Both Portal 2 and Epistile 3 end in the far distant future and provide us with little more than proof that the Earth still physically exists and has an atmosphere that can support human respiration and some crop growth.

But here's the thing: Portal 2 strongly suggests there are few if any humans left resident on Earth, and almost certainly no large planet-spanning societies. That means no massive-scale agriculture.

So where did the field of wheat come from? Well, that's just what's left. Most of Earth's fragile biodiversity has long since perished and been replaced by a fragile network of Xen, domesticated Earth, and offworld life, and that network is in decline. Some physical aspects of the climate may have reverted to mean, or even gone through many mass extinction cycles since the long-since-ended Holocene, but they can't undo... well, I'll get into that.

The ending of the series from what we're shown/told in P2 and E3 seems pretty clear to me:

• in mid-2023, following the death of Eli Vance and the closure of the Superportal over City 17's ruins, the Resistance tried to secure the Borealis, whose pseudoteleport drive was powered by more energy than anything else humanity had access to.
• After Alyx kills Judith probably at G-Man's subliminal prompting it is decided to use the Borealis directly against the Combine, as a suicide attack vessel, while they remain weakened from the City 17 detonation.
• G-Man steals Alyx away because she's valuable for some cosmic reason. Gordon is left behind and realizes the Combine are far vaster than any human effort - let alone the haphazard weaponization of the Borealis - could defeat. Through the purple Vortigaunts intercession, the submarine's explosion flings him into the far future instead of shattering him into fundamental particles we haven't discovered yet.
• Back on Earth, the Borealis appears to vanish with Alyx, Judith, and Gordon aboard. Their fates likely remain a mystery for as long as humanity remembers their names.
• Shortly after, the Combine reassert control over Earth's "last-mile" of their portal network. What happens to humanity after that depends on a lot of factors, but there aren't really any good answers. Besides the raw resources of the oceans and atmosphere, their primary interest in humanity, as demonstrated by what we see most Combine transhumans doing, is footsoldiers. One assumes humans aren't THAT special in our ability to serve as faceless goons. The existence of the Suppression Field suggests they could instantly and selectively kill all humans on the planet if they so desired- they might just do that. Alternatively, the population may be wholly transferred offworld (the Combine seems to understand how deeply undesirable most subject species find this prospect) or been winnowed down to solely willing transhumans and stalker-like creations.
• After this reprisal, whatever it is, Earth falls largely silent. Human civilization as we know it is dead and possibly rendered peramently extinct. Powerful AIs like GlaDOS, developed by humanity around the turn of the century, seem to be the dominant form of intelligence/life on Earth, but we know of only one - her - and she was essentially running in Safe Mode (No Networking) during the vast time skip between Portal and Portal 2. Her "coma" may be all that saved her from the Combine scouring of the planet.

NOW- GLaDoS is awake now, and she has expressed interest in reanimating the dead and humanity generally. But look what remains of us in that era: fragmented personality cores, brain-degraded cadavers on ice, and GLaDOS's own warped and spite-poisoned memory of her human life. Is that really the template you want a new human race to be wrought from?