Corn's genetic diversity on display in new genome study

Date:
August 5, 2021
Source:
Iowa State University
Summary:
A new study details the genomes of 26 lines of corn from across
the globe. The genomes can help scientists piece together the
puzzle of corn genetics. Using these new genomes as references,
plant scientists can better select for genes likely to lead to
better crop yields or stress tolerance.



FULL STORY ==========================================================================
The newly assembled genomes of 26 different genetic lines of corn
illustrate the crop's rich genetic diversity and could pave the way for
a better understanding of what genetic mechanisms account for crop traits prized by farmers.


==========================================================================
The mapping of the 26 genomes is detailed in an article published in the journal Science, and Matthew Hufford, first author of the study and an associate professor of ecology, evolution and organismal biology at Iowa
State University, said the genomes will help scientists piece together
the puzzle of corn genetics. Using these new genomes as references,
plant scientists can better select for genes likely to lead to better
crop yields or stress tolerance.

"It's allowing you to get a much more precise understanding of what's
driving variation of traits," Hufford said. "If a breeder really wants to select for the right variation to produce a trait they're interested in,
and they only have a foggy view of the genetic causes of variation in that trait, they're working with their hands tied behind their backs. So we're giving them a lot more information to go on." The first corn genome to
be mapped was the genetic line known as B73, a line developed at Iowa
State. Patrick Schnable, director of the ISU Plant Sciences Institute;
and Doreen Ware, adjunct professor at Cold Spring Harbor Laboratory
and USDA research scientist, led the effort to assemble the genome,
which was completed in 2009. Since then, B73 has served as the primary reference genome for corn, with a handful of additional genome assemblies becoming available only in the last few years. That means scientists
have a limited understanding of genetic sequences in other corn genomes
that aren't present in B73.

"While the first genome was invaluable, providing an initial parts
list and partial wiring diagram, we knew it was not complete," Ware
said. "It was critical to develop other genome references to understand
the genetic architecture underlying important agricultural traits."
But the 26 genomes mapped in the new study encompass a wide range of
genetic diversity, everything from popcorn to sweetcorn to field corn
from various geographical and environmental conditions. This provides
much more reference data for scientists combing maize genetics for
targets that could lead to better crop performance.

Genetic diversity poses a challenge Hufford said the sheer genetic
diversity present in corn created major hurdles for the assembly of the
new genomes. He said 85% of the corn genome is composed of transposable elements, or patterns that repeat throughout the genome.

Hufford compared those transposable elements to a jigsaw puzzle in which
the vast majority of pieces are a single color. All that repetition
makes it difficult to figure out how the parts fit together.

"If you can't find a unique color or shape that tells you where to put
the puzzle piece, you're in a world of hurt," Hufford said. "But if you
get slightly larger puzzle pieces with unique features, that simplifies
the process." Technological advancements provided just the tools
the researchers needed to overcome those hurdles, Hufford said. New
sequencing technology allows for longer sequence reads, meaning the
pieces of the puzzle are larger and more likely to contain clues that
allow the scientists to arrange them properly.

New technology may even allow for the assembly of a pangenome, or a
genomic reference that encompasses all the diversity present in corn,
Hufford said. He called such an effort "the next frontier" of this line
of research.

The research was funded by the National Science Foundation Plant
Genome Research Program. The paper includes a total of 46 authors
from Hufford and Jianming Yu's Labs at Iowa State and several other institutions including MaizeGDB, a USDA-funded genomic database also
at Iowa State; lead principal investigator Kelly Dawe's group at the
University of Georgia; co-PI Doreen Ware's group at USDA; Cold Spring
Harbor Laboratory in New York and co-PI Candice Hirsch's group at the University of Minnesota.

========================================================================== Story Source: Materials provided by Iowa_State_University. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Matthew B. Hufford et al. De novo assembly, annotation, and
comparative
analysis of 26 diverse maize genomes. Science, 2021 DOI: 10.1126/
science.abg5289 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/08/210805141202.htm

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