Citified nonfarmers worry that corn’s germplasm is shrinking into a narrow genetic spectrum. To them, all corn looks the same and is controlled by corporate agriculture. And now the truth: Fear not.

Maize is grown around the world, and its genetics are highly adaptable to changing uses and environments. That’s the latest finding of new and much more detailed genome research, published online recently in Nature.

“Our new genome for maize shows how incredibly flexible this plant is, a characteristic that directly follows from the way its genome is organized,” explains Doreen Ware, USDA genetic researcher at New York’s Cold Spring Harbor Laboratory. She led scientists at seven academic institutions and several genome technology companies in the gene mapping project.

The plant’s genomic DNA sequencing in its 10 chromosomes is very large and has a far wider “phenotypic plasticity” — i.e., the potential range in its ability to adapt — than even the human genome, she adds. “That helps us understand why maize, and not some other plant, is today the most productive and widely grown crop in the world.”

This flexibility helps explain why this plant species has been so successful since its adaptation by agriculturalists thousands of years ago. It also bodes well for its ability to grow in new places as Earth’s climate changes, and for increasing the plant’s productivity and global environmental sustainability.

Which genes are activated or silenced determines what the total set of genes enables a plant to do, Ware says. This new genome map is bringing to light how the plant’s genes are regulated in different individuals across the species.

By assembling a highly accurate and very detailed reference genome for the B73 maize line, then comparing it with genome maps for maize individuals from two W22 and Ki11lines grown in different climates, the sequencing team arrived at an astonishing realization.

“Maize individuals are much, much less alike at the genome level than people are,” points out Ware. The genome maps of two people will each match the reference human genome at around 98% of genome positions. Humans are virtually identical, in genome terms.

“But we’ve found that two maize individuals — from the W22 and Ki11 lines — each align with our new reference genome for B73 maize only 35%, on average. Their genome organization is incredibly different!”

This difference between maize individuals reflects “not only of changes in the sequence of the genes themselves, but also where and when genes are expressed, and at what levels,” explains Yinping Jiao, another Cold Springs researcher. He developed the first reference genome for maize in 2009, but acknowledges that it’s now outdated technology that yielded a genome “text” more akin to a speed-reading version than one fit for close reading.

A boon for corn breeders
Current mapping technology sheds much more light on how those genes are regulated. “Because of its amazing phenotypic plasticity,” concludes Ware, “so many more combinations are available to this plant. What does this mean to breeding? It means we have a very large variation in the regulatory component of most of the plant’s genes. They have lots of adaptability beyond what we see them doing now. That has huge implications for growing maize as the population increases and climate undergoes major change in the period immediately ahead of us.”

The new genome’s resolution of spaces between genes makes it possible to read detailed histories from the “texts” of genomes from different maize individuals. Consider, for instance, the impact of transposons — bits of DNA that jump around in genomes. This can now be assessed with specificity not previously possible. 

When transposons jump into a position within a gene, the gene can be compromised entirely, adds Ware. Other times, whether a transposon has hopped into a position just before or after a gene can determine when and how much it is expressed.