Molecular Mapping and Functional Analysis of Phenotype-determining Genes for Mendelian Traits in Pea

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 (<italic>Pisum sativum</italic>). 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 <italic>Le</italic> locus corresponds to <italic>PsGA3ox1</italic>, which encodes a gibberellin 3β-hydroxylase. Mutations at <italic>Le</italic> 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 <italic>R</italic>, identified as <italic>PsSBEI</italic> (starch-branching enzyme I). Insertion of a transposable element into <italic>R</italic> 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 <italic>A</italic> (a bHLH transcription factor) and <italic>A2</italic> (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 <italic>I</italic>, which encodes <italic>PsSGR</italic> (STAY-GREEN), a magnesium dechelatase that catalyzes a key step in chlorophyll catabolism. Loss-of-function alleles at <italic>I</italic> block chlorophyll degradation, yielding “stay-green” seeds in which chlorophyll persists beyond normal developmental stages. Pod coloration maps to <italic>Gp</italic>, corresponding to <italic>ChlG</italic> (chlorophyll synthase). Either direct loss of <italic>ChlG</italic> 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 <italic>P</italic> gene, <italic>PsCLE41</italic>, signals through the P-PXY-WOX/NAC axis to promote vascular differentiation and secondary-wall programs, while <italic>V</italic> encodes <italic>PsMYB26</italic>, 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 <italic>FA</italic>, identified as <italic>PsCIK</italic>, which participates in the CLAVATA-WUSCHEL (CLV-WUS) feedback circuit that maintains shoot apical meristem homeostasis. Mutations in <italic>FA</italic> 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, <italic>Mfa</italic>, which fine-tunes the outcome in the <italic>fa</italic> 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.