This post explains how to perform the genome browsing in the proximity of quantitative trait loci (QTL) identified through genome wide associated studies (GWAS). Naturally, performing a GWAS is a prerequisite for using this feature. If you want to learn about the GWAS procedure, you can find a step-by-step guide here: https://open.qtlmax.com/guide/wp-admin/post.php?post=302&action=edit
Figure 1 shows the “Genome browse” tab in which a set of GWAS output files were selected, and all required configuration fields are filled out.
The field labeled with “P cutoff” is for a P value threshold value to define QTL; the fields labeled with “Left margin (bp)” and “Right margin (bp)” define the window size by adding the left and right distances from a QTL marker (SNP). The combo box under the “Gbrowse servers” shows a list of gbrowse database servers. You can select a database upon a crop species you are working on. With all settings configured, pressing the [Execute] button will pop up a web browser as shown in Figure 2. Alongside with it, an item relevant to this work will be additionally listed as shown in Figure 1; each created item is clickable, allowing you to revisit the results later as needed.
(Figure 1)
Figure 2 shows a web browser popped up, which displays a list of QTL markers that met the specified P-value threshold. Each record per QTL marker has a button.
(Figure 2)
Clicking the button opens a new tab where you can view the genomic window on the genome browser server (Figure 3).
(Figure 3)
QTLmax 6.0. further supports mapping QTL markers on chromosomes. To this end, you need to use Qmapper. On the right-bottom of the current QTLmax tab page, there is button called [Qmapper]. (Figure 4)
(Figure 4)
If you press the [Qmapper] button, a new window form called “QTLmax Mapper” will pop up. (Figure 5) For more details, please visit here: https://open.qtlmax.com/guide/index.php/2026/02/09/physical-mapping-of-snps/
(Figure 5)