Jason Ayto has been working under the Brazilian former midfielder, who is departing his role at sporting director.
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Edu tendered his resignation on Monday, having rejected a significant pay rise.
He is set to take a big role for businessman Evangelos Marinakis, who owns Nottingham Forest, Olympiacos and Portugal’s Rio Ave.
Per The Mirror, Ayto is emerging as a serious candidate for Edu’s vacated post at Arsenal.
The club are considering bringing in someone from the outside, but may stick with the internal option instead.