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Cherry Genomics, 4-H License Plate

Posted by | April 25, 2012

Tiny Differences Help Scientists Take Giant Steps Forward

    Regional differences--as between the 'A' and the 'T' in the genetic sequence above--provide genomic scientists with powerful tools in their ongoing pursuit of bettern fruit.
Regional differences–as between the ‘A’ and the ‘T’ in the genetic sequence above–provide genomic scientists with powerful tools in their ongoing pursuit of better fruit.

Genetics has something in common with linguistics. If I say “po-tay-toe” and you say “po-tah-toe,” a linguist can begin to tell which part of the country each of us is from. To a linguist, a tiny difference in the pronunciation of a vowel acts as a kind of marker. So, too, with genetics: single nucleotide polymorphisms are minute differences that help geneticists differentiate between members of a single species. With DNA, though, there are only four “vowels” — A, C, G, and T — the nucleotides that can configure themselves in many (“poly”) forms (“morphisms”).

These tiny differences are, to geneticists and their partners, the plant breeders, markers of potentially interesting traits. If one plant has, say, a resistance to powdery mildew (an all too frequent disease known to farmers and gardeners) while another does not, sequencing the genomes of those two individuals and then contrasting the map of their genomes may reveal a SNP (single nucleotide polymorphism); that is, a polymorphism in a single nucleotide that makes the difference between resistance and lack of resistance to powdery mildew.

That’s why WSU plant scientists have been hard at work using various approaches to identify SNPs. WSU horticultural genomicist Amit Dhingra and his students and colleagues have helped make significant advances in efforts to breed better fruit.

Better Fruit

“Better fruit is the ultimate goal,” said Tyson Koepke, a doctoral student in Dhingra’s lab. Koepke and a team of WSU scientists recently completed work that resulted in the identification of over 2,000 SNPs in cherry.

“This represents a significant advance in genetics, genomics and breeding,” said Dhingra, especially for cherry. “Compared to peach and apple, sweet cherry lacks in genetic and genomic information, impeding understanding of important biological processes and development of efficient breeding approaches,” Koepke and his colleagues wrote in a paper published recently in BMC Genomics.

“This work also represents an all-Cougar collaboration that includes Nnadozie Oraguzie, sweet cherry breeder, and Mathew Whiting, stone fruit physiologist, both based at WSU’s Irrigated Agriculture Research and Extension Center in Prosser,” said Dhingra.

Better Efficiencies

For thousands of years, plant breeding has been incredibly inefficient. For millennia, humans bred plants by employing their senses to evaluate the organism for desirable traits. Are its kernels large and plentiful, and do they mill easily? Does the plant easily succumb to disease? Is this plant’s fruit sweet, juicy, and plentiful, or is it mealy and bland? Answering these questions required assessing multiple generations of plants. If you were looking for a better variety of wheat, you could move toward more desirable plants fairly quickly, as there is a new generation of wheat every year. If your goal was a better cherry, pear, or apple, though, you could spend your lifetime looking and still not make much progress, because it takes several years for a tree to produce fruit.

Tyson Koepke sampled the DNA from thousands of cherry plants in order to identify key SNPs.
Tyson Koepke sampled the DNA from thousands of cherry plants in order to identify key SNPs. Photo by Brian Charles Clark

Plant breeding has accelerated in recent decades thanks to the availability of new technology. Genetic analysis, in particular, has benefited from the computing revolution, as well as advances in laboratory techniques. Now, plant breeders can screen for desirable traits in plants before they ever appear in the growing plant itself. It’s these technologies that enable genomicists like Dhingra and Koepke to push the envelope and enable their plant-breeder colleagues to develop new varieties in years instead of decades.

SNPs of Yesteryear

The efforts of Dhingra and his colleagues are the result of years of innovation by a great many people all around the world. Karen Adams, the manager of Dhingra’s lab at WSU, has nearly 30 years of experience as a genetics research technician that includes being a firsthand witness to a lot of those developments.

Adams said that the ability of modern researchers to use SNPs as markers has been made possible by technological advances in genetic sequencing–the early equipment was large, slow, and expensive. “Not so long ago, people had to do their own sequencing, as there were no banks of machines to do it for us. Then, we had to do a different reaction for every nucleotide. Now, they are all done together. When I started working in this field, the results were read by hand; you were the computer. Now the process is automated,” and the quantity of data being processed is many orders of magnitude larger.

Moore’s Law

This is Moore’s Law in action, writ large and applied to every area of human endeavor that computing touches, especially the sciences. Moore’s Law, simply put, states that the number of transistors on a microchip–and thus the chip’s computing horsepower–doubles every couple of years. Humans made round trips to the moon using computers with an interface similar to a pocket calculator and with less computing power than a modern car. Computing and other technological advances now make trips to Mars, or even farther, a possibility.

Similarly, with the limitations of early genetic sequencing equipment, “we would get a few hundred base pairs of genetic sequencing information,” Adams said, an amount of data that, by today’s standards, is miniscule, “and the process of getting it could take days.” Sequencing the human genome, for example, took 13 years using the technology available between 1990, when it started, and 2003, when it was finally completed. “Today,” said Dhingra, “the genome can be sequenced in a week.”

Not only is reaction time, along with data processing and analysis, many times faster, but the raw materials have changed as well. To analyze human genetic makeup, Adams said, “we used to have to draw 50 milliliters (about two fluid ounces) of blood. Now, nearly as much information can be gleaned from the follicle from a hair.”

With hundreds of species of crop plants still to be genetically mapped, the project is huge and daunting. But every technological advance, along with the persistence and expertise of WSU researchers, brings us closer to translating the language of plant genomes into science-based solutions for the challenges faced by Washington tree-fruit growers.

–Brian Clark

Learn more about the genomics research going on in the Dhingra lab at WSU, as well as opportunities for both undergraduates and graduate students, by visiting genomics.wsu.edu.

This article is based in part on “Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3’UTR sequencing,” a paper by Koepke, et al., published in BMC Genomics. The paper is available online at http://bit.ly/JazIPw.

Washington State 4-H License Plate Bill Signed into Law

The new 4-H license plate will help support programs for youth.

Legislation to create a special 4-H license plate for the state’s largest youth development program is now in effect. On March 23, Governor Christine Gregoire signed the bill that will allow the design of a license plate with the 4-H clover. House Bill 2299, sponsored by Rep. Judy Warnick (R- Moses Lake), a former 4-H’er, permits drivers to purchase the plates for $40 and renew for $30 (in addition to the cost of standard license plates).

“The specialized 4-H license plates will be a wonderful way for current 4-H families as well as alumni and supporters to increase awareness about the 4-H program as they drive across town or across the state,” said Pat BoyEs, director, 4-H Youth Development, Washington State University Extension.

The Washington Department of Licensing will collect the fees and deposit funds after administrative expenses into the newly created 4-H programs account in the state treasury. Money raised will go toward activities to support the 90,000 youth served in the state.

In addition to support from Representative Warnick the bill was also backed by Senators Curtis King and Mary Margaret Haugen.

In February, a group of 4-H students spoke in favor of the bill in a Senate transportation hearing committee meeting. The youth were in Olympia as part of the annual WSU Extension 4-H Know Your Government Conference.

The 4-H license plates will be available in 2013.

Learn more about 4-H at 4h.wsu.edu.