The process of developing new crop varieties requires many steps and can take almost 25 years. Now, however, applications of agricultural biotechnology have considerably shortened the time it takes to bring them to market. It currently takes 7-10 years for new crop varieties to be developed. One of the tools, which make it easier and faster for scientists to select plant traits is called marker-assisted selection (MAS). The different traits and physical features of plants are encoded in the plant's genetic material, the deoxyribonucleic acid (DNA). The DNA occurs in pairs of chromosomes (strands of genetic material), one coming from each parent. The genes, which control the plant's characteristics, are specific segments of each chromosome. All of the plant's genes together make up its genome.
Some traits, like flower color, may be controlled by only one gene. Other more complex characteristics, however, like crop yield or starch content, maybe influenced by many genes. Traditionally, plant breeders have selected plants based on their visible or measurable traits, called the phenotype. But, this process can be difficult, slow, influenced by the environment, and costly - not only in the development itself, but also for the economy, as farmers suffer crop losses.
As a shortcut, plant breeders now use molecular marker-assisted selection. To help identify specific genes, scientists use what are called molecular markers which are short strings or sequence of nucleic acid which makes up a segment of DNA. The markers are located near the DNA sequence of the desired gene. Since the markers and the genes are close together on the same chromosome, they tend to stay together as each generation of plants is produced. This is called genetic linkage. This linkage helps scientists to predict whether a plant will have the desired gene. If researchers can find the marker for the gene, it means the gene itself is present.
As scientists learn where each of the markers occurs on a chromosome, and how close it is to a specific gene, they can create a map of the markers and genes on specific chromosomes. This genetic linkage map shows the location of markers and genes, and their distance from other known genes. Scientists can produce detailed maps in only one generation of plant breeding. Previously, scientists produced very simple genetic maps using conventional techniques. It was observed long ago that as generations of plants were crossed, some traits consistently appeared together in the new generations (genetic linkage). However, since researchers could concentrate on only a few traits in each attempt at cross-breeding, it took many crosses to obtain even a very simple genetic map. Using very detailed genetic maps and better knowledge of the molecular structure of a plant's DNA, researchers can analyze a tiny bit of tissue from a newly germinated seedling. They don't have to wait for the seedling to grow into a mature plant to test for the presence of the specific trait. Once the tissue is analyzed through molecular techniques, scientists know whether that seedling contains the appropriate gene. If it doesn't, they can quickly move on and concentrate analysis on another seedling, eventually working only with the plants which contain the specific trait.
Currently, molecular marker-assisted breeding, an agricultural biotechnology tool is already a routine step in breeding of most crops where the gene and the markers for a specific trait are known. This technique is being used in the efficient introgression of important genes into rice such as bacterial blight resistance, increased beta carotene content, and submergence tolerance to name a few.
Molecular markers are also used to determine the genetic profile of a line or variety. Random primers are used to scan the genomic constitution of the plant through molecular methods. The information is fed to a computer program that will analyze the relatedness of one line to another. The information on genetic diversity of the lines is utilized in selecting for extremely unrelated parents useful for hybrid seed technology. The information will also provide details on the parentage of the line, the possible traits, and the unique identity of the plant useful for germplasm collection database.
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