Wheat gene map shows how plants survive heat and drought

Wheat feeds billions, so even small gains matter a great deal. It is also vast in scope, covering more than 215 million hectares each year, according to a recent study.

A new resource maps which wheat genes turn on in different tissues and varieties. It translates gene activity into patterns that breeders can use to build tougher, higher yielding plants.

How wheat genes work

Dr. Rachel Rusholme-Pilcher of the Earlham Institute, a genetics research center in the United Kingdom, helped build a wheat-wide pan transcriptome, a catalog that shows which genes are active across multiple tissues and cultivated varieties.

The catalog explains when and where genes are turned on, and how those patterns differ between lines.

“We’ve revealed layers of hidden diversity spanning our modern wheat variations,” said Dr. Rusholme-Pilcher. Her team grouped genes into core, shell, and cloud sets, and traced which ones are shared across wheats or unique to certain lineages. That offers clues for traits that shift with climate or local pests.

Wheat is a polyploid, meaning it carries several related subgenomes, or complete sets of chromosomes.

Matching genes from these subgenomes, called homeologs, can split duties or combine forces, and the new map shows when that balance stays steady and when it shifts under different conditions.

Wheat that can handle stress

The resource traces regulatory networks, groups of genes that work together to control plant responses, not just single genes. That helps identify clusters that manage reactions to heat, drought, or poor soil, which breeders can target without using large amounts of fertilizer.

By 2050, global agricultural production will need to be about 60 percent higher than levels in 2005 to 2007, a widely cited projection. A playbook that points to the right gene networks can speed breeding toward that goal.

The catalog also puts past genome work into context. The 10+ Wheat Genomes Project, a global collaboration that mapped multiple varieties, revealed how breeders have already reshaped gene content.

This new expression atlas, a map of where and when genes are active, shows how those genes actually behave, connecting sequence to function through time and tissue.

That earlier effort assembled multiple wheat genomes and exposed large structural differences that matter to agronomy. The new atlas now layers transcription, or the reading of genes into RNA, on top of those structures, building a functional index that breeders can use right away.

Building the wheat gene map

The researchers assembled expression data, measurements of which genes were active, from roots, leaves, spikes, and grains, sampled at defined growth stages.

They used long-read and short-read RNA sequencing, a technology that reads genetic activity, to annotate, or label, genes in nine cultivars, then tracked activity levels across tissues.

“The new expression atlas allowed us to independently predict and compare the gene content of the wheat cultivars,” said Dr. Manuel Spannagl from Helmholtz Munich.

The analysis defined core genes that handle basic metabolism, the chemical reactions that keep cells alive, and DNA maintenance, shell genes enriched for stress responses, and cloud genes with more specialized roles.

Patterns were consistent across tissues for core sets, while stress-related modules varied more between cultivars.

“This work demonstrates the power of technology to reveal novel biology,” said Dr. Karim Gharbi, Earlham Institute.

Grain size and height

Plant hormones steer growth, and gibberellin, a natural chemical messenger that promotes elongation and seed formation, is a key driver of stem length and grain development.

New functional genetics show that different gibberellin oxidase genes, enzymes that fine-tune this hormone’s levels, control height and grain size in distinct ways.

A recent study identified seven GA3OX genes, which help produce gibberellin, in bread wheat. One group, GA3OX2, proved essential for normal growth, while GA3OX3 and GA1OX1 shaped gibberellin levels in developing grains.

Natural variations in these genes tracked with differences in grain size, suggesting that modern breeding has already nudged these genetic switches.

The expression atlas complements that work by showing where such hormone genes fit into wider networks. That can guide breeders toward combinations that lift grain weight without making plants overly tall.

The catalog also helps resolve trade-offs. Grain-specific hormone changes can feed back on stems through hormone movement, so seeing both the network and tissue context is vital when stacking alleles, or versions of genes, for yield.

Wheat genes and health

The atlas mapped variation in prolamin genes, which code for storage proteins that influence dough properties and, in some cases, human immune reactions.

These proteins include gliadins and glutenins, key parts of gluten that contain epitopes, small protein fragments that can trigger celiac disease, an autoimmune reaction to gluten in food.

Expression profiles for these genes differed between cultivars and growth stages. Some lines showed lower activity of epitope-rich alpha or gamma gliadins in grain, while others expressed more, adding a health-relevant dimension to quality and yield selection.

Variations in gene copy number – how many times a gene appears in the genome – within the alpha gliadin region, along with shifts in transcription factor activity (proteins that control whether genes are turned on or off), accounted for part of this diversity.

The findings point to potential breeding or gene-editing strategies that could lower the epitope burden – the total number of immune-triggering sequences – while preserving baking quality.

Such findings do not claim clinical effects on their own. They do, however, provide a clear genetic and expression map that links grain quality, processing traits, and potential immunogenicity, the likelihood of provoking an immune response.

What breeders can do now

Network modules, clusters of genes that act together, in the atlas capture sets of co-expressed genes that move in sync under stress or during development. Those modules can be turned into markers that track complex traits more reliably than single gene tests.

The same applies to the hormone pathway results. Breeders can balance height and grain size by selecting for GA3OX and GA1OX1 haplotypes, combinations of linked genetic variants, that boost grain weight in the endosperm, the seed’s nutrient layer, while keeping stems moderate in the field.

The atlas also exposes cultivar-specific expression signatures that likely reflect local breeding histories. That helps programs exchange useful diversity across regions in a targeted way, rather than through broad, slow introgressions, the gradual introduction of genes from one population into another.

It is a practical resource. With one map, teams can aim for heat resilience, nitrogen efficiency, and grain quality, then check that the underlying networks align across tissues and stages before making crosses.

The study is published in the journal Nature Communications.

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