The Johnstones had acquired the Elphinstone estates in c. 1450 by marrying the sole heiress Agnes of the last Laird, Alexander Elphinstone, who had been killed in the battle of Piperdean on 10 Sept 1435.  Agnes Elphinstone married Gilbert Johnstone, junior son of Adam of that Ilk, and the Elphinstone lands then passed to their Johnstone descendants.  The intervening generations to Mariota are not known, currently.

I have seen a suggestion that her parents were Andrew Johnstone of Elphinstone and Margaret Douglas (of an unknown family).  If that is correct, then Alec Findlater has examined the (Scots) Register of the Great Seal and produced a researched genealogy which supports this, assuming that Mariota can be inserted as the daughter of Andrew:

1. Agnes Elphinstone m. Gilbert Johnstone, a younger son of Adam J of that Ilk.  Gilbert d. aft. 1482.
|
2. Adam J, living 1498 and 1504, d. bef. 1512
|
3. Gilbert J, living 1512, d. bef.1531
|
4. Andrew J, living 1531, m. Margaret Douglas.  He died betw. 1550/65.
|__________________________
|                          |
5. James, d. by 1575   Mariota, d.1564 = David Home of Wedderburn, d. 1574
|__________________________
|                          |
6. James, d.aft 1587   Barbare  = (2) David Home of Godscroft

Andrew Johnstone of Elphinstone had another daughter Elizabeth who m. William Cranstoun of Cranstoun; see SP 2, p. 590.

The above 5. James Johnstone m. (1) c.1550, Margaret dau of William Ruthven (SP 4, p. 261), (2) c.1564 Jonet Melville, dau of John melville of Raith (see also SP 6, p. 95).
____________________