ArticleNature biotechnology2014
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
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Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 329 papers, 1 of them a synthesis that pooled it.
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329citing papers in PubMed, 1 pooled it
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Who cites it
329 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advancing crop improvement through GWAS and beyond in mung bean.Frontiers in plant science · 2024Pooled it
- Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens.The Plant journal : for cell and molecular biology · 2026Review
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Harnessing genomics approaches for heat stress resilience in wheat: from discovery to deployment.Journal of experimental botany · 2026Review
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.Nature communications · 2026Article
- Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.BMC plant biology · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Breeding Climate-Resilient Soybeans for 2050 and Beyond: Leveraging Novel Technologies to Mitigate Yield Stagnation and Climate Change Impacts.Plants (Basel, Switzerland) · 2026Review
- A telomere-to-telomere gap-free genome of the new cultivar 'Zhongtian No. 5', combined with pan-genome analysis, aids in exploration and genetic enhancement of red clover (Horticulture research · 2026Article
- An α/β-Hydrolase GmABHD6 Controls Seed Oil Content and Yield in Soybean.Plant biotechnology journal · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Genomic Signatures of Artificial Selection Underlying Oil Content Differentiation in Chinese and Uruguayan Soybean Germplasm.Plants (Basel, Switzerland) · 2026Article
- Pan-genome of wild and cultivated rice uncovers genetic diversity, lost and selected sequences during rice domestication.Rice (New York, N.Y.) · 2026Article
- Article
- On the use and misuse of pangenome and related terms.Nature communications · 2026Article
- Natural variation of theFrontiers in plant science · 2026Article
- Genetic improvement and bioactive potential of rice bean (Frontiers in plant science · 2026Review
269 more citing papers are in PubMed but not listed here.
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Authors and funding
36 authors.
Ying-hui Li1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [4].
Guangyu Zhou1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] [3].
Jianxin Ma1] Department of Agronomy, Purdue University, West Lafayette, Indiana, USA. [2].
Wenkai Jiang1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2].
Long-guo Jin1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Zhouhao ZhangNovogene Bioinformatics Institute, Beijing, P.R. China.
Yong Guo1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Jinbo ZhangNovogene Bioinformatics Institute, Beijing, P.R. China.
Yi Sui1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Liangtao ZhengNovogene Bioinformatics Institute, Beijing, P.R. China.
Shan-shan Zhang1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Qiyang ZuoNovogene Bioinformatics Institute, Beijing, P.R. China.
Xue-hui Shi1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Yan-fei Li1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Wan-ke ZhangState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China.
Yiyao HuNovogene Bioinformatics Institute, Beijing, P.R. China.
Guanyi KongNovogene Bioinformatics Institute, Beijing, P.R. China.
Hui-long Hong1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Bing Tan1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Jian Song1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Zhang-xiong Liu1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Yaoshen WangNovogene Bioinformatics Institute, Beijing, P.R. China.
Hang RuanNovogene Bioinformatics Institute, Beijing, P.R. China.
Carol K L YeungNovogene Bioinformatics Institute, Beijing, P.R. China.
Jian LiuNovogene Bioinformatics Institute, Beijing, P.R. China.
Hailong WangNovogene Bioinformatics Institute, Beijing, P.R. China.
Li-juan Zhang1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Rong-xia Guan1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Ke-jing Wang1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Wen-bin LiKey Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, P.R. China.
Shou-yi ChenState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China.
Ru-zhen Chang1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Zhi JiangNovogene Bioinformatics Institute, Beijing, P.R. China.
Scott A JacksonCenter for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
Ruiqiang Li1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center, and School of Life Sciences, Peking University, Beijing, P.R. China.
Li-juan Qiu1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.
Indexed as
AgricultureAmino Acid SequenceBiomassDisease ResistanceDNA, PlantGenome, PlantGenomicsGlycine maxMolecular Sequence DataPhylogenyPolymorphism, Single NucleotideSeedsSequence AlignmentSequence Analysis, DNADNA, Plant
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25218520What OpenQuestion holds
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