Mutation breeding in the age of next-generation sequencing and genome editing

Authors: Xin, Zhanguo; JIAO, YINPING - Texas Tech University; Burow, Gloria; Hayes, Chad; Chen, Junping; WARE, DOREEN - Cold Spring Harbor Laboratory

Submitted to: International Plant and Animal Genome IX Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/20/2022
Publication Date: 1/14/2023
Citation: Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Ware, D. 2023. Mutation breeding in the age of next-generation sequencing and genome editing. International Plant and Animal Genome IX Conference.

Interpretive Summary:

Technical Abstract: Mutation Breeding is a classical and effective approach to generate diversity and create novel traits. Thousands of varieties have been released through mutagenesis. Advances in sequencing technologies and genome editing tools have advanced mutation breeding beyond release of new varieties. We have established a Pedigreed Mutant Library in the sorghum inbred line BTx623 by mutagenizing the seeds with ethyl methane sulfonate (EMS). The BTx623 we used to make the mutant library was purified by single seed descent for six generations to achieve near uniform background. The library has 6,400 M4 seed pools and possesses a great diversity of mutant phenotypes. Over 1000 sorghum mutants with altered agronomic traits have been isolated from the mutant library. Using next-generation sequencing (NGS), we have established an effective bioinformatic pipeline to identify the causal mutations through bulk-segregant-analysis (BSA) of the whole genome sequencing data of the pooled mutants selected from F2 populations. Once an F2 backcrossed population is established, the cost to identify the causal mutation is under $200 in NGS sequencing. On the other hand, we have sequenced 1256 lines from the mutant library and generated >10 million EMS-induced mutations. All genes in BTx623 genome, except for 517 short genes, have at least one mutation that results in either an amino acid change or knockout mutation. The mutation data will be available for public search on Sorghumbase (https://www.sorghumbase.org/). The mutant library has a high mutation frequency, which enable the selection of desired traits in a manageable number of lines but also make the direct use for breeding difficult. This drawback can be overcome by precise genome editing once the causal mutations are known. A combination of mutant library, NGS, and genome editing will revolutionize plant breeding.