Journal Article

A reference-grade wild soybean genome

Tanabata, Takanari, Fu, Aisi, Wang, Xin, Qi, Xinpeng, Leung, Alden King-Yung, Xiao, Zhixia, Wong, Tin-Hang, Tong, Suk-Wah, Valliyodan, Babu, Deng, Tianquan, Ng, Ming-Sin, Xie, Min, Isobe, Sachiko, Fan, Kejing, Liu, Ailin, Foyer, Christine H., He, Lijuan, Li, Man-Wah, Ding, Qiong, Yang, Linfeng, Chung, Claire Yik-Lok, Nguyen, Henry T., Lam, Hon-Ming, Wong, Fuk-Ling, Chen, Lu, Chung, Gyuhwa, Cannon, Steven B., Chan, Ting-Fung, Wang, Zhili, He, Junxian

2019

Overview

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. Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al . report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45/23 / 45/91 / 631/208/212/2304 / 631/449/1870 / 631/449/711 / 631/61/447/8 / Assembly / Biological Evolution / Chromosomes / Copy number / Crop improvement / DNA Copy Number Variations / Domestication / Gene mapping / Genetic diversity / Genetic improvement / Genome, Plant - genetics / Genomes / Genomics - methods / Genotype / Genotypes / Germplasm / Glycine max - genetics / Glycine soja / Humanities and Social Sciences / Molecular Sequence Annotation / multidisciplinary / Peptides - genetics / Plant breeding / Plant Breeding - methods / Plant Proteins - genetics / Quantitative trait loci / Quantitative Trait Loci - genetics / Science / Science (multidisciplinary) / Seed coats / Soybeans / Translocation / Translocation, Genetic - genetics / Trypsin / Trypsin inhibitors