<p>Information on polymorphisms<br />among rice parents are very important in rice<br />breeding for tolerance to phosphorus defficiency. A study<br />was conducted at the Molecular Biology Laboratory,<br />Indonesian Center Agricultural Biotechnology and Genetic<br />Resources (ICABIOGRAD) from October 2006 to July 2007 to<br />identify polymorphism markers from 6 rice genotypes. The<br />rice genotypes, i.e., Dodokan, Situ Bagendit, Batur, Kasalath,<br />NIL-C443, dan K36-5-1-1 were analyzed for polymorphisms<br />using 496 SSR markers, which cover the rice genomes.<br />Seven of the 496 markers were used as foreground and<br />recombinant selection markers, and the rests (489 markers)<br />were used as background selection markers. PCR amplifications<br />were separated on a 5% polyacrylamide gel and<br />colored by the silver staining method. Three different markers<br />among the seven foreground and recombinant selection<br />markers were selected from each crossing, which are<br />tightly linked with Pup1 gene and have a distance less than 5<br />cM. These markers are Dodokan vs Kasalath (RM277, SSR3,<br />RM519), Dodokan vs NIL-C443 (RM277, SSR3, RM519),<br />Dodokan vs K36-5-1-1 (RM277, SSR3, RM519), Situ Bagendit<br />vs Kasalath (RM28102, SSR3, RM519), Situ Bagendit vs NILC443<br />(RM28102, SSR3, RM519), Situ Bagendit vs K36-5-1-1<br />(RM511, SSR3, RM519), Batur vs Kasalath (RM277, RM1261,<br />RM519), Batur vs NIL-C443 (RM277, RM1261, RM519), and<br />Batur vs K36-5-1-1 (RM28102, SSR3). Variations in background<br />selection primers were found in each chromosome<br />and in each parent combinations. Primers on chromosome<br />4, 5, and 12 showed the lowest polymorphisms; more<br />primers are needed for these chromosomes.</p>
A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel