Focusing On Phenomics In Specialty Crops
September 27, 2016 Not that long ago, the term “genomics” did not mean much to most people.
If anything, it was lumped into that confusing biotechnological bucket of “DNA,” “genetic engineering,” “GMO,” and “gene therapy.” Something that scientists might understand, but for many in ag it was somehow related to Roundup Ready crops and “stacked genes” in new corn and soybean releases. Or something that the television series “CSI” must have used when they employed DNA evidence to catch the bad guys.
Now, if you have $100, you can submit a sample of your DNA to a company like 23andMe and receive a detailed analysis of all the genes in your 23 chromosomes — your genome — within a few weeks.
Suddenly, more than 1 million 23andMe customers have become familiar with their very own genetic profile, based on analysis of a little tube of saliva they sent in. They can use this information on the specific genetic information they carry to assess health care choices, unravel their ancestry, and determine the probability of passing on a predisposition to certain diseases to their children.
While some applications of such personal genetic testing are controversial and significant regulatory constraints remain, it certainly seems inevitable that “genomics” is a term that is not just meaningful, but will be quite personal, to millions. Technical language around genomics is still difficult and often incomprehensible, but everyone can now have a sense of their personal genetic profile — all the DNA material that constitutes their genome.
Now ADD the Environment
What are the chances the same will soon apply to the term “phenomics?”
At its simplest, a phenome is any organism’s collection of traits: physical, biochemical, and physiological. Just as every human (or an apple) has their own unique genome, which can be termed its genotype, they have their own unique phenome, which is termed phenotype.
But this is where phenomics becomes very challenging. An organism‘s genotype is determined by the genes on the chromosome it inherits from its parents. Except for relatively rare mutations, it is a fixed set of DNA-based instructions, the blueprint for life.
An organism’s phenotype, on the other hand, is determined both by its genotype and the environment(s) in which it has existed. Biologists often express this in the simple equation: Phenotype = Genotype + Environment (P = G + E). Colloquially, we often say an individual is the product of both nature and nurture.
Nature is quite familiar to ag producers, sometimes beneficent, sometimes malevolent. Early season frost, timely rain, a spotted wing drosophila invasion, perfect harvest conditions, those biotic and abiotic factors that have positive and negative impacts on their crop.
Of course, producers attempt to manipulate their environment to optimize the quality and quantity of the end product, whether it is a rose flower, an apple fruit, an almond nut, a golf course green, or a bottle of wine.
Specialty Crop Applications
In addition to the usual crop protection measures, for most specialty crops we employ intensive and expensive management of vegetative and reproductive growth via production systems, nutrient and irrigation inputs, plant growth regulators and various cultural practices.
Furthermore, we select a specific genotype that has demonstrated it will perform well in our managed agricultural environment. With the right combination of the right cultivar and the right management (and some luck), a producer harvests the perfect phenotype.
Obviously, this simple equation is not so easily applied, given climate changes, unpredictable weather events, and ceaseless pest and disease pressures. In fact, it is amazing how effective countless generations of agriculturists have been prior to the application of modern science and technology.
Not that current scientists, blessed with the tools of genomics analysis and the digital revolution, have been much more effective in their quest to understand and optimize both the genetic potential of cultivars and management practices.
Technological advances now permit the rapid and relatively inexpensive genotyping of individual genomes, from microbes to crop plants to humans. What took millions of dollars and many years a decade ago now takes a couple hundred dollars and a few hours.
But this ability to more rapidly, affordably, and reliably obtain genomic sequences of a single individual, plant or animal, only provides a data set. This data must be interpreted, validated, and applied appropriately so we can link a genotype with a phenotype.
This is exactly what 23andMe offers its customers. Knowing the specific genetic profile you have for a given trait allows you to understand where your great-great-great grandparents called home, or if you have a specific genetic variant that you could transmit to your offspring, possibly leading to a heritable disease.
Scientific advances in crop plants can be informed by advances in human biology — which is exactly what is happening now.
National Meeting On Phenotyping
Recently, a newly-constituted entity called the Foundation for Food and Agriculture Research (FFAR) organized a national meeting held at Purdue University to initiate the North American Plant Phenotyping Network.
Gathering nearly 200 scientists and industry stakeholders for three days, FFAR, funded for $200 million in the 2014 Farm Bill, is seeking to develop a national strategic vision to propel scientific understanding of the interaction of a plant’s genotype and phenotype, emphasizing high-throughput phenomics approaches.
These approaches include everything from sensor-laden drones to laser-based imaging to precise microscopic robots. All approaches will rely on massive computer databases and intensive processing capacity, part of the “big data” revolution.
When the Human Genome Project was initiated in 1990, the words “genomics” and “phenomics” were unfamiliar to most. In 2016 genomics has meaning and real promise to improve human well-being.
I hope phenomics soon carries the same weight and researchers are not the only folks interested in solving the P = G + E equation. Ultimately, consumers will benefit from superior new cultivars and optimized production practices — enjoying their favorite specialty crop phenotypes.
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