Home > Industry Issues > Research > Interview with Dr. Fred Gmitter of IFAS on the Citrus Genome
Interview with Dr. Fred Gmitter of IFAS on the Citrus Genome
1) What does sequencing the citrus genome mean?
DNA is the molecule that codes for all genes that exist in any given organism, including our favorite citrus trees. DNA is something like a string of beads, with each bead being one of 4 nucleotides (abbreviated as A, T, C, and G). This 4 letter alphabet in various combinations makes up the “words” in the string, and we might think of these words as the genes of the citrus tree. Actually, there are 9 pairs of DNA strings in the nucleus of each cell in a citrus plant, whether the cell is in the root, flower, leaf, or fruit, all encoding the same basic information. Differences in gene expression in different tissues is what makes some cells develop into a fruit, the peel, the stem, and so on; but the information contained within the DNA strings is the same in all cells. This collection of DNA strings is what is called the genome; it is all the DNA sequence, including “words” that code for specific products as well as elements that control expression (on or off) of genes in response to the environment, pathogens, and interactions with the products of other genes.
DNA sequencing is a process starting with extraction of DNA, followed by cutting the long strings (total length in citrus is ~385 million letters long) into small pieces each of which can be sequenced; that is, a machine “reads” the sequence order of the 4 letters usually in lengths of ~700 letters at a time. Because the strings are cut randomly and there are many copies of each string in the initial extract, the end result is that there is overlap of the “reads” and by recognizing the overlapped regions, the entire sequence of the original strings can be nearly reconstructed. Once this assembly step has taken place, powerful computers and software programs can analyze the sequence to identify the many genes (“words”) coded, their controlling factors, and other elements, based on their features. By comparing these potential genes with other already sequenced genomes and genes, potential functions of specific genes can be identified. For example, it is very possible to identify all the genes involved in disease resistance that a plant has by searching its genome for features that are commonly known from disease resistance gene sequences in other plants.
The end result of sequencing the citrus genome is that the catalogue of all genes within citrus can be identified as a starting point for further analysis.
2) I’ve heard sequencing the citrus genome compared to unlocking a door that leads to a room full of research possibilities. Can you explain the analogy?
To expand on this analogy, knowing all of the genes really is just the starting point of further research, which is necessary to extract the value to growers and consumers of the genome sequence. For example, we may know the location and identity of all the genes for resistance to pathogens, but we will not know just from the sequence alone which gene confers resistance to which pathogen, or whether the form of the gene actually allows a plant to be susceptible rather than resistant to any given pathogen. Or we may be able to know that all of the genes in a pathway that leads to fruit color development, for example, may be present in a citrus plant, but we might not necessarily know how they are expressed differently in a lemon compared with a tangerine, for example; one fruit appears yellow while the other appears deep orange. The variation in traits among citrus plants can be the result of different forms (or by analogy different spellings of the “words”) of the same gene that leads to different end characteristics, just like common but different forms of genes for human eye color can result in blue or brown eyes, or different hair color, etc. So, having just one genome sequence is merely the starting point. The value in having a very solid foundational sequence comes from the ability to identify the core genes a citrus tree has; but then by comparing the various forms of specific genes (or their expression differences) among different types of citrus (sweet vs. sour, resistant vs. susceptible, cold-tolerant- vs. cold-hardy, red vs. yellow, and so on), scientists can begin to have a real understanding of the nature of the genetic variation that exists, and with that comes insights into how best to manipulate that genetic variation to developed improved citrus plants. While the focus in Florida is currently on HLB (greening) as the most significant threat, the full genome sequence is in reality a tool that can be applied to ANY trait or characteristic of importance to producers, marketers, and consumers, because ALL genes in the citrus tree can be identified and studied.
Much molecular genetic research has gone on previously in citrus to address specific problems by identifying and determining the sequences of key genes that affect these problems. In some specific cases it has taken almost ten years to accomplish this task, before the advent of modern genome sequencing technology. With a full genome sequence, citrus researchers can move directly to the identification and verification of the activity of specific gene targets immediately, for any trait of interest, saving many years of duplicated effort across many labs for many different characteristics. Still, there must be the hard and unavoidable work of looking at plants and studying their behavior, to associate specific genes with specific characteristics and traits. Having the genome sequence enables scientists to do so in a much more rapid and efficient manner.
3) What has genome sequencing done for other agricultural commodities?
It is really only very recently that plant genomes have been sequenced. In fact the first fruit plant genome sequences were just released this past summer; two different groups in Europe sequenced grape, and they were able to very quickly identify all of the genes associated with disease resistance, stress tolerances, and (importantly for grapes being used to make wine) the genes involved with flavor and pigmentation elements. Arabidopsis thaliana, the guinea pig of plant biology, was the first plant sequenced, and its gene content has been used to help identify the functions of genes in other plants; in fact, even the human genome has been useful for identifying possible gene functions in plants. The entire world biology research community, in fact, makes their information generally publicly available, and it is through this global resource that agricultural plant researchers are able to put forth hypotheses to test and to predict functions of genes in their favorite species (citrus in our case!). The rice genome has been available for a few years now, as well, and because of this certain genes for seed quality (that is, in nutritive value of the rice) have already been identified and manipulated through breeding; likewise, genes for salt and drought tolerance were very easily identified. Knowledge and understanding of these useful genes will result in increased yields and crop productivity, and currently rice researchers are looking at genome information to hasten the development of rice plants that can be productive in a time of global warming and changing climatic zones for production. A little more than 2 weeks ago a first draft genome of corn was announced. “Successfully sequencing the maize genome will have a phenomenal impact on agriculture and agricultural productivity,” said William S. Niebur, DuPont vice president, Crop Genetics Research and Development. This impact will come through an ability to more rapidly breed and select improved types of plants as well as having tools to better understand the complexities of plant behaviors and interactions with environment, to improve plants in ways not ever considered previously. The citrus research community will likewise have a tremendously valuable new resource to address the concerns of the industry, once citrus genome sequencing has been accomplished.
4) How far along are you?
Much preliminary work has been done to achieve the goal of a high quality citrus genome sequence, but much more lies ahead. Through the activities of the International Citrus Genome Consortium (ICGC), concrete plans have been developed and a reference plant has been selected that will provide the highest quality sequence assembly possible. This will be made available to all participants in the ICGC for the subsequent downstream applications, such as described above. It is anticipated to cost ~$3.2 million, and it is our goal to have completed the sequencing phase of the project within the next 12-18 months. Of course, also as pointed out above, that is the beginning point of more research aimed at current and future challenges and opportunities our industry faces.
5) Will sequencing the citrus genome get us any closer to finding a long term solution to greening?
Sequencing the genome will NOT solve greening in the short term. Having the genome sequenced, however, does place a profoundly powerful tool into the hands of the citrus research community that will allow many types of researchable questions to be raised, which could not be answered by any other means. Should differences be found in the responses of some citrus plants to HLB infection compared with others, for example a plant that developed no symptoms, or even a plant that was resistant to HLB, it becomes substantially easier for scientists to begin to determine why and how such phenomena occur and then to devise methods to exploit that information in plants that could be tolerant or even resistant to HLB. In addition, by knowing all genes that are present in citrus plants, and then by following their changing expression patterns as disease progresses, it might be possible to devise a genetic strategy using the citrus plants’ own genes to interrupt the disease progression. In fact, these are the kinds of applications of genomic science that human medical researchers now are pursuing in studies of human pathology. Knowing the genes involved in very early stages of infection by HLB might enable scientists to develop extremely sensitive detection techniques, far exceeding our current ability to detect and diagnose asymptomatic trees for removal, this being one of the keystones of the current HLB management strategies being promoted. Greater understanding of the interactions of psyllid vectors with citrus at the genetic level could potentially reveal new strategies for psyllid management not yet considered. As stated above, the citrus genome sequence is a powerful tool for discovery, and it is a tool that the citrus research community needs now not only for HLB, but for other pests and pathogens not yet here in Florida. In addition it holds great value for studying all of the other traits of interest that have captured the attention of citrus researchers over the years, such as CTV, Phytophthora, blight (remember citrus blight?), cold tolerance, high soil pH, salinity, fruit quality, yield, and so on.
