ARS | Publication request: IDENTIFICATION OF POLYMORPHISMS USING RNASEH-LTR REGIONS OF THE TY1-COPIA RETROTRANSPOSONS IN WATERMELON ACCESSIONS

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: November 30, 2003
Publication Date: January 10, 2004
Citation: Reddy, U.K., Saha, S., Nimmakayala, P., Katam, R., Levi, A. 2004. Identification of polymorphisms using rnaseh-ltr regions of the ty1-copia retrotransposons in watermelon accessions. Plant and Animal Genome XII Conference Proceedings. Abstract. pg. 329.

Technical Abstract: Retrotransposons are present in high copy number in many plant genomes and they show considerable degree of sequence heterogeneity and insertional polymorphism, both within and among species. The extremely high variability of Ty1-copia retrotransposons in several other crop genomes including pea, broad bean, Ipomoea, Vitis, Medicago and carrot warrants the current investigation. A large number of fragments that contain RnaseH-LTR regions of the Ty1-copia were amplified and cloned by following procedures developed by Pearce et al, 1999. Some modifications to the original method include hybridization of biotinylated gene-specific degenerate oligo and subsequent stringent washes of streptavidin coated paramagnetic beads after affinity separation. A PCR with nested primer from second RnaseH motif followed this capture. A study of putative transposon insertion sites and the resultant genetic variability is underway using terminal sequences of long-terminal repeats (LTR) using S-SAP (sequence-specific amplified polymorphism) in a set of watermelon genotypes. A genetic linkage map is currently available (Levy et al., 2002) for watermelon using a testcross population [Plant Accession Griffin 14113 (C. lanatus var. citroides) x New Hampshire Midget (NHM); Citrullus lanatus var. lanatus)] x U.S. Plant Introduction (PI) 386015 (C. colocynthis). As this map consists of RAPD and ISSR markers, further integration of PCR based markers based on insertional polymorphism will be useful to locate important genes.