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ARS Home » Northeast Area » Washington, D.C. » National Arboretum » Floral and Nursery Plants Research » Research » Publications at this Location » Publication #334024
Title: Genetic diversity of Danthonia spicata (L.) Beauv. Based on genomic simple sequence repeat markers

Author
item THAMMINA, CHANDRA - Rutgers University
item AMUNDSEN, KEENAN - University Of Nebraska
item Bushman, Shaun
item Warnke, Scott

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2017
Publication Date: 4/1/2018
Citation: Thammina, C.S., Amundsen, K., Bushman, B.S., Warnke, S.E. 2018. Genetic diversity of Danthonia spicata (L.) Beauv. Based on genomic simple sequence repeat markers. Genetic Resources and Crop Evolution. 65:1059-1070. Available: https://link.springer.com/article/10.1007/s10722-017-0596-z.

Interpretive Summary: Danthonia spicata, commonly known as poverty oatgrass, is a widespread perennial grass often found in low input turf settings. It has potential to be developed into a low-input turf option in areas where it is adapted. Two important factors that impact the breeding and development of an uncultivated species into one for commercial use are the amount of diversity the species exhibits and its method of reproduction (outcrossing, self fertilizing, or clonal reproduction). DNA-based markers were used to determine the level of diversity that exists among 91 plants collected from 23 locations in Washington D.C., Virginia, Maryland, and North Carolina. The results suggest that variation does exist between and within the populations; however, a number of clonal plants were identified, indicating that the primary method of reproduction is clonally through seed. These findings will help to clear up some of the confusion that exists in the literature and lead to new strategies for developing varieties of poverty oatgrass that are suitable for cultivation in low-input landscape settings.

Technical Abstract: Danthonia spicata, commonly known as poverty oatgrass, is a perennial bunch-type grass native to North America. D. spicata has dimorphic seed heads; the hypothesis is that terminal seed heads allow some level of outcrossing and axial seed heads are only self-fertilized. However, there is no genetic evidence for heterozygosity and outcrossing in the literature. Our objective was to study the diversity and reproductive biology of D. spicata using genomic simple sequence repeat markers (genomic-SSRs). Roche 454 sequenced randomly sheared genomic DNA reads of D. spicata were mined for SSRs using the MIcroSAtellite identification tool (MISA). A total of 66553 singlet sequences (approximately 37.5 Mbp) were examined, and 3454 SSRs were identified, including 1584 mono-, 997 di-, 791 tri-, 57 tetra-, 18 penta-, and seven hexa-nucleotide repeats. 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. A total of 63 candidate markers were selected for testing from the trinucleotide SSR 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 from each of 23 different locations. They amplified a total of 54 alleles ranging in size from 71 to 246 bp. Minimum and maximum number of alleles per locus were 2 and 12, respectively, with an average of 5.4. A dendrogram based on simple sequence repeat data matched with the two main groups obtained by Structure v2.3. Fourteen multilocus genotype groups were observed, providing strong evidence for asexual reproduction in D. spicata. The presence of polymorphisms unique to individuals suggests somatic mutation may be generating variability.