In the wild, dogs grab each other by the scruff of the neck as a way of asserting dominance, and mothers grab their pups and carry them around this way. If you try to grab a dog by the scruff of the neck, you should be careful, as he'll instinctively interpret this as you asserting dominance over him -- and he may not like it.
Handling your own dog by the scruff, which you may have done from early in the dog's life, essentially reinforces that you're dominant over the dog. If you do this to an unfamiliar and/or agitated dog, though, he may not appreciate or agree with your assertion of dominance. According to the dog care professionals at the website Dog Care Guide, if your own pet growls at you, you may practice grabbing the scruff of his neck while maintaining eye contact to show that you are in control and unafraid. This can help you maintain the role of leader in your established relationship. An unfamiliar dog, however, may be inclined to see you as a threat and, when you go for the scruff, he could lash out and bite. Talk to a professional trainer before introducing this tactic into a training regimen.
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