A few years ago (seems like just yesterday, don’t it? ), all of us high school students learned (in 10th-grade Biology) how the 19th-century Austro-Hungarian friar, Gregor Mendel, discovered the basic principles of genetics — by studying peas, which he planted by the thousands in the garden of his abbey. After cross-pollinating varieties and noting the proportions in which traits such as flower color occurred in their offspring, Mendel discovered the mathematical patterns of recessive and dominant inheritance — a fundamental breakthrough in genetics. But, working decades before genes were even identified as the mechanism of heredity, Mendel knew nothing about the molecular basis of his seven traits, which remained “seven riddles” [see attached article]. Today, scientists have a good idea about the causes of all seven phenotypes.
The first of Mendel’s traits to be linked to a gene was [1] seed shape. Some pea varieties have seeds that wrinkle if dried and taste sweet (sugar-rich) when served fresh. Mendel showed they have recessive “wrinkled” alleles. Peas with a dominant “round” allele stay smooth when dry and are less sweet (starch-rich), often going to soup or animal feed. In 1990, researchers at the John Innes Centre (JIC; Norwich, Norfolk, England) identified the responsible gene, which encodes enzymes that help convert sugars to starch. [The process of starch synthesis starts with glucose and uses enzymes like starch synthase, starch-branching enzyme, and ADP-glucose pyrophosphorylase.] Its dominant form packs the seeds with starch and keeps them smooth, whereas the recessive allele makes an inactive enzyme that leaves more sugar in the seeds. Scientists at JIC and elsewhere subsequently discovered the genes behind three other traits: [2] plant height, and [3] flower color, and [4] seed color.
The entire pea genome was sequenced in 2019. Researchers in China [Agricultural Genomics Institute at Shenzhen (AGIS)] went on to sequence 237 kinds of peas and compile their genetic differences into a map, published in 2024. This diversity allowed them to identify 29 million genetic markers, called single-nucleotide variants (SNVs) — which pea breeders can use to guide and accelerate crop improvement. Together, AGIS and JIC have now sequenced nearly 700 pea varieties, spanning the diversity of the collection; this has yielded 155 million SNVs that they have correlated with physical traits of the plants, allowing them to narrow down the location of important genes.
Among those genes are ones for the three remaining Mendel traits: [5] color of the pea pod, [6] arrangement of flowers, and [7] whether the pods are edible. The new details show, for example, that yellow pods occur in plants with DNA missing next to a gene involved in making chlorophyll. Cheng’s group believes the defective RNA transcribed from that DNA region interferes with chlorophyll synthesis, leading to pale pods. That particular insight might not lead directly to improved peas, but others likely will.
For example, the genetic basis for tendrils. By intertwining, these modified leaflets help pea plants stay upright (clinging to support structures) and make harvesting much easier. In the 1980s, breeders produced varieties with plentiful tendrils, a trait controlled by a gene called afila. But the same afila alleles that cause pea plants to grow more tendrils and fewer leaves — can also lower yield by somehow deleting adjacent genes that influence the number and weight of the seeds. By revealing exactly where on the genome the deletions start and stop, Cheng and colleagues hope to help breeders select afila alleles that do not delete the nearby genes.
Lastly: most, if not all, of “Mendel’s seven riddles” do not reflect transcripts or protein products of single genes but rather are determined by the combination of effects from multiple genes; these are known as polygenic traits. This occurs when two or more genes influence the expression of a single characteristic. Examples in human genetics include eye color, height, and skin color. There are anecdotal stories that — when inheritance of a trait did not “agree” with his mathematical expectations — Mendel discreetly altered some of his data; we now know that these unanticipated deviations most likely reflected the polygenic nature commonly seen in inheritance studies from virtually all organisms.
DwN
Science 25 Apr 2025; 388: 346