I'm sure this has been discussed at length, but I cannot find discussions on it, nor recall if there was a consensus, and what it was.
Suppose I use a Muto spell of sufficient duration to change a plant into one of a different type - say an apple tree into an orange tree. Then, I wait for the plant to bloom and bear fruit. I harvest the fruits, and let the spell expire. What type of fruit do I get, apples or oranges?
As a game balance issue, I would like to point out that if you allow the fruits to be natural, whether natural apples or natural oranges, you open the door to some very unsettling get-quick-rich schemes in the hands of the wrong player, probably followed by a flurry of new rulings at Tribunals...
Because what goes for apples and oranges must, logically, extend to animals as well. So if you get apples, your unscrupulous player could Muto a cow and bull into a couple of rabbits, and a few weeks later sell a dozen newborn calves, instead of the months it normally takes to get only one. Apart from the value involved, it's vis-less creation of natural food 
And if you get oranges it is even worse : take a couple of rabbits and breed yourself any animal you want in creation. Did I say animal ? I meant creature. Muto those rabbits into dragons, and you can breed real dragons, once again without spending vis.
So unless you are sure of your players' intent (a few oranges won't do much harm), I would rule that the result, whether apples or oranges, is warped and seedless, and probably some strange hybrid of apples and oranges, unless the player do some experimental research to get something which at least resembles oranges. And if you translate that to animals, I would rule the result a strange, sterile hybrid of the natural and Mut-ated creatures that promptly dies unless the creatures were close enough for an hybrid to begin with (like mules, or tiglons).
There's also the question of other Muto-like changes. I played a shapeshifter Redcap in one saga who had grown up mostly as an African wild dog. He still spent most of his time as a wild dog. He fell in love with the bitch familiar of a magus in a neighboring and rival covenant. They had a litter together. Unfortunately, the saga faded out of existence before we got to deal with the fall-out.
Chris
Noble's Parma, but won't those plants be without seed unless you use vis in a ritual?
From a modern POV, fecundation is what creates fruit and seed. I don't see Muto having an impact on the result, or if it does it won't be nourishing. Could it be seen as some sort of glamour that melts away when is separates from the parent? Or should it have a life of its own?
You should get oranges, because Muto causes real changes, just ones that are temporary in that they require the force of the magic to maintain them. While under the spell, the tree really is an orange tree and it's creative powers are directed towards oranges, not apples. The open question - and potential loophole for those concerned about game balance - is that the oranges may be magical in nature and liable to cause warping of some sort.
I would probably go with the concept of Essential nature... Ie, you get apples.
Possibly there are some effects in the offspring, but if a thing is transformed and it is fertil, then it can have it. Other thing is that the offspring (pupies, childrens, seeds) wouldn't be totally common versions, but it still being reall, they are in some stent like the footsprints or the wounds made of a transformed magi.
The Essential Nature argument gets overused, imo. If you read the text on page 79 of AM5:
There's no barrier to essential changes with Muto, it's just temporary. Transform a person into a rock and he really is a rock.
True, true...
Ah but now you´re looking at the wrong part of the argument. "must always be maintained" is the part i took as relevant. Based on assuming that any results of using the mutoed things is part of the "being maintained".
Its certainly not an ironclad argument, but it does have at least some merit.
So, you said it yourself, "it's just temporary"...
I haver a horse and a Mare; the mare gets fecundated. I turn Them into dragons for YTear duration:
Do I get a "natural" dragon offspring?
Wow
Maybe the argument for essential nature is overused, but it can get pretty silly if it does not.
Or.... I get 2 rabbits. One of them gets fecundated. I turn them into jewels (that in this period REPRODUCED) and bury them. Do I get rich?
Xavi
If a player asked me what would happen... I'd say try it and see.
Things that would be likely to happen would be one of the following:
In no case would this result in a dragon. Result could differ from one attempt to another. If it lives, the offspring may possibly have some sort of magical trait or power, either beneficial or detrimental.
Just my gut feeling. May make for an interesting research avenue for a magus.
Dragons probably object to the Lizard association with their Lineage however and Rocks Fall Everyone Dies. :mrgreen:
A Horse with physical dragon features , such as scales or gold-hoarding tendencies , cosmetic wings , etc.
Warping Flaws are much more likely than a Warping Virtue (Score of 05 only).
You need a ritual spell of minimum Level 55 (Base 50 , +01 Touch) to instill or create anything magical.
First, if you're talking about what I imagine to be a dragon -- enormously big, magical, fire breathing, very intelligent, maybe magic using -- good luck creating a Muto spell powerful enough to do this.
But let's say you're thinking about a big lizard, more of a Komodo Dragon.
In your example, if the mare is already pregnant then the offspring, if it survived, would revert to horse form at some point. However, if two "synthetic" Komodo Dragons mated and give birth (what's the gestation period for a giant lizard?) and if the offspring somehow survived, then I suppose you'd have a baby lizard. I'd imagine you'd have a very weird baby lizard, due to the effects of all this magic on its prenatal development.
I doubt it would be any more useful for a magus to do this than it would be to randomly inflict warping on animals and see what results.
A quibble: I would actually first change the horses, and then allow the (former) mare to get impregnated. Otherwise, the foal is "already there" so to speak, and its essential nature is that of a foal and not that of a dragon; so that, depending on the spell used, the foal embryo either gets turned into a dragon-embryo, is born and then reverts to horse-ness when the spell expires, or remains a foal embryo inside a dragon mother ... uhm ... not for very long (messy!).
That said, I do not really see a "game balance" problem with a covenant getting stupendously rich from breeding vast herds, or by making tons of gemstones - both because magic already offers the ability to do so for a very modest price, and because once you have the goods, you have to trade them, and that's a nice source of adventures. I do not see a "game balance" problem with the breeding of dragons, either; I can see a ton of headaches and adventures coming from it.
No, I'd really rather understand the "philosophical implications", if you wish, of the question. Going back to the apple-turned-to-orange example, I was initially tempted to agree with something close to what DIREWOLF75 suggested: you'd get fruits whose essential nature would be that of apples, though perhaps "appearing" as oranges as long as the Muto spell lasted. But Jabir changed my mind; no, as long as the magic lasts, the apple tree is really an orange tree, so it can turn soil and water and sunshine into perfectly real oranges. Otherwise, you have the problem with the cat-turned-into-a-man-eating-lion-that-explodes-after-lunch.
In Magi of Hermes , pages 10 & 13
Alexander sometimes turns his followers into bats , and feeds them.
(talk about a cheap way to save on food costs in a desert)
Duration Sun is used , so they have time to digest the food and be nourished.
The Man eaten by Lion (previously Cat) , duration Diameter , should rupture , if not actually explode violently.
Unless the muto was permanent, the item changed will always register it's Essential Nature under Intellego magics and revert to it's Essential Nature after the duration. The Essential Nature remains the same even though the item, animal, magus has taken on the qualities of the new form.
Only a Bjorner should be able to have offspring with animals when shape changed. This is because the Essential Nature of a Bjorner is that of whatever form they are in, a human and that of their Heartbeast. Where as a magus using a spell or shapechanging ability keeps their true nature and only mimics the creature. This is why you can't tell a Bjorner is anything other than a beast and a shapechanged human is really a human.
The way I run Muto is the underlying Essential Nature of something changed can always be ascertained through Intellego, as though it wants to go back to how it once was. This allows the changing of a person into stone, then after investigation and researching a spell the statue can be turned back into the person. But disallows making making statues into clones of the people they represent. Also you can always determine magically created things (gold). But that is where I deviate.
If the spell was a long enough duration the plants in the examples would gain warping points, then you can do whatever you want 
I don't think the turning bovine to rabbits to breed them is game breaking. No more than Rego Herbam. I would think the babies born would have warping or as soon as born the babies aren't targets of the spell any longer, they are no longer part of the mother, so they are morn then change into a calf immediately. Now the mother can't milk them. Bummer.
It seems to me this is covered under canon. Bloodline, under Faerie magic Page 86 or 87 of Ars Magica. Am I missing something?
Unless the Muto spell is designed with extra magnitude for potential offspring ,
and in the case of rabbits , a Group target ,
then as soon as unborn offspring reach second trimester , they immediately revert.
Thats how i see it at any rate.
With the Fertility Magic virtue you can actually make this sort of magical breeding work. I think you need a second breakthrough to apply the virtue to non-humans though. Otherwise the process is going to be very random as the magic can't be precisely targeted.
Every one of the breakthroughs from Ancient Magic has the potential to revolutionize the Order if all the implications are played out. I like that.
Just to be clear , my quote from Ancient Magic is how Hermetic magic currently works ,
not as the result of any breakthrough.