<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Dear Richard,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Yes, if you are working within a species and particularly if the strains you want to distinguish are closely related, microsatellite markers are probably the most informative markers to use. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>If there are not alot of microsatellites available for your species, you can always use AFLP, but a majority of the bands will not be informative, you know nothing about allelic relationships among bands, and you have only "dominant / recessive" information to work with.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The microsatellites are co-dominant, have multiple alleles per locus and are usually already mapped, so you usually get more information per marker from them.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I hope this is helpful.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Regards,</DIV><DIV>Susan McCouch</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><DIV>On Aug 31, 2006, at 11:13 AM, richard hampson wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2">Dear Sir/Madam</FONT></SPAN></DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2">When comparing closely related strains of the same grass species, is there any information as to which marker type is the most likely to be informatice. Are microsatellites the best bet?</FONT></SPAN></DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2">Thanks for your help, </FONT></SPAN></DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="459421015-31082006"><FONT face="Arial" size="2">Richard</FONT></SPAN></DIV> <DIV class="Section1"><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">Richard Hampson PhD<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">Oryzon Genomics<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">Parc Científic de Barcelona<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">Josep Samitier, 1-5<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">08028 Barcelona<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">Spain<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana"><O:P> </O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">phone: (34) 93 40 34 744<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">fax: (34) 93 40 34 792<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana"><O:P> </O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana">www.oryzon.com<O:P></O:P></SPAN></P><P class="MsoNormal"><SPAN style="FONT-FAMILY: Verdana"><O:P> </O:P></SPAN></P></DIV> <DIV> </DIV> <BR><P><FONT size="2">--<BR> No virus found in this outgoing message.<BR> Checked by AVG Free Edition.<BR> Version: 7.1.405 / Virus Database: 268.11.7/434 - Release Date: 30/08/2006<BR> </FONT> </P></BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>