1. Always use Parent Id instead of Parent.Id.

Example:
Use AccountId instead of Account.Id in the Query.

2. Use inner join query instead of using Parent object field reference. Make sure the parent object field is indexed for selective.

Example:

//Takes more time to execute
List < Contact > listContacts = [ 
    SELECT Id 
    FROM Contact 
    WHERE Account.Name = 'Test' 
];

//Takes less time to execute
List < Contact > listContacts1 = [ 
    SELECT Id 
    FROM Contact 
    WHERE AccountId IN ( 
        SELECT Id 
        FROM Account 
        WHERE Name = 'Test'
    ) 
];