Background on Value Web Component: Genetics
Background
The science surrounding genetic
improvement of soybean has the potential to
impact all aspects of the value chain. Genetic
resistance to biotic and abiotic (or
environmental) factors have a profound impact
on production, crop values and profitability.
“Output traits” such as compositional
improvements have the potential to expand
soybean markets and increase meal or oil values,
while simultaneously solving problems for
diverse consumers in terms of nutritional or
compositional quality. An expanded
understanding of soybean gene function (with
regards to genes controlling maturity, agronomic
characteristics, nutrient uptake and partitioning)
will make public and private soybean breeding
more efficient and responsive to changing
demands, by facilitating the selection of
desirable genes in breeding populations.
Genetic approaches to soybean
improvement include plant breeding and trait
introgression approaches, as well as transgenic
approaches – modifying the plants genetic code
to incorporate new genes or to eliminate existing
genes to produce a new plant with improved
functionality.
With the advent of genomics and
modern breeding technologies, as well as
unprecedented opportunities for research to
translate current knowledge from model species,
we are only beginning to realize the potential
gains from genetics in soybean.
Limitations to Value Realization
One major limitation faced by soybean
genetics research is the limited genetic diversity
of cultivated soybean. In other words, most of
the soybeans used in commercial production are
very much the same genetically because only a
small set of founding parents were first
introduced into the US and used for soybean
improvement. The limits in genetic variation
have historically hampered traditional breeding
efforts, specifically in the identification of a
sufficient number and density of molecular
markers that can be used for trait genetic
mapping. It continues to be an issue for the
optimization of yield and composition traits.
Limited genetic diversity for the modern
cultivated soybean is also a worry for disease
resistance: in many cases few resistance genes
are presently deployed, making the crop
vulnerable to rapidly evolving resistance in pests
and pathogens.
A second limitation faced by soybean
geneticists and physiologists is phenotyping
technology. (Phenotype is used here to describe
any measurable trait, for example seed
composition, plant size, seed yield, or the
resistance to a particular disease.) For robust
phenotyping breeders and geneticists require
massive parallelization to measure traits in
hundreds of thousands of plants simultaneously,
as well as the need for more accurate and
reproducible measurements of common traits.
The need for phenotyping creates opportunities
for collaborations between plant scientists and
engineers.
Example of Complex Issue Affecting the Genetics Component of the Value Web:
Low Genetic Diversity of Cultivated Soybean
A major limitation for continued
soybean improvement is the low genetic
diversity of cultivated soybean. Some estimate
that for as many as 40% of the genes there is no
detectable genetic diversity within the set of elite
cultivars.1 For breeding and improvement, this
means that it may be difficult to find better
performing soybean plants, or plants that have
traits that have not been the object of historical
selection programs in the germplasm that we are
currently using. This could include resistance to
emerging disease, or biochemical/composition
traits that were once difficult to screen for.
Modern soybean has been subjected to
multiple genetic bottlenecks, or events that have
reduced genetic diversity. These include the
initial domestication of soybean from wild
relatives in Asia, the selection of a small number
of Asian lines to form the basis of soybean
grown in the US, and continued selective
breeding of these lines.
Current efforts at Purdue include the
assessment of gene function as well as genetic
and phenotypic diversity across the basis of
modern soybean cultivars (Rainey Lab, the
Soybean Nested Association Mapping project).
The Ma lab exploits soybean’s wild relatives
(Glycine soja) species to identify genetic loci
involved in the domestication of soybean as well
as identify resistance for agronomic traits. The
Hudson lab is using forward and reverse genetic
approaches to understand gene function and
generate new germplasm with an emphasis on
the improvement of seed composition. This
work relies on expertise from the Yao lab, who
devise and enable high throughput phenotyping
technologies, and plant pathologists and
physiologists (Shaun Casteel, Kierstin Wise) for
field and resistance phenotyping.
Both genetic and biotechnological
(transgenic/knock-out) approaches can be used
to expand soybean genetic diversity and bring
desired traits into the market, however this is a
long and resource intensive process.
Research towards a solution
Present DNA-sequence based
technologies enabled by genomics allow the
identification and exploitation of all of the
available variability within our current cultivars
to advance breeding strategies. In addition,
expanded characterization of the genes and
genomes of soybean’s wild relatives can identify
the rare alleles that have been lost during the
selection for our current cultivars. This presents
the opportunity to locate novel variation
conferring useful traits from germplasm or
mutant collections and introduce these into elite
lines. Even with current technology, a
considerable amount of effort and a number of
seasons are required to move genes from wild
relatives into acceptable cultivars.
It is anticipated that Purdue University
will expand its soybean breeding and genetics
capability with the newly announced Plant
Sciences Initiative, which will fill in gaps in the
soybean breeding, genetics, and physiology
team.
References:
1. Hyten, D. et al. (2006) Impacts of genetic
bottlenecks on soybean genome diversity. PNAS
103:45.