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ARS Home » Southeast Area » Tifton, Georgia » Crop Genetics and Breeding Research » Research » Publications at this Location » Publication #309405
Title: Development and characterization of microsatellite markers for a little bluestem collection

Author
item Harris-Shultz, Karen
item Harrison, Melanie
item WADL, PHILLIP - University Of Tennessee
item TRIGIANO, R - University Of Tennessee
item Rinehart, Timothy - Tim

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2014
Publication Date: 12/31/2014
Citation: Harris-Shultz, K.R., Harrison, M.L., Wadl, P.A., Rinehart, T.A. 2015. Development and characterization of microsatellite markers for a little bluestem collection. Journal of the American Society for Horticultural Science. 140(1):78-87.

Interpretive Summary: Little bluestem is a native perennial grass that has been used as a forage for decades and only recently has become popular as an ornamental grass. With the national planting of only a few cultivars, we aimed to assess the ploidy level and genetic diversity of these widely used cultivars as well as the USDA National Plant Germplasm System collection. No sequence specific markers exist for little bluestem. Thus high throughput sequencing was used to generate 2812 primer sets that target sequences that contain repeats. 82 of these primer pairs were used to characterize the little bluestem accessions. The accessions examined could be classified into five groups and it was discovered that the little bluestem sequences are highly genetically similar despite the morphological variation seen in this species. These newly created markers can be used for further genetic studies or for identification of new cultivars.

Technical Abstract: Little bluestem (Schizachyrium scoparium) is a perennial bunchgrass that is native to North American prairies and woodlands from southern Canada to northern Mexico. Originally used as a grass for forage, little bluestem is now listed as a major United States native ornamental grass. With the widespread planting of only a few cultivars, we aimed to assess the ploidy level and genetic diversity among some popular cultivars and the USDA National Plant Germplasm System collection. Ten microsatellite markers, with successful amplification, were developed by using sequences available in Genbank and additional SSR markers were generated by using Ion Torrent sequencing of a genomic library created from the cultivar The Blues. A total of 2812 primer sets were designed from high throughput sequencing, 100 primer pairs were selected, and 82 of these primers were successfully amplified from the Schizachyrium accessions. The number of scored fragments per primer pair ranged from 0 (monomorphic) to 12 and only 35 primer pairs, generating 102 scored fragments, were polymorphic among S. scoparium accessions. Twenty-two primer pairs generated more than four fragments per accession. The use of a repetitive sequence identifier found that of 117 examined sequences only nine sequences did not have similarity to DNA transposons, retrotransposons, viruses, or satellite sequences. The most frequently identified fragments were the LTR retrotransposons Gypsy (177 fragments) and Copia (98 fragments), and the DNA transposon EnSpm (60 fragments). UPGMA cluster analysis of the SSR data for S. scoparium revealed five groups. Group I consisted of 13 accessions collected primarily from Texas. Group II consisted of 58 accessions including all of the forage cultivars as well as the ornamental cultivars Carousel and Blue Heaven. Group III and V consisted each of a single sample collected from Texas. Group IV consisted of a coastal little bluestem S. scoparium var littoralis. The lowest genetic similarity between little bluestem samples was 86% which was surprising due to the high degree of morphological variation seen in this species.