This analysis allows assessment of the stability of performance of lines in a population (or panel of unrelated lines) over multiple environments. In the dialog, you will use the trait list to select the traits to be analyzed (of course they will be not different traits, but evaluations of the same trait in more than one environment) and view the dot plot showing their phenotypic score arrays, distributed along vertical axes rising from points on the x-axis placed at the environment means. Selection cutoff points are shown for traits under selection. A white line connects the points representing the environment means.
The medium gray contour in the plot at bottom shows for each line the slope of the regression of its scores on the environment means, representing its environmental responsiveness (R) or inverse stability. The light gray contour shows its mean performance (P) over environments and the dark gray one the product of PxR, while each of the remaining contours shows its performance in one of the environments and is color-coded to match the name of that environment in the trait list. Each of these stats is scaled to its range over all the lines, so that all contours can fit into the same plot. In QGene, you drag in the line list, dot plot, or contour plot to view the performance of each line in every environment. Holding down the Shift key as you do this will suppress erasing. Option-click on a trait in the trait list to sort the population on performance for that trait (environment). Click in the uniplots of response, performance, or PxR to view them as histograms or (if the Command key is held down) just to sort the population on either statistic, causing the contours to be redrawn to correspond. When, for example, the population is sorted on performance, dragging with the mouse from left to right across the contour shows regression lines whose pivot point steadily descends in the plot, while when the lines are sorted on response, the slopes of the regression lines decrease steadily from positive to negative.
When you run QGene, you'll click the Save as trait button to store the current statistic in the Transformed trait for marker analysis, choose File/Save data to save the stability stats for the current set of environments, choose Edit/Show all to show all of the regression lines, and choose either of the two Edit/Copy menu items to export graphics.
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