The Augustinian friar Gregor Mendel completed his groundbreaking work on genetic inheritance more than 160 years ago, after carefully studying seven traits in peas, including the shape and colour of their seeds and pods. Yet until now, scientists still hadn’t worked out which genes drive three of those traits in the garden pea (Pisum sativum).

In a paper published on 23 April in Nature¹, researchers add a fresh chapter to Mendel’s pivotal story, perhaps in the process launching a new era in the genomic study of peas, which are a popular source of plant-based protein.

Scientists published a reference genome for P. sativum in 2019². That digital sequence — a representation of the plant’s DNA — “was a huge breakthrough”, says Clare Coyne, an adjunct plant geneticist at Washington State University in Pullman. “But I would say [the latest study] is an even larger breakthrough. It’s really just an incredible effort.”

Modern tools meet age-old mystery

Mendel, a citizen scientist, famously performed a series of experiments in the mid-nineteenth century in which he cross-bred some 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 along hereditary ‘factors’ to offspring that determined whether they inherited what turned out to be ‘dominant’ or ‘recessive’ versions of genes known as alleles. Scientists continue to study such Mendelian traits today, and have identified thousands of them in humans. However, many of these traits have yet to be linked to a particular gene — and the same had been true of three of Mendel’s original seven pea traits.

Noam Chayut, an applied crop geneticist at the John Innes Centre (JIC) in Norwich, UK, and a co-author of the current paper, says he and the other team members were intrigued by the enduring mystery and decided that “sequencing and computational tools had advanced enough to tackle the final three” genes. Using the JIC’s Germplasm Resource Unit — which houses more than 3,500 pea variants, alongside publicly available genomic data sets — the group amassed and deep sequenced nearly 700 pea genomes. These contained roughly 155 million single-nucleotide polymorphisms (SNPs) — single base-pair differences in the DNA sequences compared with the standard, or ‘reference’, P. sativum genome.

Using several methods, including selective breeding of pea plants and genome-wide association studies, which probe each genome for differences in the number and location of SNPs, the group identified the genes linked to the three remaining traits. Specifically, the researchers found that pea-pod colour is controlled by a gene that disrupts chlorophyll biosynthesis, leading to either green or yellow pods. They also identified two genes that probably help to control pod shape by inducing disruption of cell-wall thickening in the plant. And they determined that a deletion in the genetic code at a particular point in another gene can cause changes in the branching or clustering of flowers on the plants — a process known as fasciation.

A long road

Pulling together several methods meant that the work took six years to complete, and Chayut says it was possible only 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,” he says.