Comprehensive genomic map reveals unprecedented genetic diversity in the global pea collection and paves the way for genetic improvements of the legume
Researchers have created a comprehensive genomic map of the global pea collection that led Czech priest Gregor Mendel to discover heredity, revealing key traits and vast genetic diversity. The new resources are expected to revolutionize pea breeding, sustainability efforts and genetic research worldwide.
Gregor Mendel laid the foundations of the science of genetics more than 160 years ago through groundbreaking experiments on pea plants.
Today, an international team of researchers is using genomics, bioinformatics, and genetics to map the diversity in the world's pea collection. Their work is revealing new insights into the traits Mendel studied and uncovering an unprecedentedly broad genetic diversity essential to agriculture.
According to the study authors, the expanded gene pool and genomic resources now available to researchers and breeders around the world could transform pea breeding processes and advance research on this legume.
“Our collaborative work has created an extraordinarily vast genomic resource, including the complete pea genome sequence data,” said Dr. Noam Hayut, one of the original co-authors, who directs the Seed Resources Unit (GRU) at the John Innes Center.
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Already today, researchers and multinational companies are ordering seeds compatible with the new genomic resources, which will change the way peas are bred and the way scientists will study them around the world.”
A global collaborative effort
The study, published in the journalNature , was held in collaboration with the John Innes Center (JIC) and the Chinese Academy of Agricultural Sciences (CAAS), along with research groups in China, the UK, the US and France.
This work comes at a time when efforts are being made to increase the use of peas and other legumes as a source of plant protein and sustainable crops that are capable of fixing nitrogen for themselves, which reduces the need for chemical fertilizers and reduces soil and water pollution.
Pea Variety Board
"Mendel wasn't just interested in peas as a perfect research model, although they were," said Dr. Hayut. "They were also an important crop that Mendel wanted to improve to solve problems facing gardeners and farmers of his time."
“Likewise, this research not only illuminates Mendel’s fundamental findings, but also paves the way for pea cultivation in a number of countries around the world, including the UK. Peas can provide a sustainable source of plant protein and have a central role in the future of agriculture.”
How researchers cracked the genomes of the world's pea collection?
The researchers selected a representative sample of approximately 700 genotypes from more than 3,500, which were collected and preserved over decades at the BBSRC-funded GRU unit.
The process yielded 62 terabytes of raw data, comprising 25.6 trillion pieces of information, which is suitable for printing on approximately 3.6 billion 4A pages.
Using this data, the team created a global genomic map of peas, from cloned and established peas to landraces and varieties that are evolutionary close to varieties commonly used in agriculture today.
Through large-scale association studies (GWAS), regions of the genome linked to more than 70 agronomic traits have been identified. The genetic markers at each location allow for accelerated breeding processes.
In the future, combined with technologies such as genome editing and long-range sequencing of DNA and RNA, unprecedented opportunities will open up for new gene discovery and predictive breeding using artificial intelligence to create gene combinations for high-yielding, disease-resistant, and agronomically sustainable peas.
Mendel's lasting legacy
Alan Franklin, a science historian, described Mendel's work as "the best experiments ever performed."
In the early days of cell theory, before the term "gene" was defined, Mendel focused on seven traits:
- Seed shape: Round or wrinkled
- Seed color: Green or yellow
- Backpack shape: Tight or puffy
- Backpack color Green or yellow
- Flower color: Purple or white
- Plant height: Tall or short
- Flower location: Axial or final
During experiments that lasted years and used thousands of plants, Mendel formulated the basic laws of heredity and discovered how traits are passed from generation to generation, laying the foundation for the science of genetics.
Confirming classical theory with modern tools
The genomic tools developed in this study are used to reexamine the classic experiments, and these tools find the exact genes and mutations that Mendel followed.
For the bloom color trait, the researchers identified a unique mutation that allows the purple color to be returned to white flowers.
The team also found a mutation responsible for the yellow pod color, a discovery that fascinates academics due to the interaction between two nearby genes.
“Mendel discovered the laws of inheritance without knowing what a gene was,” said Professor Shi-Peng Cheng of the Institute of Agricultural Genomics in Shenzhen. “Today, with modern tools, we can identify the exact genes and specific mutations that Mendel followed.”
Professor Noel Ellis, a researcher at the John Innes Centre and co-author of the study, added: “Beyond the practical application of the data to breeders, the resources are also important for academics and genetics teachers, as the study provides an up-to-date description of Mendelian variants. The data is available and pea lines can be ordered – we hope that academics will use it freely.”
Kong Feng, a graduate student and co-author of the paper, said: “GWAS and haplotype analysis have proven to be powerful tools, and we were pleased to discover sequence-level insights into all seven classic Mendelian traits.”
Dr. Julie Hooper, a postdoctoral researcher, added: “For years, the question of what causes the color of the pod has been fraught with obstacles, but our discovery highlights the extent to which genome structure can influence gene function at the transcriptional level.”
