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ARS Home » Northeast Area » Washington, D.C. » National Arboretum » Floral and Nursery Plants Research » Research » Publications at this Location » Publication #251578
Title: Miniature inverted-repeat transposable element identification and genetic marker development in Agrostis

Author
item Amundsen, Keenan
item ROTTER, DAVID - Rutgers University
item JUNG, GEUNHWA - University Of Massachusetts
item BELANGER, FAITH - Rutgers University
item Warnke, Scott

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2012
Publication Date: 3/16/2012
Citation: Amundsen, K.L., Rotter, D., Jung, G., Belanger, F., Warnke, S.E. 2012. Miniature inverted-repeat transposable element identification and genetic marker development in Agrostis. Crop Science. 51:854-861.

Interpretive Summary: Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. DNA marker development in creeping bentgrass species is difficult. In the present study, DNA-based markers anchored to a class of mobile genetic elements (miniature inverted-repeat transposable elements; MITEs) were developed and evaluated for their use to study creeping bentgrass. The software program FindMITE, designed to identify MITEs from DNA sequences, identified 495 candidate MITEs from a set of 16,122 publicly available creeping bentgrass and colonial bentgrass DNA sequences. The software program may identify sequences that are not necessarily MITEs, so experiments were designed to test for evidence of mobilization that indicates the presence of a true MITE. There was evidence of mobilization in 79 of the candidate MITEs and DNA markers were developed to a subset of these MITEs. This is the first report of MITEs and MITE-based DNA marker development in creeping bentgrass. The novel marker system was also shown to behave normally in an experimental creeping bentgrass mapping population. This new class of DNA-based markers provides more resources for researchers studying the creeping bentgrass genome.

Technical Abstract: Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. A. stolonifera is a highly outcrossing allotetraploid making genetic marker development difficult in this species. In the present study, genetic markers anchored to miniature inverted-repeat transposable elements (MITEs) were developed and evaluated for their use to study Agrostis species. The FindMITE software program identified 495 candidate MITEs from 14,796 EST and 1,326 random sheared genomic DNA Agrostis sequences. There was evidence of transposition in 79 of the candidate MITEs based on MITE insertional polymorphisms, the first report of MITEs in this species. Genetic markers were developed from a subset of these 79 MITEs by MITE-display, a modified amplified fragment length polymorphism (AFLP) technique that anchors amplified fragments to MITEs. Four MITE-display primer combinations were screened against an Agrostis experimental mapping population and 139 polymorphic markers were developed (PIC=0.33). Twenty-eight of the polymorphic genetic markers segregated normally in the experimental mapping population. MITE-display genetic markers are a new class of genetic markers for studies of the Agrostis genome and are a resource for the development of a more detailed genetic linkage map of A. stolonifera.