DNA
LandMarks is a world leader in providing
marker-assisted breeding services. As this field
is constantly evolving at a rapid pace, we
thought it would be helpful to gain some insight
and perspective on the technology from leaders
in the science. We are pleased to present the
following installment in what will be a series
of interviews with scientists in the field of
marker-assisted breeding.
|
 Dr.
Allen Van Deynze is a molecular geneticist
and a Professional Researcher at the Seed
Biotechnology Center at the University of
California Davis. We asked him for his thoughts
on the opportunities currently provided by
marker-assisted breeding technologies and where
this field will take us in the future. |
|
How
long have you been in the field of molecular breeding?
I’ve been doing it since 1989 with RFLPs
In that time what are some of the biggest changes you've
seen?
The biggest changes were conversion to PCR markers and now
beyond, RAPDs in early 1990s, Simple Sequence repeats in mid
1990s and SNPs in late 1990s. This still made technologies
accessible only to major crops. The biggest change in the last 3
years is sequencing technology that makes markers available to
any organism, coupled with datapoints in the pennies range.
Given the power of the genomic technology available today
where do you see some of the most significant applications of
molecular breeding?
As mentioned above, sequencing technology has enabled us to
sequence parents and in the near future populations such that we
are can truly use genome assisted breeding vs following simple
marker associations to major loci. The major change is that we
can do denovo marker/quantitative trait loci (QTL) analysis on
every population vs just the most important ones. Breeders can
have access to the full genotype of plants to combine with
breeding value at the phenotypic level. They can also understand
the allelic makeup (heterozygous or homozygous at key loci) and
begin to understand what genes control complex traits. The
current throughput of technologies allows breeders and
geneticists to accumulate data on 1000’s of individuals in days
to weeks. The challenge is to handle the data.
For a long time, GMO technology has received the most
attention (good and bad) in regards to crop biotechnology while
genomics has held a lower profile. Is this changing?
The media has amazing power regardless of how good or bad a
technology is. Unfortunately, too often the flashy alarming, yet
scientifically not credible stories get promoted and published
by groups with ulterior motives. Fortunately, this is rarely the
case with genomics and it is viewed very positively in media.
Who doesn’t think it is cool that a mass murderer can be
instantly identified and convicted with a cheek swab, a small
fragment of a hair on a crime victim and a good database in less
than 1 hour. Programs like CSI do it every week and have given
the general public a flavor of the benefits of technology like
genomics. Ok it is not that fast, but the general methodology
and capability is correct. This is exactly what marker-assisted
breeding does in plants---use DNA from plants to create and
query large databases of genetic data combined with trait data
to decide which plants are likely to give us the best quality,
yield, resistances etc.
Given the
significant investments by large, multinational ag
biotech companies, where do academic institutions such as UC
Davis fit into the R&D picture?
Universities are very good at doing research and creating
knowledge whereas large multinationals are very good at
commercializing products and implementing technologies. UC Davis
is pioneering many of the applications and even the genomics
technologies themselves. Our strength comes in numbers. We have
over 100 plant scientists on campus and have access through the
latest technologies through facilities such as our centralized
Genome Center. I believe UC Davis plays a central role in
developing the biology to understand gene networks and what
controls plant traits at the whole plant level across dozens of
crop species. Our capacity to analyze the huge volumes of data
on comparative genomics – using information from one species to
understand others – is equal or larger than most multinationals.
Basically, UC Davis and many other public institutions are
populating the biological databases across many organisms that
enables marker or genome assisted breeding. With over 200 plant
commodities in California, we work closely with large and small
breeding companies to ensure we are working on the most relevant
germplasm and that our research is integrated with the seed
industry.
What should medium-sized breeding companies be focusing on to
keep pace with their larger competitors?
As any seed company CEO will tell you, germplasm (plant
varieties) is the most important asset. Developing the best
germplasm in most cost-effective and efficient way is now even
more important. There are few crop varieties that last more than
3-5 years in most major crops anymore due to increased
investment in plant breeding. Furthermore the first company out
with a new trait, such as disease resistance, quality etc gets
the lion’s share. Marker assisted breeding can decrease breeding
times from 8-10 years to 4-5 years for a variety. Only in the
last few years or so has it become cost efficient for medium
sized companies to fully use marker assisted selection and whole
genome selection on all their crosses vs just the few most
important ones. The challenge with marker-assisted selection is
that there are dozens of different technologies, with various,
cost of reagents, throughput and capital costs. Generally, cost
per sample goes down with volume and having a medium number of
samples with a medium number of markers is the most expensive.
The best systems are flexible and allow one to choose a
different set of markers for every cross or population. This is
critical as only a small subset of the markers are informative
in a given population. These systems are becoming more and more
affordable. Another question for a traditional breeding company,
is should I invest in my own lab and personnel to run markers,
or should out-source it. There are several service companies
that have decades of experience in applying markers to breeding.
These are a great choice to get started and establish marker
assisted programs as the breeding company does not need to make
capital and personnel investments and accesses experienced
personnel directly. Most often the service companies either
already have markers for your favorite crop or can develop them
specifically for a breeding company’s germplasm. As the service
company must also make a profit, the cost of marker-assisted
selection is higher. As a company, one must weigh the cost of
the capital investment, depreciation and experienced personnel
with the higher cost per datapoint through a service company. In
my opinion, marker-assisted breeding is traditional breeding now
and is absolutely required to be in business, big or small.
Breeders can now select on traits (phenotype) and genotype and
make more informed selections.
What will breeding with molecular markers look like 5 years
from now?
How about 10 years from now?
Hmm, 5 years, It will be integrated
in all breeding programs, big and small at some level. We will
shift from anonymous markers to those controlling genes. We will
be challenged with the huge volumes of data to analyze. In 10
years, we will be using genome (as opposed to marker assisted
breeding) assisted breeding and have the sequence of individuals
in every cross and have markers that represent the causative
mutation for all major traits i.e. diagnostic. As breeders,
though, we still won’t be able to predict yield, but be very
good at tracking it in every cross. Marker (genome)-assisted
selection is a powerful tool in breeding, but, we will always
need breeding and breeders and always need to test varieties in
the field.
Dr. Van Deynze can be reached
at
avandeynze@ucdavis.edu |
