Applications of genomics approaches to agriculture
Agriculture is the primary means of meeting the nutritional needs of the world’s population. The projected growth in population from the current 6 billion to 9–10 billion within 50 years will put enormous strains on the world’s food supply. At present, approximately 800 million people are malnourished. In the past, improvements in agriculture through the use of traditional breeding approaches managed to keep pace with increased demand. In the 1960s and 1970s, breeders produced new strains of rice and other crops that significantly increased yields, resulting in what was called the “green revolution.” The problem facing agriculture today is that traditional breeding requires many years to bring together desirable traits and eliminate undesirable traits. The time required for traditional breeding is one of the major reasons that agricultural researchers both in academia and in the biotech industry have turned to genomics as a source of the next green revolution. Genomics has the potential to rapidly identify genes that confer useful traits. Sequencing of the genomes of agriculturally important species allows researchers to relate a trait on a genetic map to a specific gene on the physical map.
Keywords: Agriculture, plant, sequencing, species, QTL, genes, organism
- Genomics applied to agriculture:
Agriculture encompasses two major classes of organisms: crop plants and farm animals. Among crop plants, the most important, both economically and nutritionally are rice, maize (corn), and wheat. The most studied farm animals are the large mammals—cows, pigs, and horses—as well as poultry. The genomics approaches applied to agriculturally important species are very similar for both plants and animals. Of key interest is the ability to relate an agriculturally important trait, like meat quality, to one or more genes. A first step in this process is to develop high-density genetic and physical maps. Traits occasionally segregate as simple monogenic loci, in which case they are relatively straightforward to place on a genetic map. More often, more than one gene contributes to a trait. To identify the contributions of several genes to a trait, a genetic analysis known as quantitative-trait loci (QTL) is used. For both single- and multiple-gene traits, the fastest way to identify the gene(s) of interest is to relate the physical-map location of the gene(s) to a full-genome sequence. The problem is that most agriculturally important species, both plants and animals, have very large genomes. Therefore, alternative approaches have been taken, including relying on synthetic relationships and EST libraries. Once important genes are identified, the hope is that they can be manipulated, either through breeding or through engineering, to remove deleterious traits and enhance desirable traits.
- Sequencing of plant genomes:
Most crop-plant genomes are very large; the first plant to be sequenced had no direct agricultural value. Arabidopsis thaliana is a weed related to cabbage and mustard. Nevertheless, it has become known as the plant model species. Some researchers have begun to refer to it as the “reference plant” because its physiology and development are much more similar to those of crop plants than the physiology and development of animal model systems such as Drosophila or C. elegans are to those of humans. The Arabidopsis genome sequence was published in December 2000. The genome is approximately 130 Mbp in size, which is similar to those of C. elegans and Drosophila. It contains approximately 28,000 genes, which approximately the same number is found in humans and quite a bit more than that found in C. elegans and Drosophila. The large number of genes is probably related to the fact that major portions of the genome appear to have undergone relatively recent duplications. Those so-called segmental duplications larger than 100 kb make up nearly 60% of the Arabidopsis genome. Both large-scale genome duplications and tandem repeats account for the fact that only 35% of Arabidopsis genes are unique, while 38% belong to families of more than five members.
- Sequencing strategies for grass genomes:
The structure of cereal-crop genomes has led to alternative approaches to genome sequencing that isolate the genic islands and leave behind the sea of retroposons. One approach relies on the fact that the genic islands tend to contain a lower number of methyl groups attached to the DNA than that contained by the retroposon regions. Bacteria that have enzymes which recognize and digest methylated DNA are then used to produce libraries of genomic DNA. The resulting libraries are enriched for regions of non-methylated DNA. Another approach uses the property of hybridization kinetics of DNA to enrich for genic islands. The DNA is sheared, and the two strands are separated and then allowed to renewal. Repetitive DNA will find a complementary strand faster than non-repetitive DNA.
- Genomics of farm mammals:
Genome-sequencing efforts have been initiated or are being contemplated for all of the major farm animals, including pig, cow, sheep, and poultry. For the first three, it is generally viewed that, because they are close relatives of rodents and humans, draft sequences should suffice. The idea is to use the mouse, rat, and human genomes as scaffolds upon which one can place draft sequences of the related farm animals. BAC libraries have been made for all of these species, and connoting maps are in progress. As sequencing costs fall, full-genome sequences will almost certainly become available. In the meantime, there are extensive EST libraries available for most farm mammals.
- Sequencing of agricultural pathogens:
In addition to providing information about the genomes of agriculturally valuable species, genomics can also aid in the identification and detection of pathogens that attack crop plants and farm animals. Work has already begun to sequence the genomes of both plant and animal pathogens. Among animal pathogens, most are viruses or bacteria, which have relatively small genomes. The completed sequence of Brucella suis, a bacteria that infects animals and can also cause disease in humans, revealed that many of the genes that control its metabolism perform a similar function in a plant pathogen, Agrobacterium tumefaciens. Although viruses and bacteria can infect plants as well, many of the worst plant pathogens, in economic terms, are fungi, which have relatively large genomes. This fact has meant that sequencing of plant pathogens has lagged behind that of animal pathogens. Nevertheless, some plant pathogens are now being sequenced, including Phytophtora, the fungus responsible for potato blight, and Fusarium graminearum, which causes diseases in barley and wheat.
- Bioterrorism issues:
Additional impetus for sequencing agricultural pathogens has come from worries about possible bioterrorism attacks. With the agricultural practices used on most U.S. farms, diseases can spread very rapidly. An example of the pace of disease spread was seen with the recent outbreak in the United Kingdom of foot-and-mouth disease, which was not related to bioterrorism. The economic effects of disease outbreak can be devastating. The cost to the British economy of the foot-and-mouth disease outbreak was estimated to be as much as US $48 billion. Knowledge of pathogen genomes will permit the rapid identification of the cause of a disease outbreak. Genomic knowledge may also be used in new rapid-detection technologies being developed to combat bioterrorism. In fact, the bacteria Brucella suis were considered for use as a potential bio warfare agent by the U.S. military, which tested its efficacy in 1950.
The research community must pay attention to the development of locally adapted varieties. A second Green Revolution, driven largely by eliminating production constraints, may integrate activities towards advancing the productivity frontier and transforming production systems. Genomic tools provide an infrastructure to lay bare the secrets of the genetic potential of plants to respond to a range of environments. Much foundational work remains to be done and translating this information into climate resilient crops will require additional large investments. As agricultural initiatives can take 15–30 years to yield maximal returns the required investments need to be made now. By working together, leading crop genome researchers can help safeguard future food supplies.
This article is collectively authored by Aqsa Arshad1*, Asim Munawar1, Muhammad Ishaque Mastoi2, Muhammad Ali3-1Department of Entomology, University of Agriculture Faisalabad. 2Department of Plant and Environmental Protection, NARC, Park Road Islamabad. 3 Department of Clinical Medicine and Surgery, University of Agriculture Faisalabad.