A large sequenced mutant library- valuable reverse genetic resource that covers 98% of the genes in a Sorghum genome

Authors: JIAO, YINPING - Texas Tech University; SINGH, DEEPTI - Texas Tech University; BARRY, KERRIE - Department Of Energy; DAUM, CHRIS - Department Of Energy; YOSHINAGA, YUKO - Department Of Energy; KHAN, ADIL - Texas Tech University; LU, ZHENYUAN - Cold Spring Harbor Laboratory; WANG, XIAOFEI - Cold Spring Harbor Laboratory; WEI, XUEHONG - Cold Spring Harbor Laboratory; TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory; Burow, Gloria; Hayes, Chad; Chen, Junping; MORTIMER, JENNY - Department Of Energy; Ware, Doreen; Xin, Zhanguo

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/29/2023
Publication Date: 12/15/2023
Citation: Jiao, Y., Singh, D., Barry, K., Daum, C., Yoshinaga, Y., Khan, A., Lu, Z., Wang, X., Wei, X., Tello-Ruiz, M.K., Burow, G.B., Hayes, C.M., Chen, J., Mortimer, J., Ware, D., Xin, Z. 2023. A large sequenced mutant library- valuable reverse genetic resource that covers 98% of the genes in a Sorghum genome. Plant Journal. 117(5):1543-1557. https://doi.org/10.1111/tpj.16582.
DOI: https://doi.org/10.1111/tpj.16582

Interpretive Summary: Sorghum is a drought and heat tolerance crop and an excellent model for functional genomics studies due to its small genome. In collaboration with DOE, Cold Spring Harbor Laboratory, and Joint BioEnergy Institute, ARS scientists in Lubbock, Texas sequenced 897 sorghum mutants and revealed 9.5 million EMS-induced mutations that covered 98% of sorghum's annotated genes. Additionally, the mutations in the promoter and enhancer regions of 18,000 and 11,790 genes respectively provide a resource to study the functions of cis-regulatory elements. In addition to the large number of mutations discovered, the sequencing effort also showed that EMS-induced mutations in sorghum are random and uniformly distributed in the genome. As the first comprehensive sequence-indexed sorghum mutant population, this work is very important to genomic studies in sorghum and other grasses, sorghum improvement, and bioenergy research.

Technical Abstract: Mutant populations are a valuable tool for studying gene function in plants and introducing new traits in crop breeding. Sorghum, a C4 crop with high drought and heat tolerance, is an excellent model for functional genomics studies due to its compact genome structure. In this study, we report on a comprehensive sequence-indexed sorghum mutant population. Our sequencing effort of 897 sorghum mutants revealed 9.5 million EMS-induced mutations that covered 98% of sorghum's annotated genes. Additionally, the mutations in the promoter and enhancer regions of 18,000 and 11,790 genes respectively provide germplasms to study the functions of cis-regulatory elements. The characterizations of the flanking sequences and the usage of codons of the mutations indicated a non-preferential pattern of EMS-induced mutations. As a deep-sequenced mutant population without strong selection pressure, our data provide an opportunity to study the impact of selections on the distribution of mutations by comparing with the sorghum association panel (SAP) that has strong breeding selection pressure. Our results indicate a uniform distribution of EMS-induced mutations across different regions of the genome and biased selection towards the coding sequence and UTR regions with low variation density in the SAP. Due to selection, the natural population had 40% more nonsynonymous variations than synonymous, while the mutant population had similar amounts of both types of mutations in the genic region. All resources of this mutant population are publicly searchable through the SorbMuDB. In summary, our comprehensive sequence-indexed sorghum mutant population provides an excellent platform to discover gene functions in the grass family, supporting plant biology research and crop breeding.