160 year old research opens gateway to more nutritious and sustainable pea crops

Researchers at the John Innes Centre at Norwich Research
Park have helped to solve a historical puzzle that could revolutionise the
breeding of the humble pea and other legumes leading to improvements in their nutritional
value and lessening the reliance on pesticides.

This landmark work, published in the journal Nature, comes
at a time when peas and other legumes are being called upon both as sources of
plant protein and as sustainable crops which can fix their own nitrogen. It
could result in pea and other legume crops, needing less chemical fertiliser to
grow, becoming more economically viable for future growers and potentially
lowering land and river pollution.

The groundwork for this latest study was laid 160 years ago
by Gregor Mendel, a citizen scientist. He famously performed a series of
experiments in the mid-nineteenth century where he cross-bred 28,000 pea plants
to understand how their traits were inherited by future generations. Although
at that stage the concept of genes didn’t exist, Mendel concluded that plants
were passing on hereditary ‘factors’ to their offspring that determined whether
they inherited what turned out to be ‘dominant’ or ‘recessive’ versions of
genes known as alleles.

Mendel’s work on peas was described by the science historian
Allan Franklin as “the best experiments ever done.” He focused on seven pea
traits: seed shape (round or wrinkled), seed colour (green or yellow), pod
shape (constricted or inflated), pod colour (green or yellow), flower colour
(purple or white), plant size (tall or dwarf) and position of flowers (axial or
terminal).

Over many years of experiments, involving thousands of
plants, he established fundamental rules of inheritance, how characteristics
are passed down through the generations, and single-handedly laid the
groundwork for the science of genetics.

Three of Mendel’s original seven pea traits had not been
linked to a particular gene. That is until now. An international research
collaboration between the John Innes Centre, the Chinese Academy of
Agricultural Sciences (CAAS) and other contributors in China, France and the
UK, has used genomics, bioinformatics and genetics to map the diversity  of a global pea collection and revealed the genes
associated with the remaining three Mendel pea traits.

This new set of gene bank and genomic resources which will
now be available to researchers and breeders worldwide could revolutionise pea
breeding and research into this environmentally important crop.

Dr Noam Chayut, one of the study’s leading authors, at the
John Innes Centre, said, “Our collaboration has created a genomic resource of
extraordinary depth and breadth that includes the whole genome sequence data
for the 700 pea types representing the global species diversity. We already
have researchers and multi-national companies ordering seeds corresponding to
the novel genomic resources which will revolutionise how companies breed peas and
how scientists study them, right across the world.” 

“In Mendel’s time, pea was an important crop that he wanted
to improve by solving problems that were facing gardeners and growers at the
time. This study not only shines a light on Mendel’s fundamental discoveries,
but it also opens the route to growing pea in many parts of the world,
including the UK. Pea is a crop which can deliver a sustainable source of
plant-based protein and has a major role to play in the future of farming.

“The six-year study was only successful because of the
interdisciplinary nature of the team, with each member bringing a necessary
skill to the partnership. The most important and beautiful part of this
research is the collaboration”.

The study’s researchers selected a genetically representative
sample of around 700 pea accessions from the collection of 3,500 held at the
John Innes Centre’s Germplasm Resource Unit, a national capability, funded by
BBSRC. This generated 62 terabytes of raw data, comprising 25.6 trillion pieces
of information which, if printed out, would cover 3.6 billion sheets of A4
paper.

From this data, amassed from the 700 pea genomes the team
created a global genomic map of pea, from the highly bred and cultivated pea,
through to locally adapted varieties from all around the world; called
landraces, and wild relatives.

Using this map and a technique called Genome Wide
Association Studies, they identified regions of the genomes that corresponded
to valuable trait variation. The research has connected more than 70 agronomic
traits to corresponding genomic locations. The many different genetic markers
at each of these locations can be used to accelerate pea improvement.

Looking forward, the new resource, coupled with other modern
technologies such as gene editing, long-read DNA and RNA sequencing, will open up
unprecedented opportunities for novel gene discovery. It will also pave the way
for more predictive breeding such as using AI models which can
combinations of genes to deliver better yielding, disease-resistant,
agronomically viable pea plants.

Prof Shifeng Cheng of the CAAS Agricultural Genomics
Institute at Shenzhen, said, “Mendel discovered what we now call the laws of
inheritance without knowing what a gene was. Today, using modern tools, we can
see the exact genes and the precise mutations that he unknowingly tracked.”

The market for pea protein is among the fastest-growing of
those for all alternative protein sources and researchers want to learn more
about creating productive pea plants specially studying genes associated with
pod size, plant yield, seed protein content and resistance to disease.