Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Yang, T and Liu, R and Luo, Y and Hu, S and Wang, D and Wang, C and Pandey, M K and Ge, S and Xu, Q and Li, N and Li, G and Huang, Y and Saxena, R K and Ji, Y and Li, M and Yan, X and He, Y and Liu, Y and Wang, X and Xiang, C and Varshney, R K and Ding, H and Gao, S and Zong, X (2022) Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nature Genetics, 54. pp. 1553-1563. ISSN 1546-1718

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Abstract

Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.

Item Type:	Article
Divisions:	Center of Excellence in Genomics and Systems Biology
CRP:	UNSPECIFIED
Uncontrolled Keywords:	functional genomics, crop breeding, next-generation sequencing (NGS) technology, Genomic polymorphism
Subjects:	Mandate crops > Chickpea Mandate crops > Pigeonpea Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	30 Oct 2023 04:36
Last Modified:	30 Oct 2023 04:36
URI:	http://oar.icrisat.org/id/eprint/12255
Official URL:	https://www.nature.com/articles/s41588-022-01172-2
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We thank L. Li, B. Redden and J. Hu for their support in sample collection and preparing materials. We are grateful to Biomarker Technologies Corporation, Beijing and Novogene Bioinformatics Institute (Beijing, China) for technical support with PacBio sequencing, NGS, 10x Genomics sequencing and Hi-C sequencing. We thank Grandomics Biosciences, Beijing for technical support with Bionano sequencing. This work was supported by the National Key R&D Program of China (2018YFD1000701/2018YFD1000700 to T.Y.), the Youth Innovation Promotion Association of Chinese Academy of Science (2017140 to Y.F.L.), the funding of Agricultural Variety Improvement Project of Shandong Province (2019LZGC017 to H.F.D.), China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08 to X.X.Z) and National Natural Science Foundation of China (31801428 to R.L.). This work was also supported by the Subject Team of Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences (CXGC2018E15 to H.F.D.), the Crop Germplasm Resources Protection (2130135 to X.X.Z), Industry Team of Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences (CXGC2016A02 to H.F.D.), Coarse Cereals Innovation Team of Modern Agricultural Industry Technology System of Shandong Province (SDAIT-15-01 to H.F.D.), Agricultural Science and Technology Innovation Program (ASTIP to X.X.Z) in CAAS, Youth Research Fund of Shandong Academy of Agricultural Sciences (2016YQN19 to D.W.) and Food Futures Institute of the Murdoch University, Australia.
Links:	Google Scholar

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