Science breaks through corn’s genetic barrier

Few crops are as genetically diverse as corn and that has made it somewhat complicated for plant breeders to achieve desired results.

Now, a new study from Iowa State University details the genomes of 26 different lines of corn, which is hoped to make research quicker and more predictable.

The genomes will help breeders better select for genes that could lead to improved yields or better stress tolerance, for example.

“The 26 lines that were selected for assembly in this project have been used for many years as a representative cross section of the diversity of (corn),” said Matthew Hufford, associate professor of ecology, evolution and organismal biology and first author of the study. “These lines include tropical and temperate corn, as well as popcorn and sweet corn.”

The first corn genome that was mapped was the genetic line called B73 developed at Iowa State University. That genome was completed in 2009.

Since then, B73 has been the primary reference genome for corn with only a few genome assemblies becoming available in the years since. That has limited scientists’ understanding of genetic sequences in other corn genomes that were not present in B73.

Hufford said that while the first genome provided an initial “parts list” and partial wiring diagram, it was incomplete. It was critical to develop other genome references to get a better understanding of the genetic architecture influencing essential agricultural traits.

Corn actually has more genes than humans. It was first domesticated about 9,000 years ago in Mexico when native people selectively bred a wild grass called teosinte.

“Teosinte is also outcrossing, or open-pollinated, meaning plants interbreed. The long-term size of teosinte populations has provided lots of opportunities for mutations to accumulate and increase in frequency as they proved adaptive to particular environments. The interbreeding has allowed for mixing of these mutations among plants, creating even more diversity,” said Hufford.

The 26 genomes that were mapped encompassed a sweep of genetic diversity from popcorn to sweetcorn to field corn and various geographical and environmental conditions. The diversity revealed a substantial variation in both disease resistance and flowering time.

“We discovered presence/absence variation in what are known as ‘NLR’ disease resistance genes that could help clarify how particular lines are susceptible to disease and others are not,” he said. “We also uncovered instances where transposable elements, or ‘jumping genes,’ insert near a flowering-time gene and affect the extent to which it is turned on or expressed. This may explain, for example, why certain tropical lines of maize (corn) take much longer to flower than temperate lines. Both disease resistance and the length of the growth cycle will be important for farmers given changing and extreme weather conditions.”

One of the challenges of the study was that 85 percent of the corn genome is composed of transposable elements, or patterns that repeat themselves throughout the genome. It is as though the genome uses a copy-and-paste mechanism in which the exact duplicated sequence is inserted into a new genomic location.

“As this is repeated thousands of times, certain types of transposable elements may occur in the genome with thousands of almost identical sequences,” he said. “This is like trying to put together a jigsaw puzzle that has thousands of pieces the exact same colour. It’s really difficult to know where the puzzle pieces fit.”

However, recent technological advances have allowed for longer DNA sequences, which has simplified the genome puzzle when it comes to identifying which genes are responsible for which traits.

Next, the research team plans to use the PacBio sequence data to assemble a pan-genome or a genomic reference that encompasses all the diversity present in corn. Hufford called it the “next frontier” of this line of research.

“Our plan is to construct a pan-genome that represents a comprehensive catalogue of corn diversity. Once this is generated, it (will be) possible to use what are known as haplotype graphs to quickly reconstruct the genome of any newly sequenced line using a minimal amount of sequencing data. This could vastly improve the speed and accuracy in finding the sequence variation that is controlling agronomic traits.”

Currently, researchers are working on genome assemblies to help fill in the gaps in the current catalogue of corn diversity. Then they will work on building the tools to help build up the catalogue for more understanding of the genetic basis of agronomic traits, so that corn breeders will be better enabled to improve the crop.

The research was recently published in the journal Science.