"I hear that train a'coming. It's coming down the line."


Although the rest of that old Johnny Cash song may not fit what's happening with corn, soybean and other major crop genome sequencing, the first two lines are appropriate. There is a train coming, and it's headed our way. According to Jim Specht, professor of agronomy and horticulture, University of Nebraska, it's being pulled by a locomotive that is still building speed. With that ever-increasing speed comes new discoveries and potential improvements in crop productivity.


If you feel like you've heard that promise as often as you've heard the Folsom Prison refrain, there's good reason. Announcements in the past year of mapping the maize and soybean genome, like the 2005 announced mapping of the rice genome, have been accompanied by anticipations of great improvements in quality and productivity. While advances are being made, it's hard to credit a single event like mapping of the genome. So, what does it mean for input suppliers, growers and others?


The fact is that mapping a single genome is neither the beginning nor the end. It is a major benchmark along the way, one that helps that locomotive build more momentum. It means researchers now have a basic roadmap for mapped crops, one they can use to gather more information in a process that has been underway since natural selection gave way to man's selection process and modern crops were born.


Speeding Up Progress


Throughout the 19th and 20th century, man's knowledge of and ability to identify and work with genes and the traits they represented grew rapidly. Each discovery served as fuel for the next. By the end of the 20th century, plant breeders had begun to identify traits by markers along the genetic map; however, knowledge was sporadic. "It was like having a sign post every 50 or 100 miles," said Specht, part of a team that reported identifying 20 linkage groups in 1999.


By 2004, he and his research team had identified, mapped and manipulated one of those linkage groups or QTLs (quantitative trait loci) to increase soybean seed protein by two percentage points. "Once we identified the QTL segment, we had to drag it into a cultivar to see what impact it had," recalled Specht. "It was a five to six year process of removing the junk genes and moving in what we wanted."


With full genome mapping, those occasional road markers have been replaced with a detailed description of every brick in the roadway — all 46,000 genes and 1.1 billion nucleotides. What took Specht years can be done in a single season. "We can identify the parts of the sequence that relate to a particular gene, look at it and plug it into a variety to understand what it does," explained Specht. "Then we can find the actual genes that will have the impact we want and put them to work."


With the map in hand, where a gene can be found is no longer the question to be asked, but rather what does it do. Using a novel technique developed in Specht's lab, his team has found an amino acid transporter gene on one chromosome. Since amino acid production determines protein and oil levels in the seed, identifying this transporter gene opens the door to manipulating those levels.


"Without the genome sequence map, we would have no idea this gene existed," said Specht.


He is quick to point out that the published genome map is only for Williams 82, one of the last publically developed soybean varieties released. Now Specht and others are comparing that map with other varieties and other mapped legumes, looking for commonalities and differences that can be exploited for improved pest resistance and enhanced seed qualities. Knowing where a particular gene is on Williams 82 and what it does, it is simple to look for it on another variety.


Specht and USDA colleagues David Hyten and Perry Cregan are evaluating the 19,000 samples in the USDA soybean germplasm collection, which includes developed cultivars as well as wild ancestors. "Most of the U.S. cultivars trace back to only 20 ancestors," explained Specht. "Regional breeders tended to cross the best lines for that region. We want to know if there were genes that were missed that could contribute to a significant boost in yield or defense against pests."


Corn Genetics Prove Complicated


Although that task seems daunting for soybeans, it may be simple compared to work with maize. "The genetic difference between varieties in soybeans is similar to the genetic difference between humans," explained Scott Jackson, professor of agronomy, Purdue University. "The contrast between two inbred lines in corn is like comparing humans to chimpanzees. The difference is due to soybeans being self-pollinating, while maize is very out bred. Other crops are even more complicated."


Even so, having a map of a single corn line, Maize B73, like the map of Williams 82 for soybeans, is immensely valuable, noted Shawn Kaeppler, professor, agronomy, University of Wisconsin. For the past 20 years he has been investigating the corn genome and applying the information through breeding.


"We can use the information to help select individuals based on their genotype," he said. "Traditionally, we had to grow a cross of two lines out in the field and select for traits. Now we can make predictions based on the DNA they carry and focus on the top 25 percent."


Prior to sequencing of Maize B73, corn breeders had information on roughly 1 percent of the 50,000 genes dispersed across 20 chromosomes. Today, they have information on each of the 50,000 genes. Where Kaeppler used to spend years gathering a few hundred data points, today he can get hundreds of thousands of data points in a week. This information is helping as he focuses on corn root structures. Knowing which QTLs are responsible, he can now compare root structures from different varieties and then compare their causal QTLs. Superior traits will then be used in future breeding efforts.


"What we are doing is looking at corn root structures as they relate to drought tolerance, low nitrogen and phosphorous levels and other stresses and measuring the characteristics of the root system, angles, size, amount of root branches," explained Kaeppler. "We are using lots of sequencing and high-density genotyping. The information helps to characterize genetic models and the differences in the various genotypes."


Bottlenecks Expected


Kaeppler cautioned that retailers and growers may not see tangible results from the work his team is doing. But the information being gathered will improve stability and yield over time. "The large private breeders are extensively using the information to facilitate breeding programs and selection of genotypes."


Jackson pointed out that bottlenecks remain. Genomics are somewhat nailed down, and comparing sequences of one variety with the reference genome is very cost effective. A major challenge is matching up genotype information with phenotype delivery. Even if a plant breeder like Kaeppler is now only looking at a quarter of the progeny from crossing two lines, he still needs someone to do the field analysis necessary.


"Field-based phenotyping is the real slowdown today," said Jackson. "There simply aren't enough people trained in collecting and integrating field data with genomics. The next generation of plant breeder will have to be as adept at phenotyping as genotyping."


He is seeing seed companies doing some cross training of their own personnel. Colleges like Purdue are getting pressure from students and their potential employers in industry for this type of training; however, making changes is expensive relative to college budgets.


"I expect we will see university and industry partnerships," Jackson said. "Some of that is happening already."


Another bottleneck is a result of the evolution to privately developed and patented varieties and hybrids in the 1980s. They are not available for the type of germplasm comparison work that Specht is doing. How these bottlenecks and others yet to be identified will be resolved will determine how quickly the promise of genome sequencing is delivered. One thing that Specht is confident of is that delivery will occur. The momentum of scientific knowledge will overcome the problems, and that train will arrive at the station as promised.


"I have to constantly remind myself to never underestimate the locomotive power of science," said Specht.