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Nat Biotechnol. 2014 Oct;32(10):1045-52. doi: 10.1038/nbt.2979. Epub 2014 Sep 14.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.

Author information

1
1] 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].
2
1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] [3].
3
1] Department of Agronomy, Purdue University, West Lafayette, Indiana, USA. [2].
4
1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2].
5
1] 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.
6
Novogene Bioinformatics Institute, Beijing, P.R. China.
7
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China.
8
Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, P.R. China.
9
Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
10
1] 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.

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.

PMID:
25218520
DOI:
10.1038/nbt.2979
[Indexed for MEDLINE]

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