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. 2023 Mar 2;55(3):507–518. doi: 10.1038/s41588-023-01302-4

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — After heat stress (H) for 21 d, only a small proportion of leaves exhibited wilting relative to the control (CK) group; leaves showed physiological changes (MDA) for up to 21 d, suggesting that pearl millet exhibits strong heat resistance. Significant differences were tested using a two-tailed t-test (**P < 0.01). We leveraged multi-omics analyses to reveal a possible mechanism of heat tolerance in the ER transport system: (1) compared with maize and rice, pearl millet showed a higher proportion of ER-related genes that were differentially expressed, indicating a quicker response to heat stress in this system; (2) this heat stress led to the production of misfolded proteins that could be recognized and degraded via the cooperation of ER-related proteins such as CRT, CNX, BiP, NEF, PDA6 and HSP. HSF genes might be involved in the heat response because their expression is upregulated and they can coregulate HSP genes^45,46. SVs surrounding 11 ER-related genes probably contributed to this response. For instance, one SV was associated with the expression of an ER-related gene, HSP70, which plays a role in the degradation of misfolded proteins. Additionally, 27 genes enriched in the ER system were located in regions with differentiated SV distributions between two populations in temperate and tropical zones; (3) furthermore, an RWP-RK gene (PMF0G00024.1) from an expanded transcription factor family was confirmed as a positive regulator involved in heat resistance and was coregulated by ER-related and HSF genes. We finally used dual luciferase assays to confirm that this PMF0G00024.1 gene could transactivate genes encoding ER-related BiP (PMA2G00107.1) and OST (PMA4G03758.1).