biostudies-literatureFeng CBiotechnology and Biological Sciences Research Council980-989https://www.ebi.ac.uk/biostudies/studies/S-EPMC12221995biostudies-literatureUnknown642(8069)Mendel¹ studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes^2-7, including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-NatureGenomic and genetic insights into Mendel's pea genes.PMC12221995BB/J004561/1BB/W510695/1Hofer JHoward ASpanner RBarclay JEWingen LVickers MJiang MSawada CFeng CShi YWang LZhao XCheng SWu ZHorler RVigouroux MChayut NBendahmane ASayers LHiguera-Poveda PWu TZhang CCheng HMoreau CZhao HTsanakas GEllis NVikeli ESong BSteuernagel BDomoney CYuan QChundakkad SLi PChen BSun YAmbrose MLu LCheema JLi XHou JDalmais MFouchal AWouters RHuang ZDeng XWLeSignor CfalseGenomic and genetic insights into Mendel's pea genes.Mendel¹ studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes^2-7, including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-2025-01-01T00:00:00Z2025 Jun2026-06-01T15:39:36.469Z2026-04-08T13:39:26.841ZS-EPMC122219954026916710.1038/s41586-025-08891-6