Abstract
Mendel established the laws and laid the foundation of modern genetics through his famous hybridization experiments on seven pairs of classic traits in the garden pea (Pisum sativum). However, the molecular bases underlying these traits have only come into sharp focus in recent years. Leveraging advances in traditional map-based cloning, TILLING, long-read resequencing, population genetics, and GWAS, this article synthesizes current knowledge of ten genes governing seven traits—plant height, seed shape, flower color, seed color, pod color, pod morphology, and flower position—by summarizing each gene’s identity, chromosomal localization, and functional pathway. For plant height, the classical Le locus corresponds to PsGA3ox1, which encodes a gibberellin 3β-hydroxylase. Mutations at Le impede the biosynthesis of the bioactive hormone GA1, and the resulting deficiency leads to a dwarf or reduced-stature phenotype. Seed shape is determined by R, identified as PsSBEI (starch-branching enzyme I). Insertion of a transposable element into R restricts amylopectin synthesis, perturbing endosperm starch architecture and resulting in the wrinkled seeds noted by Mendel. Flower color is specified by the coordinated action of A (a bHLH transcription factor) and A2 (a WD40 scaffold). Together, they assemble the canonical MYB-bHLH-WD40 (MBW) regulatory complex, which co-activates structural genes in the anthocyanin pathway to determine pigment accumulation and floral hue. Seed color is governed by I, which encodes PsSGR (STAY-GREEN), a magnesium dechelatase that catalyzes a key step in chlorophyll catabolism. Loss-of-function alleles at I block chlorophyll degradation, yielding “stay-green” seeds in which chlorophyll persists beyond normal developmental stages. Pod coloration maps to Gp, corresponding to ChlG (chlorophyll synthase). Either direct loss of ChlG function or readthrough-fusion transcriptional interference caused by a large upstream deletion suppresses chlorophyll biosynthesis in developing pods, resulting in the yellow-pod phenotype. Pod morphology depends on two convergent regulatory pathways. The P gene, PsCLE41, signals through the P-PXY-WOX/NAC axis to promote vascular differentiation and secondary-wall programs, while V encodes PsMYB26, a transcription factor that drives secondary wall thickening in fiber cells. Acting in concert, these modules ensure robust secondary-wall deposition in the fiber layer lining the inner pod wall; disruption of either component compromises wall thickening and leads to pleated or wrinkled pods. Flower position (inflorescence determinacy at the shoot apex) is controlled by FA, identified as PsCIK, which participates in the CLAVATA-WUSCHEL (CLV-WUS) feedback circuit that maintains shoot apical meristem homeostasis. Mutations in FA destabilize this self-regulatory loop and promote terminal flowers at the apex. The expressivity of this determinacy phenotype is further modulated by a recessive modifier, Mfa, which fine-tunes the outcome in the fa background. Across these loci, convergent evidence highlights the central role of structural variation in generating the classical Mendelian phenotypes. Building on this clarified molecular landscape, we outline practical implications for quality improvement and the deliberate “design” of traits. Looking ahead, we envisage a next generation of legume genetic improvement anchored on three mutually reinforcing pillars: high-quality reference genomes to deliver contiguous, structurally faithful assemblies; comprehensive pan-genomes to capture presence/absence variation and structural polymorphism across germplasm; and precise gene editing to target coding, regulatory, and structural features alike. Together, these tools chart a path toward mechanism-based breeding, enabling purposeful, design-driven trait improvement in peas and, by extension, other legumes.
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Claims 16
Claim · model-written summary
The Le locus corresponds to PsGA3ox1, encoding gibberellin 3β-hydroxylase.
- Taxon
- garden pea (Pisum sativum)
Lathyrus oleraceuse7 - Gene
- PsGA3ox1e0
- Outcome
- gibberellin 3β-hydroxylasee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the classical Le locus corresponds to PsGA3ox1, which encodes a gibberellin 3β-hydroxylase”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Le mutations impede GA1 biosynthesis and produce dwarf stature.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- Lee0
- Outcome
- dwarf or reduced-stature phenotypee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Mutations at Le impede the biosynthesis of the bioactive hormone GA1, and the resulting deficiency leads to a dwarf or reduced-stature phenotype”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
The seed-shape locus R is PsSBEI.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- PsSBEIe0
- Outcome
- Seed shapee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Seed shape is determined by R, identified as PsSBEI (starch-branching enzyme I)”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
A transposable-element insertion into R disrupts amylopectin synthesis and yields wrinkled seeds.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- Re0
- Outcome
- wrinkled seedse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Insertion of a transposable element into R restricts amylopectin synthesis, perturbing endosperm starch architecture and resulting in the wrinkled seeds noted by Mendel”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
A and A2 coordinate flower color through the MBW regulatory complex.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- Ae0
- Outcome
- floral huee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Flower color is specified by the coordinated action of A (a bHLH transcription factor) and A2 (a WD40 scaffold). Together, they assemble the canonical MYB-bHLH-WD40 (MBW) regulatory complex, which co-activates structural genes in the anthocyanin pathway to determine pigment accumulation and floral hue”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Seed color locus I encodes PsSGR, a chlorophyll catabolism enzyme.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- PsSGRe0
- Outcome
- Seed colore0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Seed color is governed by I, which encodes PsSGR (STAY-GREEN), a magnesium dechelatase that catalyzes a key step in chlorophyll catabolism”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Loss of I prevents chlorophyll degradation and yields stay-green seeds.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- Ie0
- Outcome
- “stay-green” seedse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Loss-of-function alleles at I block chlorophyll degradation, yielding “stay-green” seeds in which chlorophyll persists beyond normal developmental stages”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Pod coloration locus Gp corresponds to ChlG.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- ChlGe0
- Outcome
- Pod coloratione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pod coloration maps to Gp, corresponding to ChlG (chlorophyll synthase)”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
ChlG loss or transcriptional interference suppresses chlorophyll synthesis and produces yellow pods.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- ChlGe0
- Outcome
- yellow-pod phenotypee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Either direct loss of ChlG function or readthrough-fusion transcriptional interference caused by a large upstream deletion suppresses chlorophyll biosynthesis in developing pods, resulting in the yellow-pod phenotype”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
PsCLE41 promotes vascular differentiation and secondary-wall programs.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- PsCLE41e0
- Outcome
- vascular differentiation and secondary-wall programse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The P gene, PsCLE41, signals through the P-PXY-WOX/NAC axis to promote vascular differentiation and secondary-wall programs”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
PsMYB26 drives secondary wall thickening in pod fiber cells.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- PsMYB26e0
- Outcome
- secondary wall thickening in fiber cellse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“V encodes PsMYB26, a transcription factor that drives secondary wall thickening in fiber cells”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Disruption of either pod wall component produces pleated or wrinkled pods.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Outcome
- pleated or wrinkled podse0
- Qualifier
- either componente0
Not reportedGene
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“disruption of either component compromises wall thickening and leads to pleated or wrinkled pods”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
FA is PsCIK and regulates shoot apical meristem homeostasis.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- PsCIKe0
- Outcome
- shoot apical meristem homeostasise0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“FA, identified as PsCIK, which participates in the CLAVATA-WUSCHEL (CLV-WUS) feedback circuit that maintains shoot apical meristem homeostasis”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
FA mutations promote terminal flowers at the apex.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- FAe0
- Outcome
- terminal flowers at the apexe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Mutations in FA destabilize this self-regulatory loop and promote terminal flowers at the apex”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Mfa modulates expression of the fa determinacy phenotype.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- Mfae0
- Outcome
- determinacy phenotypee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The expressivity of this determinacy phenotype is further modulated by a recessive modifier, Mfa, which fine-tunes the outcome in the fa background”
e7“garden pea (Pisum sativum)”
Claim · model-written summary
Structural variation contributes to the classical Mendelian phenotypes.
- Taxon
- garden pea (Pisum sativum)Lathyrus oleraceuse7
- Gene
- structural variatione0
- Outcome
- classical Mendelian phenotypese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“convergent evidence highlights the central role of structural variation in generating the classical Mendelian phenotypes”
e7“garden pea (Pisum sativum)”