Rosdeep Kular, 33, is due to appear at the Edinburgh Sheriff's Court tomorrow over the death of Mikaeel Kular, who was reported missing on Wednesday evening, prompting a massive search operation.
Kular was detained on Friday night and arrested and charged yesterday after Mikaeel's body was found by officers in woodland behind her former home in Kirkcaldy, Fife, where she lived before moving to Edinburgh.
She was charged after almost 24 hours of questioning, as police confirmed the body was that of her missing son. The body was removed by officers for an autopsy.
Kular, a mother of five, told police that she put her son to bed at 9pm on Wednesday, but when she went to wake him up at 7:15am the following morning he was missing.
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She also said that on the night when Mikaeel allegedly disappeared, he was sleeping alone in the bedroom he normally shared with his twin sister Ashika.
It later emerged that Mikaeel had not been at his nursery school for almost a month because of an apparent chest infection.
Neighbours said they had not seen Mikaeel for some time and that the little boy's domestic circumstances were complex.
He had never met his biological father, who is of Pakistani origin, and his mother was estranged from her husband, Omotoso Adekunle Adekoya, 35, a taxi driver from Nigeria who lives nearby.
It has been claimed that the parents of her estranged husband had reservations about her lifestyle which they believe contributed to the collapse of her marriage.
Scotland's First Minister Alex Salmond said: "This is a tragic development in this harrowing story and the news that we have all been dreading.
"The hearts of everyone across Scotland and beyond have been touched by the events of recent days. We should at this difficult time remember the work of the officers of Police Scotland who have responded to this difficult task and investigation and shown such professionalism and dedication.