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Nat Commun. 2019 Mar 14;10(1):1216. doi: 10.1038/s41467-019-09142-9.

A reference-grade wild soybean genome.

Author information

1
Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
2
BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China.
3
Wuhan Institute of Biotechnology, Wuhan, 430075, Hubei, China.
4
Department of Biotechnology, Chonnam National University, Gwangju, 550-749, Jeonnam, South Korea.
5
Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Chiba, Japan.
6
Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, 65211, USA.
7
Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, Iowa, 50011-4014, USA.
8
Faculty of Biological Sciences, Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, Yorkshire, UK.
9
Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China. tf.chan@cuhk.edu.hk.
10
Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China. honming@cuhk.edu.hk.

Abstract

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.

PMID:
30872580
PMCID:
PMC6418295
DOI:
10.1038/s41467-019-09142-9
[Indexed for MEDLINE]
Free PMC Article

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