Since 1995, the genomes of nearly 50 plants have been sequenced and thanks to advances in technology, the rate at which these sets of genetic instructions are being deciphered is increasing rapidly.
Just 10 plant genomes were sequenced between 2000 and 2008. In 2012, by comparison, 13 genomes were published and 12 more in 2013. They include corn, wheat, barley, rice, soybeans, hemp, cotton, flax, apple, peach, watermelon, tomato and the list goes on. “Having these increasingly comprehensive collections of DNA allows us to mine useful genes more efficiently and make better use of them,” says Owen Hoekenga, research molecular biologist for Cornell University.
Once the genome has been sequenced, genotyping tools can be used to determine the genetic variants that any individual plants might possess. Genotyping provides information about the complete genetic makeup of a particular plant variety or species. It allows breeders to quickly identify desirable traits that can potentially be deployed across varieties of the same species, and in some cases across different plant species using transgenic technologies.
“As genotyping tools become increasingly inexpensive, it’ll be more straightforward to deploy traits into a wider range of germplasm for broader impact,” says Hoekenga.
In November 2012, a team of international scientists announced that they had sequenced the wheat genome that contains 96,000 genes and is five times larger than the human genome. That was followed by sequencing of the barley genome in October 2012, which has 5.3 billion letters of genetic code. Because the genomes of plants such as barley and wheat are so large, scientists use a technique called shotgun sequencing, which essentially breaks the genome into smaller, more manageable segments for analysis and then reassembles them.
“Shotgun sequencing is routinely applied to increasingly large and complex organisms,” says Hoekenga. “It’s so much more efficient in terms of how much information you recover from a single experiment.”
DNA Mapping and Sequencing
Many people mistake DNA mapping and sequencing for the same thing, but they are different processes that provide different information. A DNA (or genetic) map shows where certain things (identified with genetic markers) are located and in what order on the chromosome of a genome. DNA sequencing (of a genome) is much more comprehensive and reveals not just where things are on the chromosome, but also what they look like and what they do.
Genetic sequencing identifies the specific genes or forms of a gene (alleles) that confer or control traits or functions that could be useful to plant breeders, such as those that influence yield, oil or protein content.
“It’s now more time and cost efficient to use genome sequencing to ask genetic mapping questions because for the same amount of time, effort and cost, we can get 100,000 pieces of information simultaneously, rather than 10,” says Hoekenga.
Gene Silencing Technology
Understanding how plants turn specific genes on and off to perform certain functions or defend themselves may pave the way for new varieties with increased pest and disease resistance through the use of gene silencing technology. One of these technologies, RNA interference (RNAi) is being employed by major seed companies. Monsanto is trying to provide resistance to pests such as corn rootworm.
“RNAi is one of a number of mechanisms by which genes can be silenced or turned off,” says Hoekenga. “Part of RNAi relies on the fact that in plants there are sensing mechanisms that can recognize RNA molecules that they regard as being pathogens in some way. If you can introduce into a plant a sequence that creates an RNA molecule that matches the gene you want to turn off, the plant will recognize this trigger and turn off the target gene. Gene silencing can not only be used to silence genes that exist in the plant, but they can also be used to silence genes of organisms that interact with the plant [like diseases and pests].”
Two genetic discoveries in 2013 may help raise global crop yields. An Israeli agri-tech company hopes to increase crop yields without the aid of genetic modification by speeding up the multiplication of crop genomes using a technique called genome doubling. Genome doubling occurs in nature, but takes thousands of years. Hoekenga explains that although this may be a new way to use genome doubling (also called polyploidy), it’s not a new technology.
Cornell researchers also announced the discovery of a scarecrow gene, which leads to more efficient plant photosynthesis. Researchers say the discovery opens the door to the transference of C4 plant mechanisms into C3 plants, such as wheat and rice, which would allow them to be grown in hotter, dryer environments with less fertilizer and still achieve up to 50 per cent higher yields.
Pests and Diseases
The genomes of pests such as the pea aphid and the diamondback moth have been sequenced and researchers are closer to improved resistance to soybean cyst nematode. For years, growers have been planting soybeans with just one gene, Rhg1, as a defense against SCN. A U.S. research team has discovered that Rhg1 is actually three genes located next to each other on the chromosome, which work together to provide SCN resistance and, if this gene group can be identified in multiple varieties, should provide more options to develop better resistance.
Diseases are also being examined at the molecular level. An international team of scientists in 2010 cracked the genetic code of a plant pathogen, Hyaloperonospora arabidopsidis, that causes downy mildew. This “stealth bomber” of plant pathogens is able to sneak undetected past a plant’s immune defenses and understanding the genetic mechanisms it uses to do this will be useful in developing better resistance to a variety of plant pathogens. Angela Lovell