Winter’s cool indifference had already embraced the snow-tipped peaks of the Tian Shan mountain system, winds whispering the tall trees into a state of undress.

“It is cold,” said Alexey Raspopov, a guide with Trekking Club Kazakhstan, pointing to the dashboard thermometer of his 4x4 as we ascended, leaving Kazakhstan’s second city Almaty to disappear beneath a layer of smog.

One could see with his own eyes that this beautiful site was the origin of the cultivated apple

After driving for about two hours to the Turgen Gorge, we abandoned the vehicle and continued on foot. The climb was not difficult, but biting gusts threatened to take the feeling from my fingertips and steal the words from my lips as I asked Raspopov, who has led hikes in the region for the past 30 years, about the landscape that unfolded before us.

“It has changed a lot,” he said, calling upon the dissolution of the Soviet Union, the thickening pollution and a shrinking glacier to illustrate his point – not that he needed to. The near disappearance of the forests of Malus sieversii, or wild apple, that once blanketed the foothills of the Trans-Ili Alatau section of the Tian Shan mountains (which also stretches to Kyrgyzstan), are testament enough to the changing times.

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When storied Russian scientist Nikolai Vavilov first identified the Malus sieversii as the progenitor of the domestic apple, Malus domestica, in 1929, the region’s forests were thick and their harvests bountiful.

“All around the city one could see a vast expanse of wild apples covering the foothills,” wrote Vavilov of his visit to Almaty, then Kazakhstan’s capital. “One could see with his own eyes that this beautiful site was the origin of the cultivated apple.”

Vavilov based these words on his idea that the ‘centres of origin’ of a species lie in the places where you find its highest genetic diversity. His observations that all domestic apples may originate from Almaty has since been confirmed by modern genetics.

“At some point, either seeds, trees or budwood from desirable trees was taken out of the [Malus sieversii] forests by humans and grown elsewhere,” said Gayle Volk, a research plant physiologist at the United States Department of Agriculture (USDA). “In some cases, those trees could have hybridised with wild apple species growing in other regions. The selection process continued.”

Silk Road trade is believed to have scattered the fruit far and wide, eventually reaching North America with European colonists.

Despite being the first to scientifically assert Almaty’s association with the apple, Vavilov was not the first to observe fruit’s influence on the region. “Almaty used to be called Alma-Ata [the Russian name for the city],” Raspopov told me at the apogee of our ascent. “It means ‘father of apples’,” he added, before handing me an acid-green fruit the size of a child’s fist.

Zesty, sweet and deliciously crisp, it was not plucked from one of the nearly naked branches in front of us, which, when in season, bear apples of all shapes, sizes, flavours and textures – and, as Raspopov warned me, are rarely edible. Instead, this apple was a triumph of farming and cultivation, sadly the very same human endeavours that have ravaged the wild apple’s natural habitats. This thought did not stop me from accepting another though, listening as Raspopov continued: “Kazakh people, Almaty people, they are very proud of the apple. It comes from here.”

That pride is worn plainly for all to see throughout the city. Billboards bearing images of apples and Almaty’s tagline, ‘the city of [a] thousand colours’, advertise nothing else but the famous fruit, injecting bold pops of red along otherwise grey highways. At the A Kasteyev State Museum of Arts, Kazakhstan’s biggest art museum, apples appear in oil paintings and metal sculptures. On a larger and more public scale, murals depicting the fruit adorn the sides of buildings, and a giant granite apple-shaped fountain is a point of attraction at Kok Tobe mountain, one of the city’s major landmarks. On my way to the cable car that takes visitors to its peak, I waited patiently in line to take a picture of a sunshine-yellow, Soviet-era car, stuffed full of plastic apples; the licence plate read ‘I love Almaty’.

In the city’s Green Bazaar, a farmers’ market thronging with locals wrapped up against the chill, precarious towers of apples fastidiously organised according to hue, size and shape beckoned. Slices were deftly cut and devoured, offered with a steady stream of Russian – the lingua franca here – and gratefully received with a grin and a quiet “spasiba” (Russian for ‘thank you’, and about the sum of my knowledge of the language).

Kazakh people, Almaty people, they are very proud of the apple

Just as the Malus sieversii is the progenitor of modern apples, the Green Bazaar is ground zero for Kazakh cuisine. Each aisle presents another ingredient or element fundamental to the country’s culinary history. There is the corner dedicated to horsemeat, from an animal so sacrosanct to the once-nomadic Kazakh people that it is considered a delicacy. Then there are countless Korean specialities, emblematic of the diaspora that led many Koreans to settle in Central Asia after being forcibly deported from Soviet Russia by Stalin in 1937, where they had fled following the breakdown of the Chosun dynasty in 1910. And there are pickles of almost every type imaginable, garnished with generous amounts of dill.

Everything needed to make some of the country’s signature dishes can be found here. Take plov, a Central Asian rice dish that each country has adapted slightly. In Kazakhstan, the twist comes in the form of apples, which are added to the customary lamb, carrots and onions for a bit of additional sweetness.

But while the region has gladly accepted the Malus domestica as its own, Kazakhstan’s wild apples have been decidedly neglected.

Malus sieversii is currently listed as ‘vulnerable’ on the ICUN Red List (last assessed in 2007), with its population ‘decreasing’. Threats to the few remaining forests include residential and commercial development, livestock farming and deforestation. Moves have recently been made to preserve those that remain in the Trans-Ili Alatau foothills by Italy’s Slow Food foundation (which requires permits for visitors to enter the forest) with funding from Cultures of Resistance Network.

“Again and again, Slow Food has demonstrated that slowing down and paying attention to what we eat is not just a matter of the lifestyle choices of the affluent,” said Iara Lee, director of Cultures of Resistance Network. “It’s about highlighting models of agroecology that provide alternatives to environmentally destructive corporate farming, where profit becomes the driving concern. We need alternative models now more than ever.”

Whether Vavilov foresaw such destructive human activity when he first visited Almaty is impossible to imagine. However, the visionary scientist made certain to collect Malus sieversii seeds to protect the species and help prevent any future famine. He added them to his collection of 250,000 seeds, fruits and roots at one of the world’s first gene banks in Leningrad (now St Petersburg).

During the Siege of Leningrad from 1941 to 1944, several botanists who worked at the gene bank chose to starve to death rather than eat the seeds stored there. Vavilov also died of starvation, imprisoned in the gulag for falling out of favour with those in power. Thankfully, though, his legacy survives to this day. Now named the Vavilov Institute of Plant Industry (VIR), the gene bank is the only facility of its kind in Russia.

“We collect, evaluate, maintain and use the collection according to Vavilov’s theories and approaches,” said Igor Loskutov, the head of the institute’s rye, barley and oats genetic resources department. “We are working to prevent the loss of genetic diversity and genetic erosion. The VIR is important not only for Russia, but for the whole of mankind.”

Volk agreed: “The wild species in their native habitats will always be important, however, gene banks increase accessibility to the wild species and can serve as a partial backup in case of unexpected circumstances,” she said.

In the case of Almaty’s wild apple forests, let’s hope those unexpected circumstances never arise.

Back in the birthplace of the modern apple, the work of Vavilov, along with his courageous colleagues and his contemporaries, is a footnote in the story of a city whose identity is entwined with the fruit. To celebrate their work, and to satisfy a sudden craving, I stepped into a street-side stall and bought a mottled green-and-red apple. It was delicious.

CORRECTION: A previous version of this article misidentified the car filled with apples as a Volga. We regret the error.

Culinary Roots is a series from BBC Travel connecting to the rare and local foods woven into a place’s heritage.

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