Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Genetic Linkage Map Of Sugarcane (Saccharum spp.) Based On SRAP, TRAP And AFLP Markers

Sreedhar Alwala¹ , John C Veremis² , Kenneth A Gravois³ , Collins A Kimbeng¹

¹  Agronomy and Environmental Management, Louisiana State University, Baton Rouge, LA 70803 USA

² USDA-ARS, SRRC, Sugarcane Research Unit, 5883 USDA Rd, Houma, LA 70360 USA

³ St.Gabriel Sugar Research Station, Louisiana Agricultural Experimentation Station, 5755 LSU Ag. Rd, St.Gabriel, LA 70776 USA

Sugarcane cultivars are complex aneuploids/polyploids with chromosome numbers ranging from 100 - 140. They were derived from interspecific crosses involving Saccharum officinarum and S. spontaneum. The complex genome of sugarcane has been resolved using several molecular marker techniques. Sequence Related Amplified Polymorphism (SRAP) and Target Region Amplification Polymorphism (TRAP) are two relatively new PCR-based marker techniques. SRAP primers are 17 to 18 nucleotides long and are supposedly designed to amplify open-reading frames. The primers consist of 10 to 11 filler sequences at the 5’ end followed by either AATT or CCGG, which are believed to target introns or exons, respectively. The 3’ end consists of three selective nucleotides. In TRAP markers, one primer is designed from EST or gene sequences while the other is similar to a SRAP primer. We are constructing a linkage map of sugarcane using SRAP, TRAP and AFLP markers. Eighty-eight individuals from a cross between La Stripe (S. officinarum) x SES147B (S. spontaneum) have been screened using 33 SRAP, 17 TRAP and 10 AFLP primer combinations. Polymorphic markers were scored for SRAP (185), TRAP (87) and AFLP (130). Single dose markers (103 for SRAP; 61 for TRAP and 93 for AFLP), segregating in a 1:1 ratio, were used to construct the map using a LOD score of 3.0 to 7.0, a threshold recombination value of 0.4 and the Kosambi mapping function. Of the 257 single dose markers mapped so far, 131 grouped into 43 cosegregation groups covering 1451 cM of genome with an average of approximately 10 cM between any two linked markers.