[en] 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.
Disciplines :
Agriculture & agronomy
Author, co-author :
Feng, Cong ✱; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Chen, Baizhi ✱; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Hofer, Julie ✱; John Innes Centre, Norwich Research Park, Norwich, UK
Shi, Yan ✱; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Jiang, Mei ✱; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Song, Bo ; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Cheng, Hong; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Lu, Lu; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Wang, Luyao; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Howard, Alex; John Innes Centre, Norwich Research Park, Norwich, UK
Bendahmane, Abdel ; INRAE UMR 1403, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
Fouchal, Anissa; INRAE UMR 1403, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
Moreau, Carol; John Innes Centre, Norwich Research Park, Norwich, UK ; Paleogenomics Laboratory, INRAE Clermont-Auvergne-Rhône-Alpes, CS 60032, Clermont-Ferrand, France
Sawada, Chie; John Innes Centre, Norwich Research Park, Norwich, UK
LeSignor, Christine ; INRAE UMR1347-Agroecologie pôle GEAPSI, DIJON Cedex, France
Zhang, Cuijun ; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Vikeli, Eleni; John Innes Centre, Norwich Research Park, Norwich, UK
Tsanakas, Georgios; John Innes Centre, Norwich Research Park, Norwich, UK
Zhao, Hang ; Université de Liège - ULiège > TERRA Research Centre ; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Cheema, Jitender; John Innes Centre, Norwich Research Park, Norwich, UK ; EMBL-EBI, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, UK
Barclay, J Elaine; John Innes Centre, Norwich Research Park, Norwich, UK
Hou, Junliang; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Sayers, Liz; John Innes Centre, Norwich Research Park, Norwich, UK
Wingen, Luzie ; John Innes Centre, Norwich Research Park, Norwich, UK
Vigouroux, Marielle ; John Innes Centre, Norwich Research Park, Norwich, UK
Vickers, Martin ; John Innes Centre, Norwich Research Park, Norwich, UK
Ambrose, Mike; John Innes Centre, Norwich Research Park, Norwich, UK
Dalmais, Marion; INRAE UMR 1403, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
Higuera-Poveda, Paola; John Innes Centre, Norwich Research Park, Norwich, UK
Li, Pengfeng; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Yuan, Quan; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Spanner, Rebecca; John Innes Centre, Norwich Research Park, Norwich, UK ; Department of Plant Pathology, University of Minnesota, St Paul, MN, USA
Horler, Richard; John Innes Centre, Norwich Research Park, Norwich, UK
Wouters, Roland ; John Innes Centre, Norwich Research Park, Norwich, UK
Chundakkad, Smitha; John Innes Centre, Norwich Research Park, Norwich, UK
Wu, Tian; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Zhao, Xiaoxiao; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Li, Xiuli; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Sun, Yuchen; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Huang, Zejian; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Wu, Zhen; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
Deng, Xing Wang ; State Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
Steuernagel, Burkhard ; John Innes Centre, Norwich Research Park, Norwich, UK
Domoney, Claire; John Innes Centre, Norwich Research Park, Norwich, UK
Ellis, Noel ✱; John Innes Centre, Norwich Research Park, Norwich, UK. Noel.Ellis2@jic.ac.uk
Chayut, Noam ; John Innes Centre, Norwich Research Park, Norwich, UK. Noam.Chayut@jic.ac.uk
Cheng, Shifeng ; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. chengshifeng@caas.cn
The authors thank J. J. Doyle, M. Bennett, S. Huang, B. Lucas, D. Sanders and G. Moore for their invaluable support and comments for this project; colleagues for assistance in pea field trial and phenotyping work from experimental stations across northern and southern China; Y. Zhong and S. Liu; and L. Zhang for providing ZW1 genome assembly and annotation for comparison in this work; E. Jones and E. Crawford for plant phenotype data; M. Trick and S. Griffiths for valuable discussions at the John Innes Centre (JIC); the JIC NBI Computing Infrastructure for Science and JIC Bioinformatics groups for support in data handling and analysis; the JIC Field Trials and Horticultural Services teams for support with field and glasshouse experiments; the Molecular Genetics, Genotyping and DNA Extraction Platforms for support in experimental biology; and Bioimaging and Scientific Photography Platforms for phenotype visualization. This work was supported by the Program for Guangdong \u2018ZhuJiang\u2019 Introducing Innovative and Entrepreneurial Teams (2019ZT08N628), the National Natural Science Foundation of China (32022006), the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2021-AGIS-ZDRW202101), the Shenzhen Science and Technology Program (AGIS-ZDKY202002), the National Key Research and Development Program of China (2023YFF1000100), and the National Key R&D Program of China (grant number 2023YFA0914600) to S. Cheng, and the National Natural Science Foundation of China (32401853) to Y. Shi. The work in the UK was possible due to the long-term investment of the UK Research Infrastructure Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) through Institute Strategic Programme (ISP) grants, Institute Development Grant funds, and the Germplasm Resources National Capability Programme (BBS/E/J/000PR8000) and the National Bioscience Research Infrastructure grant (BBS/E/JI/23NB0001). We also acknowledge support from UKRI-BBSRC grants BB/J004561/1, BB/W510695/1 and BBS/E/J/000PR9799, the UK Department for Environment, Food, and Rural Affairs (Defra) through the Pulse Crop Genetic Improvement Network (grants CH0103 and CH0111) and the Provision and Maintenance of the Pea Genebank to Facilitate R&D Need grant (C5515), and JIC through its Institute Strategic Fund. We acknowledge the source of the TILLING mutant used in the analysis of gp as UMR1403-INRAE-IPS2, UMR1347-Agroecologie, France and the European Union FP6 Integrated Project Grain Legumes, FOOD-CT-2004-506223.
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