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, Abdelhafid Bendahmane, Anissa Fouchal, Carol Moreau, Chie Sawada, Christine Le Signor, Cuijun Zhang, Eleni Vikeli, Georgios F. Tsanakas, Hang Zhao, Jitender Cheema, J. Elaine Barclay, Junliang Hou, Liz Sayers, Luzie U. Wingen, Marielle Vigouroux, Martin Vickers, Mike Ambrose, Marion Dalmais, Paola Higuera-Poveda, Pengfeng Li, Quan Yuan, Rebecca Spanner, Richard Horler, Roland H. M. 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, Shifeng Cheng
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. Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their molecular details and provides tools for further studies in pea genetics, functional genomics and crop improvement.