Comparative analysis of sorghum EMS mutants and natural populations

Authors: WANG, LIYA - Cold Spring Harbor Laboratory; LIPZEN, ANNA - Joint Genome Institute; LU, ZHENYUAN - Cold Spring Harbor Laboratory; Chen, Junping; WANG, XIAOFEI - Cold Spring Harbor Laboratory; TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory; BARRY, KERRIE - Joint Genome Institute; MORTIMER, JENNY - Joint Bioenergy Institute (JBEI); Ware, Doreen; Xin, Zhanguo

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 6/7/2021
Publication Date: 6/7/2021
Citation: Wang, L., Lipzen, A., Lu, Z., Chen, J., Wang, X., Tello-Ruiz, M.K., Barry, K., Mortimer, J., Ware, D., Xin, Z. 2021. Comparative analysis of sorghum EMS mutants and natural populations. bioRxiv. https://doi.org/10.1101/2021.06.06.447271.
DOI: https://doi.org/10.1101/2021.06.06.447271

Interpretive Summary: Chemical mutagenesis is a technique that allows the introduction of random mutations (or DNA changes) using a chemical such as EMS, in the genome. The technique is commonly used to treat seeds and study the effects of such mutations in the plant. This is particularly useful to elucidate the specific combination of DNA changes (or the underlying genes) that is responsible for favorable traits in the plant, such as higher crop yield, tolerance to drought, resistance to disease, or improved quality. This work analyzed 4.2 million mutations in 445 mutagenized sorghum lines together with spontaneous DNA changes naturally occurring in the population and previous EMS efforts, and concluded that nearly 70% of sorghum genes present at least one (deleterious) mutation predicted to disrupt a gene's function (deleterious). As expected, EMS appears to promote more deleterious mutations than it occurs in nature, making chemical mutagenesis more powerful in elucidating sorghum gene functions on a large scale and requiring less work in validating candidate genes responsible for specific traits. All data (importantly, genes with noteworthy mutations) is being made available through web applications known as BSAseq and SciApps.org.

Technical Abstract: To build a large-scale genomic resource for functional validation of sorghum genes through EMS-mutagenized BTx623 seeds, we deep sequenced (30-60X) an additional 445 phenotyped EMS mutant lines. 4.2 million EMS mutations are called with nearly 36,800 mutations that could have a disruptive effect on functions of over 15,500 genes. Combining variants carried by both the natural population and previous EMS efforts, over 69% of sorghum coding genes (23,644) are now presented with one or more mutations that are, or are predicted to be, disruptive to their functions. Our results show that the EMS population carries more significant mutations but less in each sample than the natural population, which makes it more powerful in elucidating sorghum gene functions on a large scale and requiring less work in validation of candidate causal genes. We have made the data available through two ways, one is the integration with the BSAseq workflow that supports retrieving independent EMS samples carrying the same genes with significant mutation for complementary testing, and the other is a web application for directly querying genes with significant mutations on SciApps.org.