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Question one: Which of the following sentences are grammatically correct?

1) What differentiate apples from oranges are their colors and sizes.

2) What differentiates apples from oranges is their colors and sizes.

3) What differentiates an apple from oranges is its colors and sizes.

4) What differentiates an apple from oranges are their colors and sizes.

5) What differentiate apples and oranges are their colors and sizes.

Question two: Do you have any alternatives for the above sentences?

I've searched the web to understand which expression to use, but I could not find a specific rule.

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The choice between is and are here is investigated in Verb Agreement in English Wh-Clefts: A Corpus-Based Study_ Seung-Ah Lee; the precis states:

This paper presents a corpus-based analysis of verb agreement in English wh-clefts. The copula in wh-clefts displays a number agreement alternation if the focused element is a plural noun phrase, as in

“What we want is/are more books in the library”.

Pedagogical grammars that address this variation hold opposing views on which of the two variants is preferred in formal English.

To resolve this issue, the research for this paper examines the entire British National Corpus. An analysis of the present-tense copulas in the relevant wh-cleft constructions reveals that singular agreement is the predominant choice—the author’s analysis found 328 occurrences of singular (61.3%) versus 207 occurrences of plural (38.7%). However, in academic prose, the most formal register, the plural copula occurs slightly more frequently (56.6%) than the singular copula (43.4%). The preference for plural verb agreement in academic prose resembles the agreement pattern of there-constructions.

From this, I'd say that

2) What differentiates apples from oranges is their colors and sizes.

and

5') What differentiate apples from oranges are their colors and sizes.

(both with internal agreement)

are both acceptable. 'What' = 'the set of things that' in (2) and = ''things that' in (5').

1

it'd be better to say:
what differentiates between apples and oranges is their size and color.
the word "differentiate" refers to "what", therefore, takes an "s" at its end. there's no need to use plural form for "size and color", since you're talking about a single quality, i.e, comparing the color of an apple and orange.

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