A reference-grade wild soybean genome

Authors: MIN, XE - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); YIK-LOK, CLAIRE CHUNG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); MAN-WAH, LI - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); FUK-LING, WONG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); XIN, WANG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); AILIN, LIU - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); ZHILI, WANG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); KING-YUNG, ALDEN LEUNG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); TIN-HANG, WONG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); SUK-WAH, IRIS TONG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); ZHIXIA, XIAO - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); KEJING, FAN - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); MING-SIN, NG - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); LINFENG, YANG - BGI SHENZHEN; TIANQUAN, DENG - BGI SHENZHEN; LIJUAN, HE - BGI SHENZHEN; LU, CHEN - BGI SHENZHEN; AISI, FU - WUHAN INSTITUTE OF TECHNOLOGY; QIONG, DING - WUHAN INSTITUTE OF TECHNOLOGY; JUNXIAN, HE - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); GYUHWA, CHUNG - CHONNAM NATIONAL UNIVERSITY; SACHIKO, ISOBE - KAZUSA DNA RESEARCH INSTITUTE; BABU, VALLIYODAN - UNIVERSITY OF MISSOURI; NGUYEN, HENRY - UNIVERSITY OF MISSOURI; Cannon, Steven; FOYER, CHRISTINE - UNIVERSITY OF LEEDS; TING-FUNG, CHAN - THE CHINESE UNIVERSITY OF HONG KONG (CUHK); HON-MING, LAM - THE CHINESE UNIVERSITY OF HONG KONG (CUHK)

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2019
Publication Date: 3/14/2019
Citation: Min, X., Yik-Lok, C., Man-Wah, L., Fuk-Ling, W., Xin, W., Ailin, L., Zhili, W., King-Yung, A., Tin-Hang, W., Suk-Wah, I., Zhixia, X., Kejing, F., Ming-Sin, N., Linfeng, Y., Tianquan, D., Lijuan, H., Lu, C., Aisi, F., Qiong, D., Junxian, H., Gyuhwa, C., Sachiko, I., Babu, V., Nguyen, H., Cannon, S.B., Foyer, C.H., Ting-Fung, C., Hon-Ming, L. 2019. A reference-grade wild soybean genome. Nature Communications. 10:1216. https://doi.org/10.1038/s41467-019-09142-9.
DOI: https://doi.org/10.1038/s41467-019-09142-9

Interpretive Summary: Plant breeders and scientists work to identify what genes are responsible for important traits (yield, nutrition, etc.) and where these genes are located within the species of interest’s DNA. Sequencing a species’ genome, down to the level of individual DNA bases, helps researchers link genes with traits. The soybean genome sequence, developed from one variety, has been available for the last eight years and has enabled many discoveries about gene function. However, more rapid progress could be made if multiple genome sequences, for distinct soybean varieties, could be examined to see how DNA changes alter particular traits. The work reported here is the complete, high-resolution sequence of approximately one billion DNA bases for the closest wild relative of soybean (Glycine soja). This sequence will allow researchers to determine how changes during domestication occurred. For example, identifying genes that changed wild soybean from a vine with small, hard seeds, into domesticated soybean, a robust, short plant with larger, softer seeds. The genome sequence for wild soybean is also of use because it will help researchers more finely pinpoint regions responsible for valuable traits. This will assist breeders and other scientists to more rapidly develop improved soybean varieties, to benefit farmers and consumers worldwide.

Technical Abstract: Efficient crop improvement is dependent on the application of accurate genetic information contained in diverse germplasm resources. To date, genomic analysis of soybean has largely depended on the genome sequence of the single elite soybean line, Williams 82. Here we report the assembly of the first high quality reference genome of a wild soybean, accession W05, providing a much broader pool of alleles and increased precision of population genetic analysis. A combination of methods including single-molecule real time sequencing (PacBio), next-generation sequencing (Illumina), optical mapping (Bionano), and Hi-C sequencing (Dovetail) was used to generate the final 1013.2 Mb assembled genome that consists of 20 superscaffolds and has a contig N50 of 3.3 Mb, with a high base-level fidelity. The power of the W05 genome and the range of useful applications are demonstrated through the refinement of quantitative trait loci (QTLs), genes, and alleles, including genomic regions with complex structural variations. Moreover, different major structural variations in soybean genomes were revealed by comparisons of cultivated and wild soybean varieties originating from or popularized in the USA and Asia, in combination with optical mapping.