Q1: What information can we get from the Marker ID?
A1: Each Marker ID consists of three parts. The first part is a single number from 1 to 5, standing for the specific chromosome on which the marker is located. The second part is the BAC accession number on NCBI (http://www.ncbi.nlm.nih.gov/), representing the BAC clone on which the marker is located. The third part is a four-digit number, indicating the relative physical location of the marker on the chromosome. With such a marker ID, researchers can quickly estimate the physical position of the marker.
Q2: How can we obtain clear gel picture with the AMP markers?
A2: Please use the recommended PCR condition for markers on AMP, which has been experimentally tested. If markers can't effectively amplify even in the recommended condition (sometimes happens for different PCR systems in different laboratories), we suggest researches try lower annealing temperature or additional Mg2+ or DMSO to optimize the PCR reaction. Furthermore, we recommend 4% agarose gel to be used for electrophoresis when PCR amplicons are less than 300bp. Sometimes, even higher concentrations of agrose should be used as the variation between Col-0 and Ler-0 is even smaller than 8bp.
Q3: How can we find the fine-mapping markers in the interval?
A3: There are several ways to find your interested markers on AMP.
Firstly, on the AMP homepage (http://amp.genomics.org.cn/), all the markers are arranged along the chromosomes according to their relative physical distances. Each red bar stands for an individual marker. With the two buttons in the lower left quarter, the scale can be magnified or reduced; and the greatest magnification is 28 fold. One can choose a suitable magnification at which the distribution of markers on chromosomes is clear, and obtain detailed information of each marker in the region of interest.
Secondly, if you have mapped the mutation to an interval with several BACs, it will be convenient to search markers on the "Marker" webpage, with your interested BAC name or its accession number on NCBI, and the detailed marker information will be shown on the right (see Figure 1). Thirdly, if you have known the physical region of your interval on the chromosome, you can click the "By Chromosome" button on the "Marker" webpage. Input the chromosome number and the base pair number of your interested region, and you will get all the markers in this interval, which are listed on the left (see Figure 2).
Lastly, if you want to see all the marker information on each chromosome, you can just input the chromosome number on the "By Chromosome" page and click the "search" button, then you will see all the markers of this chromosome on the left part (see Figure 3).
Q4: How can we find the mutant information in the mapping interval?
A4: To find a mutant, the most direct way is to check the mutant information on the AMP homepage. Each blue spot is represented an individual mutant from TAIR (http://www.arabidopsis.org/), Arabidopsis Hormone Database (AHD, http://ahd.cbi.pku.edu.cn/), the SeedGenes database (http://www.seedgenes.org/) or some published papers. With the two buttons in the lower left quarter, the scale can be magnified or reduced. The greatest magnification is 28 fold. One can choose a magnification level at which the distribution of mutants on the chromosomes is clear, and obtain detailed information of each mutant in your interested region.
Another direct way is to search the mutant information on the "mutant" page. Take the two boundary markers of your specific interval as the "Left Marker" and "Right Marker", respectively. Click the "Search" button and the mutants between them will be listed in the following part (see Figure 4). In addition, researchers can look for mutants with the physical distance (e.g., the base pair number) on the chromosome (see Figure 5).