The field of botanical genetics is booming with calls for more and more information about the ways in which plants pass on their characteristics, gather up nutrients that are important for human sustenance, maintain their defenses against predators and disease, and produce chemicals and fibers that are essential to a lot of our medicines, industrial applications, and textiles. In other cases, we need to know how to keep problematic species from invading and taking over, or at least how to make use of them in ways that benefit mankind.
Botanical geneticists look at the complex traits of plants from a genetic, physiological and molecular basis. In some cases the attempt is to identify traits that affect the plant's performance and metabolic functions. In other cases, we want to examine the traits that allow plants to accumulate or to produce compounds and substances that are essential for nutrition, such as minerals, heavy metals and phytochemicals.
Mostly, plant genetics study begins with the phenotype, or the observable characteristic or trait of a plant. Then there is the genotype, or the set of instructions for replicating the phenotype from generation to generation. There is, of course, a difference between what the instructions say and what the plant actually does with the instructions, given the environmental challenges that the plant faces. (Willhem 1911).
Next, the quantitative trait loci or QCL of the plant can be identified and examined at the molecular level. QCL are little bits of DNA that are closely linked to the genes that cause the trait that is being examined. From there, segments of the plant genome that underly a specific trait can be mapped. Eventually the exact genes can be identified and sequenced. From there, the possibilities of cloning the plants to create the best characteristics, such as resistance to disease, hardiness in drought areas, and the best metabolisms for producing or gathering chemicals and nutrients.
Amplified fragment length polymorphism PCR (AFLP) is the most common way of "snipping and putting together" of fragments of DNA. So the genetic botanist will be working with restriction enzymes, as well as the polyacrylamide gels, and the autoradiography or fluorescence methodologies that allow the material to be put into visually observable form. There are also microarrays and metobolomic analyses that can be done when metabolism is being studied.
From there, the qualities of plants can be experimented with through natural husbandry, such as grafting or chemical treatments, or through cloning to create more hardy plants that will survive in drought conditions; to create sterile plants that will reduce problematic populations by failing to reproduce; to create plants that will be more effective in gathering up nutrients and producing chemicals. There are fields of plant conservation genetics where plants are maintained and studied in botanical gardens, many of which can be found at universities which have genetic biology research programs and curriculum.