographic distance matrices (r = 0.31, P = 0.009). Based on these results, we recommend that two germplasm sources of western prairie clover be developed for use across the collection area, one from the Deschutes River region and the other encompassing Idaho, Washington, and eastern Oregon collection sites. The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform August 202