Scientists finally solve the 160-year-old problem of Mendel's peas
Feng, C., Chen, B., Hofer, J. et al, 'Genomic and genetic insights into Mendel's pea genes', Nature (2025). doi.org/10.1038/s41586-025-08891-6
In 1856, an Austrian monk named Gregor Johann Mendel began experimenting on pea plants to understand how traits are passed on from parent to offspring. He worked diligently for eight years, experimenting on more than 10,000 plants, before presenting his results in a meeting of the Brunn Natural History Society in 1865.
His work was published the following year in a small journal of the society called Proceedings of the Natural History Society of Brno. His findings received very little attention at the time. Mendel died in 1884, unaware that his work would go on to become the foundation of the field of genetics.
Crossing plants
In 1900, 16 years after Mendel's death, three scientists — Hugo de Vries, Carl Correns, and Erich von Tschermak — independently rediscovered his work. They realised that Mendel had answered the question of whether some traits of the parents are passed on to their offspring more frequently than others.
Mendel had studied the inheritance patterns of seven traits in pea plants, each with two clearly distinguishable forms. For example, one of the traits he examined was seed shape, where the seeds were either round or wrinkled. Mendel observed that when he crossed plants with opposing traits, one form would consistently dominate the other. That is, crossing plants with round seeds and those with wrinkled seeds always produced first-generation offspring with round seeds.
Interestingly, when two such first-generation plants were crossed, the wrinkled form reappeared, though at a much lower frequency. Mendel found that the ratio of round to wrinkled seeds in this second generation was consistently around 3:1. For reasons unknown at the time, the round form appeared to 'dominate' the wrinkled form, and this same pattern held true for all seven traits he studied, the remaining six being: seed colour (yellow or green), flower colour (purple or white), pod shape (inflated or constricted), pod colour (green or yellow), flower position (along the stem or at the end), and plant height (tall or short).
Predictability of inheritance
Mendel's observations became the basis for understanding how traits are inherited through discrete units of heredity, which we now call genes.
Scientists later realised that for each trait, an organism carries two versions of a gene, one inherited from each parent. These versions, known as alleles, can differ in their effect on the offspring's appearance. In many cases, one allele masks the effect of the other, explaining why only one form of the trait appeared in first-generation plants.
This work provided the first clear evidence that inheritance follows predictable patterns — an insight that eventually led to the development of the chromosome theory of inheritance, the identification of genes as specific units on chromosomes, and paved the way for the emergence of modern genetics.
However, the original question of what genetic differences gave rise to the two forms of each of the seven traits Mendel studied remained unanswered for a long time. Although efforts to identify the genetic locations involved had begun to make progress by 1917, it took the scientific community another 108 years to fully understand why Mendel observed what he did.
Mountain of information
A paper published in Nature on April 23, has now identified the genetic factors responsible for the final three traits, that had remained unresolved, while also uncovering additional alleles involved in the four traits that were previously characterised.
The team achieved this by selecting more than 697 well-characterised variants of the pea plant and sequencing the total DNA content of all these plants using a technique called next-generation sequencing. This resulted in almost 60 terabases of DNA sequence information. That's the equivalent of nearly 14 billion pages of text, or a stack of A4 sheets stretching 700 km into the sky.
The answer to the problem of Mendel's traits was buried within this colossal mountain of information.
Opening new doors
The authors of the study analysed this data to create a comprehensive map so that they could begin searching for patterns. This revealed several interesting findings.
First, while it is well accepted that the genus Pisum, to which the pea plant belongs, has four species, genetically they appear to form eight groups. The four species are spread across these groups due to multiple crosses and admixtures between them, revealing that the plants have a more complex population structure than previously recognised.
Second, while four of Mendel's seven traits — viz. seed shape, seed colour, plant height, and flower colour — were well characterised, the team identified additional allelic variants that contribute to the observed traits. For instance, the team found a new variant that, when present in white-flowered plants, causes them to produce purple flowers again, showing that the genetic picture is more complex than Mendel originally observed.
Third, they identified genes that are involved in the remaining three traits — pod colour, pod shape, and flower position — that remained uncharacterised until now. Specifically, they found that a deletion of a segment of DNA present before a gene called ChlG disrupts the synthesis of chlorophyll, the pigment that gives plants their green colour, resulting in the yellow pods. Changes near the MYB gene and changes in the CLE-peptide-encoding genes together resulted in the constricted pod trait. And a small deletion in the DNA containing the CIK-like-coreceptor-kinase gene, along with the presence of another DNA segment called a modifier locus, was associated with the flowers appearing at the end of the stem.
Finally, the map that the team generated shows multiple other genome-wide interactions that Mendel did not study, including 72 agriculturally relevant traits such as the architectures of the seed, pod, flower, leaf, root and plant.
While closing the doors on this 160-year-old scientific mystery, the scientists involved in the study have paved the way to something greater. The depth of genetic information they had uncovered holds enormous promise for future research, with a lot of implications for increasing crop yield, enhancing disease resistance, and improving environmental adaptations.
It is incredible to think that all of this owes its origin to a 19th century monk, who, while tending to his garden, chose to ask why.
Arun Panchapakesan is an assistant professor at the Y.R. Gaitonde Centre for AIDS Research and Education, Chennai.
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