Chance observation leads to plant breeding breakthrough

A reliable method for producing plants that carry genetic material
from only one of their parents has been discovered by plant
biologists at UC Davis. The technique, to be published March 25 in
the journal Nature, could dramatically speed up the breeding of crop
plants for desirable traits.

The discovery came out of a chance observation in the lab that could
easily have been written off as an error.

“We were doing completely ‘blue skies’ research, and we discovered
something that is immediately useful,” said Simon Chan, assistant
professor of plant biology at UC Davis and co-author on the paper.

Like most organisms that reproduce through sex, plants have paired
chromosomes, with each parent contributing one chromosome to each
pair. Plants and animals with paired chromosomes are called diploid.
Their eggs and sperm are haploid, containing only one chromosome from
each pair.

Plant breeders want to produce plants that are homozygous — that
carry the same trait on both chromosomes. When such plants are bred,
they will pass the trait, such as pest resistance, fruit flavor or
drought tolerance, to all of their offspring. But to achieve this,
plants usually have to be inbred for several generations to make a
plant that will “breed true.”

The idea of making a haploid plant with chromosomes from only one
parent has been around for decades, Chan said. Haploid plants are
immediately homozygous, because they contain only one version of
every gene. This produces true-breeding lines instantly, cutting out
generations of inbreeding.

Existing techniques to make haploid plants are complicated, require
expensive tissue culture and finicky growing conditions for different
varieties, and only work with some crop species or varieties. The new
method discovered by Chan and postdoctoral scholar Ravi Maruthachalam
should work in any plant and does not require tissue culture.

Ravi and Chan were studying a protein called CENH3 in the laboratory
plant Arabidopsis thaliana. CENH3 belongs to a group of proteins
called histones, which package DNA into chromosomes. Among the
histones, CENH3 is found only in the centromere, the part of the
chromosome that controls how it is passed to the next generation.

When cells divide, microscopic fibers spread from each end of the
cell and attach at the centromeres, then pull the chromosomes apart
into new cells. That makes CENH3 essential for life.

Ravi had prepared a modified version of CENH3 tagged with a
fluorescent protein, and was trying to breed the genetically modified
plants with regular Arabidopsis. According to theory, the cross
should have produced offspring containing one mutant gene (from the
mother) and one normal gene (from the father). Instead, he got only
plants with the normal gene.

“At first we threw them away,” Chan said. Then it happened again.

Ravi, who has a master’s degree in plant breeding, looked at the
plants again and realized that the offspring had only five
chromosomes instead of 10, and all from the same parent.

The plants appear to have gone through a process called genome
elimination, Chan said. When plants from two different but related
species are bred, chromosomes from one of the parents are sometimes
eliminated.

Genome elimination is already used to make haploid plants in a few
species such as maize and barley. But the new method should be much
more widely applicable, Ravi said, because unlike the process for
maize and barley, its molecular basis is firmly understood.

“We should be able to create haploid-inducing lines in any crop
plant,” Ravi said. Once the haploid-inducing lines are created, the
technique is easy to use and requires no tissue culture — breeders
could start with seeds. The method would also be useful for
scientists trying to study genes in plants, by making it faster to
breed genetically pure lines.

After eliminating half the chromosomes, Chan and Ravi had to
stimulate the plants to double their remaining chromosomes so that
they would have the correct diploid number. Plants with the haploid
number of chromosomes are sterile.

The research also casts some interesting light on how species form in
plants. CENH3 plays the same crucial role in cell division in all
plants and animals. Usually, such important genes are highly
conserved — their DNA is very similar from yeast to whales. But
instead, CENH3 is among the fastest-evolving sequences in the genome.

“It may be that centromere differences create barriers to breeding
between species,” Chan said. Ravi and Chan plan to test this idea by
crossing closely related species.

Chan, who arrived UC Davis in 2006 in his first academic position,
described the result as a “game changer” for his laboratory, opening
up new research areas, funding sources and recognition.

The work was supported by a grant from the Hellman Family Foundation.