Chinese Bulletin of Botany ›› 2020, Vol. 55 ›› Issue (4): 403-406.DOI: 10.11983/CBB20096

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A 360-degree Scanning of Population Genetic Variations—a Pan-genome Study of Soybean

Guangtao Zhu1,Sanwen Huang2,*()   

  1. 1The CAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming 650500, China
    2Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
  • Received:2020-05-26 Accepted:2020-06-07 Online:2020-07-01 Published:2020-06-17
  • Contact: Sanwen Huang

Abstract: Soybean (Glycine max) is an important oil and protein crop. The abundancy of genetic diversity within the species provides an essential resource for traits exploration and breeding improvement. However, one reference genome is inadequate for discovering all genetic diversity of a species. Pan-genome provides a new solution to overcome this limitation. Recently, Prof. Zhixi Tian’ Group and Prof. Chengzhi Liang’ Group from the Institute of Genetics and Develop- mental Biology, Chinese Academy of Sciences, selected 26 representative soybeans from 2 898 sequenced accessions. Together with three previously published genomes, they constructed a pan-genome and a graph-based genome of wild and cultivated soybean germplasm. The core, dispensable, and private genes as well as all the vast majority of genetic variations within this species were identified and characterized. These data comprehensively revealed allelic variations and gene fusion event of maturity gene E3, the haploid types of seed coat color gene I and their evolutionary relationship, and structural variations affecting gene expression and regional adaptation selection of ferric ion transporters. This study provide a new mode for crop genomics, and will facilitate genetic variations identification, traits exploration and germplasm innovation of soybean.

Key words: soybean, pan-genome, graph-based genome, genetic variation, agronomic traits