Example of Complex Issue Affecting the Genetics Component of the Value Web

Example of Complex Issue Affecting the Genetics Component of the Value Web:

Low Genetic Diversity of Cultivated Soybean

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 onlya 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 torapidly 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 inhundreds 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.

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.

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.

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.

It is anticipated that Purdue University will expand its soybean breeding and genetics capabilitywith 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.