Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression

Authors: ZHANG, JUNLI - University Of California, Davis; XIONG, HONGCHUN - University Of California, Davis; BURGUENER, GERMAN - University Of California, Davis; WOODS, DANIEL - University Of California, Davis; LIU, QIUJIE - University Of California, Davis; DEBERNARDI, JUAN - University Of California, Davis; AKHUNOVA, ALINA - Kansas State University; Garland-Campbell, Kimberly; Kianian, Shahryar; Brown-Guedira, Gina; POZNIAK, CURTIS - University Of Saskatchewan; Faris, Justin; AKHUNOV, EDUARD - Kansas State University; DUBCOVSKY, JORGE - University Of California, Davis

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2023
Publication Date: 9/13/2023
Citation: Zhang, J., Xiong, H., Burguener, G.F., Woods, D.P., Liu, Q., Debernardi, J.M., Akhunova, A., Garland Campbell, K.A., Kianian, S., Brown Guedira, G.L., Pozniak, C., Faris, J.D., Akhunov, E., Dubcovsky, J. 2023. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proceedings of the National Academy of Sciences (PNAS). 120(38) e2306494120. https://doi.org/10.1073/pnas.2306494120.
DOI: https://doi.org/10.1073/pnas.2306494120

Interpretive Summary: The study of the function of wheat genes is complicated by the complexity of the wheat genome. The TILLING population of Kronos Durum wheat has been useful to evaluate specific genes with variants caused by mutation using a databased of gene sequences from the members of the TILLING population . This paper describes additional sequence data from the upstream promoter regions of genes. Variation for many traits in plants is caused by promoter sequence differences which regulate gene expression. This report of the promoter sequences adds to the genetic tools available for the study of wheat gene function.

Technical Abstract: Background: Wheat is an important contributor to global food security and further genetic improvements are required to feed a growing human population. New functional genetics and genomics tools can help us understand the function of the different wheat genes and engineer beneficial changes. Results: In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, discovered 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more non-synonymous substitutions and 49% more truncation-mutations than in the original study. To show the biological value of the new promoter dataset, we selected two mutations in the VRN-A1 vernalization gene promoter within predicted transcription factor binding sites, and showed that both significantly altered VRN-A1 expression, and one mutation reduced the number of spikelets per spike. Conclusions: This publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where lack of regulations can accelerate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.