Luckily E. Helleborine is a diploid plant with just two of each chromosome per cell. This greatly simplifies the possibilities. If there is an enzyme deficiency due to a genetic defect it is most likely due to the inheritance of a rare recessive from both parent plants, or self pollination by a plant carrying the recessive genetic defect. Heterozygotes - carriers of the genetic defect with one normal and one affected gene - would produce sufficient of the enzyme or protein to supply a normal amount of chlorophyll. Thus the defect would have to be present on both chromosomes; homozygosity for the affected gene.
The genetic defect could be a single point mutation of the DNA; one base substituted for another. However the product of these mutations often do have some functionality. Their function is compromised but not destroyed. Even the inheritance of two such genes can lead to some functional product. However a point mutation which leads to an amino acid substitution at the critical active site of an enzyme product may lead to zero functionality.
Sometimes it is a mutation at an intron-exon region of a gene that occurs. The product of such a gene is normal, but the quantities produced can be compromised. This happens with persons who are homozygotes for the commoner forms of á-thalassaemia (Mediterranean anaemia). They have a low level of normal haemoglobin A, but even in the most affected types there is some normal product.
A `nonsense' mutation can lead to zero product. This would be when the gene template is changed for example, so that a termination codon is created before it would be normally found (in terms of gene transcription). The m-RNA produced will not lead to any functional enzyme.
Gene transcription is regulated by small DNA sequences close to the gene, Again, mutations of these will compromise the rate of gene transcription and thus the amount of protein produced, but normally there would be some. Thus in terms of an enzyme required for chlorophyll synthesis there would still be some chlorophyll produced, not a total absence.
Gene deletion leads to a state where no gene product can be made. Genes can be deleted at meiosis by unequal cross-over of chromosomes. Crossing over of chromosomes is a normal situation and helps lead to random gene association. Genes are often duplicated on a chromosome. The crossover can occur between the leftward gene on one chromosome and the rightward of the second. One chromosome ends up with two copies of a gene and the other none. Gene deletion is the basis of human ŕ-thalassaemia. Those who are heterozygotes for ŕ-thalassaemia, where one of the globin chains of blood haemoglobin is affected, have normal(ish) haemoglobin levels and are asymptomatic. Only in the homozygous state is there no gene product. This pattern fits well with what we see with the `achlorophyllous Helleborine'.

If it is a genetic defect that causes the chlorophyll deficiency, it could be from a point mutation, a nonsense mutation or a gene deletion. Whichever it is, the end result is the same. Self pollination of a heterozygote for the genetic defect would more or less guarantee progeny plants with chlorophyll deficiency. Assuming a single gene defect, 25% of the progeny would be normal, 50% would be heterozygotes (one affected and one unaffected gene) which would be phenotypically normal, and 25% would be homozygotes (two affected genes) expressing chlorophyll deficiency. These figures still apply regardless of the rarity of the variety. We do not see many achlorophyllous plants at all and there is but one at the quarry. Therefore self pollination of a parent is unlikely.
Allogamic pollination of two parents, heterozygous for the affected gene, will result in progeny in the same proportions as above but is less likely to happen, reflecting the rarity of the phenotype. If the abnormal gene frequency is 1/1,000 then just 1/1,000,000 pollinations would lead to a double dose the abnormality. This scenario is closer to what we see with this helleborine.
If a single faulty gene offers no benefit or minimal disbenefit to a species the gene will persist at a stable or only minor fluctuating level over the generations. Epipactis species show a capability to be able to obtain energy from their fungal partners independently of sunlight via chlorophyll. E. helleborine populations show a high degree of out-crossing between populations which is reflected in the diversity of flower colours seen within a colony. This prevents recessive genes becoming amplified within a colony, yet helps preserve and disperse those recessive genes. They may yet prove useful. A mutation of one such gene may confer an advantage sometime in the future.

* The DNA genetic code leads to proteins such as enzymes being produced. Each set of three DNA bases codes for a particular amino acid. The sequence of these triplet codons determines the order of the amino acids that make up the protein product of the gene. Genes commonly have coding sequences called exons, and non-coding sequences called introns. The first product of gene transcription, hn-RNA, contains both types of sequence, but the non-coding parts are spliced out to form functional m-RNA. It is this which acts as the template for protein synthesis. Each gene terminates with a Stop codon, which is self-explanatory