The iconic pea plant experiments of Gregor Mendel laid the foundations for the science of genetics. Now 160 years on, an international research collaboration has used genomics, bioinformatics and genetics to map the diversity of a globally important pea collection—revealing secrets behind the traits that Mendel made famous and uncovering agriculturally useful genetic diversity on an unprecedented scale.
The new set of gene bank and genomic resources available to researchers and breeders worldwide could revolutionize pea breeding and research into this environmentally important legume crop, say the authors of a new study.
“Our collaboration has created a genomic resource of extraordinary depth and breadth, including the whole genome sequence data for pea,” said one of the co-corresponding authors Dr. Noam Chayut, who manages the Germplasm Resource Unit (GRU) at the John Innes Centre.
“We already have researchers and multi-national companies ordering seeds corresponding to the novel genomic resources, which will revolutionize how companies breed peas, and how scientists study them, across the world.”
The
research
, which can be found in the journal
Nature
is developed through a partnership between the John Innes Centre (JIC) and the Chinese Academy of Agricultural Sciences (CAAS), along with additional research teams in China, the UK, and France.
This significant research emerges as peas and other legumes are increasingly recognized for their role as sources of plant-based proteins and environmentally friendly crops capable of fixing atmospheric nitrogen independently. As such, these crop varieties require minimal synthetic fertilizers during cultivation, possibly reducing soil and water contamination.
Dr. Chayut stated, “Mendel’s interest in peas wasn’t solely due to them being ideal model organisms; they were also a significant crop he aimed to enhance by addressing issues faced by gardeners and cultivators of his era.”
Just as this research illuminates Mendel’s key findings, it also paves the way for cultivating peas across various regions globally, such as in the UK. The pea stands out as a crop capable of providing a sustainable supply of plant-derived proteins and will have a significant part to play in shaping agriculture’s future.
What methods did scientists use to decode the genomes of a worldwide pea collection?
Scientists chose a representative sample of approximately 700 pea varieties from a collection of 3,500, which were gathered globally over several decades and are kept at the GRU.
This produced 62 terabytes of unprocessed data, consisting of 25.6 trillion individual pieces of information that, when printed, would span across 3.6 billion pages of A4 paper.
Using this information, the team developed a comprehensive genomic chart of peas, ranging from extensively bred and farmed types to regionally adapted strains known as landraces, all the way to their wild progenitors.
By employing this map and utilizing a method known as Genome-Wide Association Studies, researchers pinpointed sections of the genome associated with beneficial trait variations. This study has linked over 70 agricultural characteristics to their respective genomic positions. These numerous genetic markers across all these sites can help expedite advancements in pea breeding.
In the future, this new resource, along with advanced technologies like gene editing, long-read DNA and RNA sequencing, will present unparalleled chances for discovering new genes. Additionally, it will facilitate more accurate breeding methods—for instance, employing AI models capable of selecting specific gene combinations to produce high-yield, disease-resistant, and agriculturally feasible pea varieties.
Mendel’s enduring legacy
Allan Franklin, a science historian, referred to Mendel’s work with peas as “the finest experiments conducted.”
In the formative era of cell theory, prior to the advent of genetic knowledge, he concentrated on these seven characteristics: whether pea seeds were round or wrinkled, their color which could be green or yellow; the pod’s shape being constricted or swollen; pod color ranging from green to yellow; flower hue varying between purple and white; plant height distinguished as tall or short; and finally, the positioning of flowers either axially or terminally.
Through numerous years of experimentation with tens of thousands of plants, he uncovered basic principles of heredity, detailing how traits are transmitted across generations, thus independently establishing the foundation for the field of genetics.
The advanced genetic instruments developed through this contemporary scientific partnership are now being employed to reassess these seminal studies, thereby illuminating the genetic basis of Mendelian characteristics. In their investigation of floral pigmentation, the group identified an uncommon form of spontaneous mutation that reinstates the purple hue in what were previously white-flowering pea plants.
The group also identified a mutation leading to the yellow pod characteristic, which is highly intriguing to scholars due to its origin from an interplay between two neighboring genes.
“One of the primary researchers in this study, Professor Shifeng Cheng from the CAAS Agricultural Genomics Institute located in Shenzhen, stated that Mendel uncovered what we currently refer to as the principles of heredity without being aware of the concept of a gene,” she explained. “With today’s advanced technologies, we have the ability to observe the specific genes and exact mutations that he inadvertently identified.”
Professor Noel Ellis, a renowned Mendel scholar and co-corresponding author of the study from the John Innes Centre, noted: “These accessions along with their related information offer significant benefits to plant breeders. For geneticists and educators, they represent invaluable assets as well since our research provides current insights into Mendelian variations. All this data is accessible now, and the pea lines can also be requested—our wish is for researchers to utilize these tools without hindrance.”
Cong Feng, a graduate student working with Professor Cheng and one of the lead authors of the study, mentioned, “The genome-wide association studies (GWAS) along with haplotype analyses turned out to be extremely potent methods. It was exhilarating for us to reveal detailed genetic information about each of Mendel’s traditional traits.”
Mei Jiang, who is also a co-first author, mentioned, “This initiative intensified my interest in peas, genetics, and Mendel’s heritage. It turned into not just a scientific endeavor but a deeply personal exploration as well.”
Dr. Julie Hofer, who is also a co-first author of the study and a postdoc at the John Innes Centre, commented, “Despite significant efforts over many years, the genetic foundation behind pod color remained elusive. This finding sheds light on how intricately the genome’s architecture can affect gene activity from a transcriptional perspective.”
The research highlights the significance of teamwork in scientific endeavors, as stated by Dr. Chayut: “Our potential for success greatly increases when we join forces.”
More information:
Shifeng Cheng, Insights from Genomics and Genetics into Mendel’s Pea Genes
Nature
(2025).
DOI: 10.1038/s41586-025-08891-6
.
www.nature.com/articles/s41586-025-08891-6
Supplied by the John Innes Centre
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