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Title: Short-read DNA sequencing yields microsatellite markers for Rheum

Author
item Gilmore, Barbara
item Bassil, Nahla
item Barney, Danny
item KNAUS, BRIAN - Forest Service (FS)
item Hummer, Kim

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2013
Publication Date: 1/1/2014
Citation: Gilmore, B.S., Bassil, N.V., Barney, D.L., Knaus, B.J., Hummer, K.E. 2014. Short-read DNA sequencing yields microsatellite markers for Rheum. Journal of the American Society for Horticultural Science. 139:22-29.

Interpretive Summary: Identifying culinary rhubarb cultivars using physical characteristics is difficult. Individuals vary in appearance because of the environment, plant age, and other factors. There are multiple cultivar names for the same genotype, and the seedlings may look similar to a parent. Other investigators have reported on genetic fingerprinting techniques for rhubarb. Our project tried a different type of marker than previously reported. We created microsatellite markers for fingerprinting the USDA ARS clonal rhubarb collection. We also physically evaluated 47 rhubarb accessions for descriptive information. The accessions exhibited substantial variability with wide overlap between different accessions in terms of many characters including petiole and leaf blade dimensions and total soluble solids and pH of the petiole juice. These results suggest that identifying genetic identity and relationships based on morphological and phytochemical characteristics is unreliable. Our marker results were compared with a previous report of identifying genetic relationships. Our results produced a family tree of the relationships between cultivars.

Technical Abstract: Identifying culinary rhubarb (Rheum ×hybridum Murray) cultivars using morphological characteristics is problematic due to variability within individual genotypes, variation caused by environmental factors, plant and leaf age, similarity between genetically diverse genotypes, multiple cultivar names for the same genotype, and the existence of genetically similar seedlings arising intentionally or accidently from cultivars. Other investigators previously reported on genetic fingerprinting techniques for Rheum, including Randomly Amplified Polymorphic DNA markers (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Inter-Simple Sequence Repeats (ISSRs), and Simple Sequence Repeats (SSRs). The project described here expands the use of SSRs for identification of culinary rhubarb and details the sequencing methods used to create microsatellites for fingerprinting the USDA ARS clonal Rheum collection. We also made physical evaluations of 47 of the Rheum accessions used in these SSR trials. The accessions exhibited substantial intra- and interaccession variability with wide overlap between different accessions in terms of petiole and leaf blade dimensions and total soluble solids and pH of the petiole juice. These results suggest that identifying genetic identity and relationships based on morphological and phytochemical characteristics is unreliable. Our SSR results were compared with a previous attempt to identify genetic relationships between Rheum clonal accessions using morphological and phytochemical characteristics and AFLPs. The SSR results produced a dendrogram in which accessions clustered similarly to those produced using AFLPs.