Same as how breeders line breed specific traits... they just find the small percentage of fishes born naturally with shorter bodies (in the beginning it will be rare) and separate them to different tanks, then keep breeding only the shorter body ones and only picking the shorter body offspring, through many generations of breeding only the shorter bodied fishes, more and more of the offsprings also inherit the short body characteristics, then eventually there will be a stable line of short bodied versions of the fish.
Only thing with such line breeding is the inbreeding level is much higher and the gene pool becomes much smaller, so such intensively line bred fishes tend to be less hardy and more prone to deformities. Short bodied fishes also can't swim as fast or as agile as their normal versions, so their behaviors also change too.
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