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United States Department of Agriculture

Agricultural Research Service


Location: Crop Genetics and Breeding Research

Title: Development and characterization of seashore paspalum SSR markers

item Harris-shultz, Karen
item Raymer, Paul
item Scheffler, Brian
item Arias De Ares, Renee

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/19/2013
Publication Date: 9/27/2013
Citation: Harris-Shultz, K.R., Raymer, P., Scheffler, B.E., Arias De Ares, R.S. 2013. Development and characterization of seashore paspalum SSR markers. Crop Science. 53:2679-2685.

Interpretive Summary: Seashore paspalum is a warm season perennial turfgrass species of which many accessions or cultivars can grow in saline soils. The increasing use of secondary water sources for irrigation, which is highly linked to salinization, creates a demand for salt tolerant turf. The objective of our long term research is to identify the genetic regions from seashore paspalum that are associated with salt tolerance and to use and transfer this knowledge to other salt susceptible species. To accomplish this, molecular tools must be developed. We identified thousands of simple sequence repeats (SSR) which can be used as DNA markers. Eighty of these SSR markers were created and used to determine genetic relationships among seashore paspalum accessions/cultivars. Polyploids, those seashore paspalum accessions/cultivars which have genomes larger than a diploid, were identified in our study by genotyping and using a technique called flow cytometry. The information generated from this work is useful for population creation and genetic map construction, which is needed for the identification of regions associated with salt tolerance in seashore paspalum.

Technical Abstract: The increasing use of secondary water sources for irrigation, which is highly linked to salinization, creates a demand for salt tolerant turf. Seashore paspalum (Paspalum vaginatum Swartz) is a warm-season turfgrass that survives in sand dunes along coastal sites, brackish ponds, and in estuaries. Some seashore paspalum accessions/cultivars are far more salt tolerant than others. In order to identify genetic regions that are associated with salt tolerance, molecular tools must be developed. In this study, genomic libraries, enriched for microsatellites, were generated using the salt tolerant accession HI33. High throughput sequencing and subsequent assembling of these libraries resulted in 18,967 contigs and 158,595 singletons. The number of simple sequence repeats (SSR) detected in contigs and in singletons was 3,511 and 31,949, respectively, and the number of primer sets designed within each group was 937 and 1,667. A total of 80 SSR markers, including five markers previously developed, were used to assess genetic relationships among 18 Paspalum accessions. Two major clusters were identified from the seashore paspalum accessions. Accessions that are likely polyploids, all with coarse leaves, grouped together whereas accessions with fine-to mid-fine leaves formed a second group. Some cultivars, such as Seadwarf, Temple 2, SeaIsle 1, and Taliaferra reported to have been collected from all over the world, were found to be very genetically similar. Furthermore, 33 seashore paspalum SSR markers cross-amplify in bahiagrass (Paspalum notatum Flugge) and these markers can be a useful tool in this species.

Last Modified: 10/19/2017
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