Rice Genetics IV - IRRI books - International Rice Research Institute

Association between SSRs and transposable elementsPoly(AT)n SSRs were frequently found in association with dispersed miniature invertedrepeat transposable elements (MITEs) in rice, and this was postulated to helpexplain the low amplification frequency of this particular motif (Temnykh et al 2001).MITE sequences that reside in regions flanking the poly(AT)n motifs may form hairpinstructures that make it difficult for SSR primer pairs to bind to the DNA. Whenbinding does occur, primers in these regions may recognize many targets dispersedthroughout the genome and this results in weak or smeared amplification patterns. Asa consequence of this finding in rice, BAC end sequences homologous to knownrepetitive elements or to other BAC end sequences are considered poor templates forSSR marker development.Genetic mapping with SSR markersCurrently, more than 500 microsatellite markers have been integrated into the existinggenetic map of rice (Fig. 4). This provides an average density of one SSR markerevery 4 cM on the IR64/Azucena doubled-haploid (DH) map (Guiderdoni et al 1992,Huang et al 1994). As more genomic sequence information becomes available forrice, additional polymorphic microsatellite markers can be easily designed to saturatethe genetic map at predicted densities of one SSR per 20–50 kb, and, in regions ofparticular interest or where overall polymorphism is not a limiting factor, higher densitycoverage (up to one SSR per 3–10 kb) is likely. Most SSR markers can be mappedas co-dominant single-locus markers and have easily scoreable banding patterns.Among the markers mapped in our laboratory, a total of ten (RM4, RM20, RM81,RM233, RM238, RM456, RM464, RM465, RM473, and RM476) amplified complexbanding patterns, which segregated independently and mapped to multiple loci.All markers genetically mapped in our laboratory were assigned RM locus namesaccording to the following nomenclature guidelines: RM1–100 indicate markers froma randomly sheared library made from cv. IR36 (Panaud et al 1996) (with RM1–59for di-nucleotides, RM60s for tetra-nucleotides, and RM70s and RM80s for ATT andTCT, respectively); RM101–199 indicate markers derived from EST sequences inGenBank; RM201–350 indicate markers from the Tsp509-digested library, withRM201–320 for poly-di-nucleotides and RM321–345 for poly-tri-nucleotides;RM346–351 indicate markers from other genomic libraries; and RM 400–600 indicatemarkers derived from BAC end sequences. Markers that mapped to more thanone locus were given a suffix (A, B, C) following the RM designation.Information about all microsatellite markers developed in the author’s laboratoryis available at the Gramene Web site (http://www.gramene.org/). Available data includethe locus name, GenBank ID, accession number, clone name, SSR motif description,primer sequences, and polymorphism survey results, including allele number,PIC value, and allele molecular weight range based on a panel of 13 O. sativagenotypes described in Cho et al (2000). Markers identified in our automated searchesthat showed sequence similarity to those previously reported by Akagi et al (1996)124 McCouch et al