An international team of researchers has achieved a major milestone in plant genetics by finally identifying the genetic foundations of all seven traits studied by Gregor Johann Mendel often referred to as the ‘Father of Modern Genetics.’ Thus, a puzzle that persisted over 160 years has been solved. This discovery answers some of the oldest unresolved questions in classical genetics and paves the way for more precise breeding techniques, enhanced pea cultivation, and sustainable agriculture.
The research was led by Shifeng Cheng of the Agricultural Genomics Institute at Shenzhen (AGIS), part of the Chinese Academy of Agricultural Sciences, in collaboration with the John Innes Centre in the United Kingdom, and other international partners. The findings were published in the April 2025 edition of the journal, Nature.
Mendel’s Experiments
In the mid-19th century, Mendel, an Austrian monk, embarked on scientific research that laid the foundation of genetics. Starting in 1856, he cultivated and crossbred over 10,000 pea plants (Pisum sativum) to explore how traits are transmitted across generations. Despite presenting his findings in 1865 and publishing them a year later in a small journal of the society, Proceedings of the Natural History Society of Brno, his work received little attention during his lifetime. Mendel passed away in 1884, unaware of the revolutionary impact his experiments would have.
It was not until 1900 that the significance of Mendel’s experiments was acknowledged, when three scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak, independently rediscovered his publication. They recognised that Mendel had uncovered consistent patterns in traits inheritance, particularly that certain forms of a trait dominate others in hybrid offspring.
Mendel focused on seven traits of pea plants, each with two distinct forms: (i) seed shape (round or wrinkled), (ii) seed colour (yellow or green), (iii) flower colour (purple or white), (iv) pod shape (inflated or constricted), (v) pod colour (green or yellow), (vi) flower position (axial—along the stem or terminal—at the end), and (vii) plant height (tall or short). When he crossed plants with contrasting traits, one variant always appeared in the first generation (F1). The suppressed form reemerged in the second generation (F2) in a predictable 3:1 ratio, laying the groundwork for the principles of dominance and segregation.
Emergence of Modern Genetics
Mendel’s findings eventually led to the understanding that traits are inherited through specific units, now known as genes. Each organism carries two versions of a gene, known as alleles, which together determine the expression of traits. One allele can dominate and mask the expression of the other. Mendel’s work illustrated that inheritance follows structured rules, that later supported the chromosome theory, which laid the groundwork for gene mapping, and became the foundation of modern genetics.
However, despite the pivotal nature of his findings, the precise molecular genetic basis of Mendel’s seven traits remained elusive for decades. Although some progress was made in identifying genetic factors by 1917, three of the seven traits—pod colour, pod shape, and flower position—remained unresolved.
Sequencing and Mapping the Pea Genome
The full pea genome was first sequenced in 2019, allowing researchers to explore genetic diversity in depth. Scientists in China subsequently sequenced 237 pea types, creating an initial map of genetic variations and identifying about 29 million single nucleotide polymorphisms (SNPs).
In this study, the research team examined over 697 genetically distinct pea plant variants representing global diversity from cultivated verities, land-races, and wild relatives. Next-generation sequencing technology was used, producing approximately 60 terabases (60 trillion bases) of DNA sequence data, equating to about 14 billion pages of text or a stack of A4 sheets reaching 700 km high. Processing this data generated 62 terabytes of raw information, covering 25.6 trillion individual data points, which would fill about 3.6 billion printed A4 pages.
An SNP, (pronounced ‘snip’) refers to a variation at a single base pair position within the DNA sequence. These variations serve as biological markers that assist scientists in identifying genes linked to specific diseases or other traits, present in at least 1 per cent of population.
Decoding Mendel’s Remaining Traits
The study clarified the three traits that had remained unexplained: pod colour, pod shape, and flower position.
For pod colour, a deletion in DNA preceding the ChlG gene disrupts chlorophyll synthesis, resulting in yellow pods. Defective RNA transcribed from this region interferes with chlorophyll production.
In the case of pod shape, changes near MYB gene and mutations in genes encoding CLE peptides led to the constricted form.
The position of the flowers was linked to a small deletion near the Clk gene like coreceptor-kinase gene, combined with another nearby DNA segment known as a modifier locus, which together influenced the development of flowers at the tip (terminal) rather than along the stem (axial).
Additional Insights
While four of the Mendel’s traits (seed shape, seed colour, flower colour, and plant height) were previously mapped, this study discovered new allelic variants, such as a mutation restoring purple flower colour in plants that typically produce white flowers. Also, the research revealed that the genus pisum, traditionally thought to have four species, actually comprises eight genetically distinct groups due to extensive historical crossbreeding and admixture.
Global Collaboration, Research Approach, and Processing
The research was a result of a global collaboration between institutions in China, the UK, and other countries. The effort was led by Shifeng Cheng along with Noam Chayut and Noel Ellis of the John Innes Centre.
The team assembled over 700 accessions selected from a larger global collection of 3,500 pea variants maintained at the Germplasm Resource Unit, a national capability funded by the Biotechnology and Biological Sciences Research Council (BBSRC). This selection was essential to ensure the inclusion of rare and diverse genetic traits. These accessions were introduced into China after 2019, and grown in both southern and northern regions.
They employed advanced methods in genomics and computational biology to revisit Mendel’s foundational experiments. Using genome-wide association studies (GWAS), they connected genomic regions with specific trait variations that provided a global pea-genome map that is now one of the most comprehensive in legume research.
Future Applications and Agricultural Impact
Beyond Mendel’s seven traits, the team identified 72 agriculturally important traits, including those affecting seed, pod, flower, leaf, root, and overall plant architecture. And with new genomic resources, breeders and researchers now have powerful tools at their disposal. These include whole genome sequences and access to diverse seed stocks and precise trait-linked markers. These open the door to predictive breeding using technologies such as gene editing, long-read DNA, and RNA sequencing, and artificial intelligence to develop better performing crops.
The significance of peas as a sustainable crop is also highlighted by this study. Peas, like other legumes, have the ability to fix nitrogen in the soil, reducing the need for chemical fertilizers and improving soil health.
Revisiting Mendel’s Legacy with Modern Tools
Mendel’s experiments are now revisited through the lens of modern science. The study has identified unique mutations, affecting traits like flower colour and pod pigmentation, offering a deeper understanding of the molecular mechanism behind these variations. For instance, how a naturally occurring mutation allowed white flowers to revert to purple, and how neighbouring gene interactions created the yellow pod trait.
The ability to pinpoint these mutations at the molecular level highlights the contrast between Mendel’s era and present genomic precision. The researchers emphasised that the genetic data and resources generated would be valuable not only for breeding but also for academic purpose. It provides an up-to-date account of Mendel’s work and enabling free access to genetic data for academic use.
By solving one of the oldest mysteries, this research has not only honoured Mendel’s pioneering work but further laid the foundation for future innovation in agriculture and genetics. With vast genetic data now publicly available, the possibilities for advancing plant breeding, improved food security, and deeper understanding of inheritance are greater.
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