Genomic and genetic insights into Mendel’s pea genes

Cong Feng, Baizhi Chen, Julie Hofer, Yan Shi, Mei Jiang, Bo Song, Hong Cheng, Lu Lu, Luyao Wang, Alex Howard, Abdel Bendahmane, Anissa Fouchal, Carol Moreau, Chie Sawada, Christine LeSignor, Cuijun Zhang, Eleni Vikeli, Georgios Tsanakas, Hang Zhao, Jitender Cheema, J. Elaine Barclay, Junliang Hou, Liz Sayers, Luzie Wingen, Marielle Vigouroux, Martin Vickers, Mike Ambrose, Marion Dalmais, Paola Higuera-Poveda, Pengfeng Li, Quan Yuan, Rebecca Spanner, Richard Horler, Roland Wouters, Smitha Chundakkad, Tian Wu, Xiaoxiao Zhao, Xiuli Li, Yuchen Sun, Zejian Huang, Zhen Wu, Xing Wang Deng, Burkhard Steuernagel, Claire Domoney, Noel Ellis (), Noam Chayut () and Shifeng Cheng ()
Additional contact information
Cong Feng: Chinese Academy of Agricultural Sciences
Baizhi Chen: Chinese Academy of Agricultural Sciences
Julie Hofer: Norwich Research Park
Yan Shi: Chinese Academy of Agricultural Sciences
Mei Jiang: Chinese Academy of Agricultural Sciences
Bo Song: Chinese Academy of Agricultural Sciences
Hong Cheng: Chinese Academy of Agricultural Sciences
Lu Lu: Chinese Academy of Agricultural Sciences
Luyao Wang: Chinese Academy of Agricultural Sciences
Alex Howard: Norwich Research Park
Abdel Bendahmane: Institute of Plant Sciences Paris-Saclay
Anissa Fouchal: Institute of Plant Sciences Paris-Saclay
Carol Moreau: Norwich Research Park
Chie Sawada: Norwich Research Park
Christine LeSignor: INRAE UMR1347-Agroecologie pôle GEAPSI
Cuijun Zhang: Chinese Academy of Agricultural Sciences
Eleni Vikeli: Norwich Research Park
Georgios Tsanakas: Norwich Research Park
Hang Zhao: Chinese Academy of Agricultural Sciences
Jitender Cheema: Norwich Research Park
J. Elaine Barclay: Norwich Research Park
Junliang Hou: Chinese Academy of Agricultural Sciences
Liz Sayers: Norwich Research Park
Luzie Wingen: Norwich Research Park
Marielle Vigouroux: Norwich Research Park
Martin Vickers: Norwich Research Park
Mike Ambrose: Norwich Research Park
Marion Dalmais: Institute of Plant Sciences Paris-Saclay
Paola Higuera-Poveda: Norwich Research Park
Pengfeng Li: Chinese Academy of Agricultural Sciences
Quan Yuan: Chinese Academy of Agricultural Sciences
Rebecca Spanner: Norwich Research Park
Richard Horler: Norwich Research Park
Roland Wouters: Norwich Research Park
Smitha Chundakkad: Norwich Research Park
Tian Wu: Chinese Academy of Agricultural Sciences
Xiaoxiao Zhao: Chinese Academy of Agricultural Sciences
Xiuli Li: Chinese Academy of Agricultural Sciences
Yuchen Sun: Chinese Academy of Agricultural Sciences
Zejian Huang: Chinese Academy of Agricultural Sciences
Zhen Wu: Chinese Academy of Agricultural Sciences
Xing Wang Deng: Peking University
Burkhard Steuernagel: Norwich Research Park
Claire Domoney: Norwich Research Park
Noel Ellis: Norwich Research Park
Noam Chayut: Norwich Research Park
Shifeng Cheng: Chinese Academy of Agricultural Sciences

Nature, 2025, vol. 642, issue 8069, 980-989

Abstract: Abstract 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 genes2–7, 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-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the ‘semi-leafless’ form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.

Date: 2025
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DOI: 10.1038/s41586-025-08891-6

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