The pasta puzzle: Decoding durum wheat’s DNA for a sustainable future

An Italy that can’t grow its own wheat for pasta? It’s a race against time. Using a shared database in a Microsoft super‑computer, scientists from Italy and other countries are working together to develop new strains of durum wheat that can better withstand heat and drought caused by climate change.

As Luigi Cattivelli tells it the story of durum wheat starts more than 10,000 years ago, when some Neolithic farmers began cultivating a wild grass called emmer.These farmers selected seeds that exhibited traits that made emmer easier to harvest and eat. Over generations, through selective cultivation and crossbreeding, human beings developed durum wheat and, later, bread wheat.

As small groups of people migrated from the Fertile Crescent, an area of the Middle East where the first farming is believed to have taken place, they brought seeds with them, further adapting the plants to the climates and conditions in new lands – including Italy, where durum became the source of pasta.

Cattivelli, an expert on the wheat genome, says the next chapter of the story deals with our immediate future; scientists must develop new varieties of wheat and other staple crops to meet the rapid pace dictated by climate change.

Climate change driving a sense of urgency

Cattivelli directs the Genomics Research Center in Fiorenzuola, which is part of the Italian government’s Council for Agricultural and Economic Research (CREA). Cattivelli and his colleagues, along with teams of crop geneticists from other parts of the world, are using high-performance computing in the Microsoft Azure cloud to try to unlock the genetic secrets of durum and other varieties of wheat. In the Pangenome Project, they are sifting through the genomes of about 40 varieties of wheat and its ancient ancestors for traits that would help the crop thrive in extreme conditions, be more efficient in use of natural resources and be resistant to disease and pests, reducing the need for fertilizers and pesticides.

It’s not just a question of pasta for Italians; it’s an urgent quest because growing enough staples like wheat, rice and corn is essential to human survival.

Wheat makes up about 20% of calories consumed by humans globally. And climate change is a direct threat to the production of crops globally, from drought and heat as well as ial rains and other extreme weather events, such as the recent floods in eastern Spain.

Working together with Microsoft, CREA built a framework in the Azure cloud that eventually could house and analyze multiple petabytes of genetic data from the genomes of many varieties of wheat from multiple sources.

That data, which is stored in Microsoft’s Northern Italy Data Center Region, is then processed and analyzed in what is known as a “pipeline,” also housed in Azure. A pipeline is a series of data processing stages, in this case created with open-source coding. This particular genomic pipeline is designed to deal with billions of small sequences that have to be ordered to make the 14 chromosomes of the durum wheat genome. The pipeline is a tool that helps the scientists’ piece together that elaborate jigsaw puzzle. This genomic puzzle can be seen and worked on by teams of scientists wherever they are in the world. Knowledge and information extracted from the genomic puzzle will be embedded in new varieties that will be made available to farmers in the coming years.

Curtis Pozniak, a geneticist who directs the Crop Development Center at the University of Saskatchewan, Canada, is among the founders of the Pangenome Project.

“We’re generating petabytes of information that we need to filter down into something meaningful,” Pozniak says. “The only efficient way to do that is through cloud-based platforms where the same data can be shared with a whole range of experts at the same time. “It took me the better part of my Ph.D. to clone a single gene that was important for a wheat trait,” Pozniak recalls. “With the kind of data and analysis tools we have at our disposal now, we’re doing that in a matter of weeks or months. It’s an exciting time to be a scientist.”

Scientists working globally to genome codes

The researchers at CREA are using a multidisciplinary approach called genomics to get a granular understanding of wheat (pun intended). Genomics combines biology, bioinformatics and information technology to analyze and interpret biological data. The tools are different, but the goals are the same as they have been for thousands of years – selecting traits to ensure the best possible harvest.

The genome of wheat for bread was completed, to much fanfare, in 2017. But that is only one step. The genome, essentially a list of genes that makes up a life form, contains billions of DNA bases, and they are constructed in sequences (if you recall your introduction to biology class, those sequences are made up of an alphabet of four letters, A, C, G and T).

Those sequences are elaborate codes that spell out how a life form functions in the most intricate and minute detail. Wheat has a particularly elaborate genome – durum wheat has 10.5 billion bases and bread wheat has about 15 billion bases– that’s three times more than the human genome, the scientists at CREA say.

To return to the jigsaw puzzle metaphor, the Azure cloud creates the table where scientists can put all the pieces together. Faccioli, Mario Giorgioni, an ICT specialist at CREA, and Wolfgang De Salvador, a Microsoft specialist in high-performance computing and artificial intelligence infrastructure, worked together to construct a cloud architecture for pipeline orchestration.

This architecture leverages a workflow orchestrator called Nextflow, created and supported by the Microsoft partner Seqera. This system in the Azure cloud made it possible for teams to work together using the same sequence of open-source programs to reach reproducible results. Giorgioni says they built this centralized research platform with tools that address the three main pillars of any high-performance computing system: fast shared storage, high-performance computing resources and fast network interconnects.

The infrastructure, built using Azure CycleCloud and leveraging Azure HPC services, allows researchers to easily scale computational resources as needed. Azure Blob-based shared storage serves as the backbone, offering the necessary bandwidth and scalability for data-intensive research projects.

“Researchers have access to a wide range of computing resources to tackle the most intricate challenges in their daily work,” he says.

This genomic puzzle can be seen and worked on by teams of scientists wherever they are in the world. Knowledge and information extracted from the genomic puzzle will be embedded in new varieties that will be made available to farmers in the coming years.

Read the full story on Microsoft Source.