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Reference genome sequence and population genomic analysis of peas provide insights into the genetic basis of Mendelian and other agronomic traits

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Abstract

Peas are essential for human nutrition and played a crucial role in the discovery of Mendelian laws of inheritance. In this study, we assembled the genome of the elite vegetable pea cultivar ‘Zhewan No. 1’ at the chromosome level and analyzed resequencing data from 314 accessions, creating a comprehensive map of genetic variation in peas. We identified 235 candidate loci associated with 57 important agronomic traits through genome-wide association studies. Notably, we pinpointed the causal gene haplotypes responsible for four Mendelian traits: stem length (Le/le), flower color (A/a), cotyledon color (I/i) and seed shape (R/r). Additionally, we discovered the genes controlling pod form (Mendelian P/p) and hilum color. Our study also involved constructing a gene expression atlas across 22 tissues, highlighting key gene modules related to pod and seed development. These findings provide valuable pea genomic information and will facilitate the future genome-informed improvement of pea crops.

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Fig. 1: Chromosomal features of the P. sativum var. ZW1 genome.
Fig. 2: Phylogenomic relationships, population structure and genomic diversity of Pisum accessions.
Fig. 3: GWAS analysis of Mendelian traits.
Fig. 4: GWAS- and BSA-based identification of candidate genes responsible for pod form.
Fig. 5: Integration of GWAS and BSA to identify candidate genes responsible for seed hilum color.
Fig. 6: Identification of genes related to seed, pod and root nodule development.

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Data availability

The genome sequencing and assembly data of Pisum sativum cultivar Zhewan1 (PeaZW1) have been deposited at National Center for Biotechnology Information under the BioProject PRJNA1042956. The whole-genome sequencing of 237 accessions has also been deposited at NCBI under the BioProject PRJNA1035516. Transcriptome data from different tissues can be found under the BioProject PRJNA1108961. Source data are provided with this paper.

Code availability

All codes and tools used in this study are described in Methods and the Reporting Summary.

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Acknowledgements

We are grateful to Biomarker Technologies Corporation, Beijing and China National Gene Bank (CNGB), Beijing Novogene Co. Ltd for technical support with PacBio HiFi sequencing, Hi-C sequencing, Iso-seq, RNA-seq and whole genomics sequencing. This work was supported by the Zhejiang Provincial Important Science and Technology Specific Projects (grant no. 2021C02065 to N.L., grant no. 2022C02016 to Y.G.), State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products (grant no. 2021DG700024-ZZ202206 to N.L.), National Natural Science Foundation of China (grant no. 31872114 to N.L.) and Zhejiang Basic Public Welfare Research Project (grant no. LGN20C150006 to N.L., grant no. LGN21C150007 to Z.F.).

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Author notes

  1. These authors contributed equally: Na Liu, Xiaolong Lyu.

Authors and Affiliations

  1. State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China

    Na Liu, Xueying Zhang, Guwen Zhang, Zhijuan Feng, Jinwen Ou, Bin Wang, Yuanpeng Bu & Yaming Gong

  2. College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

    Xiaolong Lyu, Ziqian Zhang, Xueying Guan, Qiang Gao, Wanghong Shi, Yayuan Deng, Kuang Sheng, Yumeng Zhu, Mingfang Zhang, Liangsheng Zhang & Ting Zhao

  3. Station of Zhejiang Seed Management, Hangzhou, China

    Xiaoyang Chen

  4. Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China

    Xiaoming Yang

  5. Hainan Institute of Zhejiang University, Sanya, China

    Wanghong Shi, Yayuan Deng & Mingfang Zhang

  6. Yazhouwan National Laboratory, Sanya, China

    Liangsheng Zhang

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  1. Na Liu
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Contributions

Y.G., N.L., L.Z., T.Z., X.L. and M.Z. conceived the project and designed the study. N.L., T.Z., L.Z., X.L., Z.Z., Y.Z., Z.F., Q.G., K.S., W.S. and Y.D. performed data analyses. N.L. and T.Z. drafted the manuscript. G.Z., X.Z., X.L., X.C., X.Y., Z.F., J.O., B.W. and Y.B. collected samples and performed experiments. N.L. and X.L. wrote the manuscript, and X.G., M.Z., L.Z. and T.Z. revised the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to Mingfang Zhang, Liangsheng Zhang, Ting Zhao or Yaming Gong.

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Liu, N., Lyu, X., Zhang, X. et al. Reference genome sequence and population genomic analysis of peas provide insights into the genetic basis of Mendelian and other agronomic traits. Nat Genet 56, 1964–1974 (2024). https://doi.org/10.1038/s41588-024-01867-8

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