ARS | Publication request: FROM RAPDS TO SNPS: THE DEVELOPMENT OF MORE EFFECTIVE AND EFFICIENT MOLECULAR MARKERS IN CUCUMBER (CUCUMIS SATIVUS L.)

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 15, 2005
Publication Date: January 15, 2006
Citation: Robbins, M.D., Delannay, I.Y., Nam, Y., Staub, J.E. 2006. From RAPDS to SNPS: the development of more effective and efficient molecular markers in cucumber (cucumis sativus l.) [abstract]. Plant and Animal Genome Conference. p. 130.

Technical Abstract: The genetic base of cucumber is narrow (3-8%), and thus, the recovery of new markers from screening experiments is typically low. The majority of markers on current genetic linkage maps are RAPDs, which are inefficient for genotyping numerous individuals during marker-assisted selection (MAS). Therefore, we employed two methods to convert many of these RAPDs into more efficient (ability to multiplex) and effective (stable and codominant) SCAR, STS, and SNP markers. Firstly, 64 dominant RAPD bands were sequenced to create 22 (15 dominant, seven codominant) SCAR markers (34%). Ten SNP markers were created from the sequences of 16 (63%) non-polymorphic SCAR markers. Secondly, the amplicons of six dominant markers (five SCAR and one RAPD) linked to important yield traits with no internal SNPs were used to probe a cucumber BAC library to create adjacent markers. From 65 BAC end sequences, 10 STS (four codominant, six dominant) and nine SNP markers (29%) were created. The two methods yielded a total of 51 new markers. Of the 64 initial RAPDs, 33 (52%) were converted into SCARs, STS or SNPs and to date, 7 have proven effective and efficient in MAS.