Alternative explanation: genotype and phenotype
The phenotype of a plant describes what a plant looks like: all its traits. Examples of traits are its color, its length, its leaf shape etc. Also its inner appearance, such as disease resistance, sugar content, or types of proteins and fibers formed are part of the phenotype.
The genotype of a plant is all the information present in its DNA. Some parts of the DNA are genes: they are transcribed and code for proteins that play a role in the physiology and performance of the plant. Genes have effect through the processes of transcription and translation. Some other parts of the DNA do not code for proteins and are called non-coding areas. Both genes and non-coding areas make up the genotype.
The environment greatly influences the appearance and performance of the plant. A plant receiving sufficient light and nutrients AND containing many genes that positively affect growth will probably result in a plant with a high biomass.
Qualitative and quantitative traits
Qualitative traits are discrete traits that have two or several character values in clearly distinct discrete classes (like eye color in humans). They are often controlled by a single gene with a major effect, or few genes with large effects and they are not much influenced by non-genetic factors like the environmental conditions. A specific gene has a specific place on a specific chromosome, called a locus. Since the effect of the gene is so large, typically a breeder can conclude from the phenotype of each plant whether it carries the one or the other allele of the gene, so the genotype is readily deduced from the phenotype (although not every genotype may be a distinct class, as in the case of dominant genes). However, as we will see later, it still may be very efficient to select on the basis of molecular markers rather than on the basis of phenotype.
A well-known example of a qualitative trait in plant breeding is seed coat of peas. In the nineteenth century, Gregor Mendel discovered that the traits 'smooth' or 'wrinkled' seed coats of peas were inherited from the parents and that these traits were controlled by two 'factors': two alleles of one gene. He formulated the basic 'Laws of heredity'. Mendel's first law of equal segregation comes down to saying that heridatory factors (now called: genes) in an individual appear in pairs (now called: alleles) of which two variants segregate into equal proportions in the egg cells or in the sperm/pollen cells. At fertilization these fuse at random to produce progeny individuals, giving rise to recognizable mathematical ratios, in the progeny population, such as 1:1, 1:2:1 (in case of codominant genes) or 3:1 (for dominant genes in an F2) for the different variants, as was the case for smooth/wrinkled seed coat of peas.
Quantitative traits, such as yield or plant height, often (but not always) have a continuous distribution. The variation in the values of the trait is usually influenced by multiple genes. and, in addition, to quite some extent also by non-genetic factors, environmental conditions. Each of the genes involved may therefore contribute only a relatively small part to the total phenotypic variation, but some large-effect genes may also be present. The exact location and identity of the contributing genes is often unknown but an association between the trait values and variation in a certain region on the genome can be discovered by statistical tests. Such a region is called a quantitative trait locus (QTL) and the discovery of QTLs is called QTL analysis. QTLs are loci (or regions, and hence, no genes by themselves!) on the genome that have a statistical association with a quantitative trait. Here the application of markers will be necessary, in research but also for a plant breeder to determine which of the plants have desirable alleles and which ones have undesirable alleles influencing the trait. A reported QTL could indicate that there is a gene or that there are multiple genes present in the region that influence the trait. However, as in any statistical analysis, false positives are also possible: detected associations that are not corresponding to actual genetic differences.