The genes for all seven of Mendel's traits have now been identified

The seven traits that Gregor Mendel worked with were: seed shape (R/r), cotyledon color (I/i), seed and flower color (A/a), pod shape (V/v), pod color (Gp/gp), flower position (Fa/fa), and stem length (Le/le). The last trait is also known as Tall (T) and short (t).

The genes for four of these traits (seed shape, cotyledon color, flower color, and stem length) were identified and characterized many years ago. The genes for the remaining three traits have now been identified. The results were published in the June 25, 2025 issue of Nature (Feng et al., 2025).

Seed shape (R/r)

The normal shape of the peas in a pea pod is smooth and round (R). The seed catalogues of the mid-19th century listed a variety with wrinkled peas (r). The wrinkled pea phenotype is caused by a transposon insertion in the last exon of the gene for starch branching enzyme (Bhattacharyya et al. 1990). Starch synthesis is very similar to glycogen synthesis. The main polymerization enzyme is starch synthase and it works just like glycogen synthase [Glycogen Synthesis]. Both starch and glycogen synthesis require an additional enzyme to create new branches. In plants this enzyme is starch branching enzyme.

In the absence of this enzyme, starch synthesis is partially blocked and the developing peas have a higher concentration of sucrose. (In plants, glucose is transported as the disacharide sucrose.) This causes the mutant peas to absorb more water than normal peas and they swell to a larger size. When the seeds begin to dry out the peas with the defective enzyme lose more water and their outer surface takes on a wrinkled appearance. One copy of the active gene for starch branching enzyme is sufficient so the presence of one defective allele has no observable phenotype. When two mutant alleles are present the wrinkled phenotype is expressed because there's no active starch branching enzyme. The mutant allele is recessive to the wild type allele.

Cotyledon color (I/i)

In wild-type peas the seeds turn yellow as they mature (I) but certain mutants exhibit a "stay-green" phenotype where the peas retain their green color (i). The figure shows seeds from a plant with the II genotype (top) and the ii genotype (bottom). The seed coat has been removed from the lower pair of each group of four peas.

The gene responsible for the stay-green phenotype is called sgr (stay-green). It encodes an enzyme that is localized to chloroplasts and plays a role in the degradation of chlorophyll during senescence and maturation of seeds. When the enzyme is defective, chlorophyll isn't broken down and the tissue stays green. The recessive allele studied by Mendel is probably due to a transposon insertion (Armstead et al. 2007; Armstead et al. 2006; Thomas, 1987; Thomas et al. 1996; Thomas and Stoddart, 1975). [Identity of the Product of Mendel's Green Cotyledon Gene (Update)]

Flower color (A/a)

Pea plants normally have purple flowers (A) but varieties with white flowers (a) were well-known in Mendel's time. The purple color is due to the production of anthocyanin—a pigment derived from phenylalanine. The white version studied by Mendel is caused by a mutation in the gene for transcription factor bHLH that regulates expression of the genes for anthocyanin synthesis. The variant allele (a) that Mendel studied was almost certainly due to a splice donor site mutation in intron 6 that causes missplicing (Hellens et al., 2010).

Pod shape (V/v or P/p)

Misshapen pods are due to the lack of a sclerenchyma layer at the end of the pod where it attaches to the stem. There are two genetic loci (V and P) that control the recessive phenotype and it's not clear which one Mendel studied.

The V locus contains the gene for a transcription factor that regulates the expression of genes for sclerenchyma formation in pea pods (Psat05G0804500). The gene is homologous to the Arabidospis MYB26 gene (Feng et al., 2025). Expression of this gene is reduced in plants with the recessive phenoptye (v) and this is probably due to the insertion of a retrotransposon upstream of the gene.

The P locus contains the gene (Psat01G0420500) that encodes a dodeca-CLE peptide that regulates an inhibitory factor involved in synthesis of zylem. The p phenotype is due to an allele with a premature stop codon (Feng et al., 2025).

Pod color (Gp/gp)

The normal pod color is green but Mendel studied a variety with yellow pods. The mutant phenotype is due to a lack of chlorophyll and the trait maps to the gene for chlorophyll synthase (ChlG) (Feng et al., 2025). The mutant allele responsible for the yellow phenotype contains a 100 kb deletion upstream of the ChlG gene and this deletion interferes with the expression of the gene leading to diminished levels of the enzyme and a deficiency of chlorophyll.

Feng et al. constructed a null mutation of the ChlG gene and found that plants that were homozygous for the null allele did not produce viable progeny. This confirms that plants homozygous for the original allele (100 kb deletion) still produce enough chorophyll for survival.

Flower position (Fa/fa)

The term "fasciation" is used to refer to defects in the growth of the apical meristem at the tip of the stem. Normal pea plants have a single flower at the end of a stem but the mutant variety has multiple flowers clustered at the tip of the stem (umbrella phenotype). There are several loci that affect fasciation but the one that Mendel studied was Fa located on chromosome 4.

The locus contains the gene Psat04G0031700, which encodes a regulatory kinase enzyme that controls the structure of the apical meristem. The fa phenotype is explained by the presence of a 5 bp deletion in exon 2 creating a premature stop codon (Feng et al, 2025).

Stem Length (Le/le) or Tall (T) and short (t)

The gene responsible for stem length has been identified and cloned (Martin et al., 1997; Lester et al., 1997). It encodes an enzyme called GA 3β-hydroxylase. This enzyme is responsible for one of the last steps in the synthesis of the hormone gibberellin GA1. The recessive allele (le) is a substitution mutation that converts an alanine residue to theonine resulting in a considerable reduction in enzyme activity and a much lower concentration of gibberellin and slower growth (shorter plants). [Mendel's Stem Length Gene (Le)]

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[Photo Credits: The photograph of mutant and wild-type pea seeds is taken from Figure 1 of Sato et al. (2007)]. The other photos with the black background are from Feng et al. 2025.

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Feng, C., Chen, B., Hofer, J., Shi, Y., Jiang, M., Song, B., Cheng, H., Lu, L., Wang, L., Howard, A. and et al. (2025) Genomic and genetic insights into Mendel’s pea genes. Nature 642:980-989. doi: [doi: 10.1038/s41586-025-08891-6]

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