What is the sentence structure uses after "that"?

The first is the plethora of small businesses, from family-run corner shops and ice-cream parlours to hardware stores, that by and large are as scruffy as they were back then, eke out a meagre existence and remain stubbornly cash-only.

We usually see , sub+ verb/ only verb after "that",but in this sentence, uses by after "that" and uses "and". How do construct this sentence? And waht is the meaning of sentence?