Some varieties have to be picked green - as are certain, but not all, bell peppers - but ones that mature green have a gene that prevents the chlorophyll in the immature pepper from breaking down and going away when the pepper ripens. The retention of chlorophyll in the ripe pod is what causes an otherwise red ripe pepper to appear brown. Retention of chlorophyll in a yellow-ripe pepper causes it to mature green.Â
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You can make any brown pepper mature green by crossing it with a yellow pepper and then selecting for two recessive genes, the one that causes the yellow color and the one that causes chlorophyll retention. There are also various shades in between a mature light green and dark brown based on a combination of the immature pod color (a light yellow-green to a dark green due to how much chlorophyll the pods produce) and the mature pod color.