Bread, like wine, is pivotal in Judeo-Christian rituals. Both products exemplify the use of human ingenuity to re-create what nature provides, and the fermentation they both require must have seemed nothing less than magical to ancient minds. When toasted, rubbed with garlic and tomato, doused with olive oil and sprinkled with salt like the Catalans do, there are few things more delicious than bread.

Wheat is the most widely cultivated crop on the planet, accounting for about a fifth of all calories consumed by humans and more protein than any other food source. Although we have relied on bread wheat so heavily and for so long (14,000 years-ish), an understanding of its genetics has been a challenge. Its genome has been hard to solve because it is ridiculously complex. The genome is huge, about five times larger than ours. It's hexaploid, meaning it has six copies of each of its chromosomes. More than 85 percent of the genetic sequences among these three sets of chromosome pairs are repetitive DNA, and they are quite similar to each other, making it difficult to tease out which sequences reside where.

The genomes of rice and corn—two other staple grain crops—were solved in 2002 and 2009, respectively. In 2005, the International Wheat Genome Sequencing Consortium determined to get a reference genome of the bread wheat cultivar Chinese Spring. Thirteen years later, the consortium has finally succeeded.

Hexawhat?

Humans are diploid. That means we have two copies (one pair) of each of our chromosomes (one from each parent). But bread wheat—Triticum aestivum L.—is a combination of three different grasses, each of which contributed both of its seven pairs of chromosomes. The first two grasses linked up about 500,000 years ago to make Triticum turgidum, an ancestor of durum wheat that has "only" four copies of each chromosome. Then, about 8,000 years ago, the third grass threw its chromosome pairs in to make the ancestor of our bread wheat.

The new reference genome published this week shows that most wheat genes are present in all three subgenomes, but some appear in only one or two out of three. One such gene, granule bound starch synthase (GBSS), “is a key determinant of udon noodle quality.”

Among the most valuable data from the study are the regulatory networks it revealed. With bread wheat, as in all organisms, where and when your genes are active can be as important as which genes you have. This analysis monitored which genes are active only in certain tissues, which are active only during certain times during development, and which are active when the wheat was exposed to different stressors.

There were 8,592 families of related genes that had additional members in the wheat genome compared to the nine other grass genomes examined. These genes were associated with fertility, tolerance to cold and salt, and processes important for grain yield and quality, like seed maturation and germination. Many gene families that are relevant for breeding—i.e., targets for future tinkering—were expanded, including one for disease resistance, one for drought tolerance, and one for winter survival. The expansion of these genes in the wheat genome is thought to have enabled the crop to produce high-quality grain across different climates and environments.

Solid

Breeding for important agricultural traits can be difficult if those traits are controlled by multiple genes, and those genes are each affected by their environment. This reference genome has identified genetic markers, much like diagnostic markers, that can be linked to particular traits. For example, about 26 genes are differentially active in wheat varieties with solid stems and those with hollow stems; this analysis revealed one gene where the number of copies varies reliably with stem thickness. This gene can now be used to select strains with solid stems in future wheat breeding programs. (Stem solidity confers resistance to drought and insect damage.)

Despite what you may have heard, modern bread wheat is not higher in gluten content than earlier varieties. (This sequencing effort didn’t show that; this fact had been demonstrated already.) Neither is the wheat we eat genetically modified. But with this genome now solved, breeders may now find it easier to tell which genes are valuable in agronomic traits, allowing them to more precisely adapt the crop to our rapidly changing environment and maintain stable yields.

Science, 2018. DOI: 10.1126/science.aar7191 (About DOIs).