College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.
Nat Genet. 2023 Mar;55(3):507-518. doi: 10.1038/s41588-023-01302-4. Epub 2023 Mar 2.
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.
珍珠粟是一种重要的世界性谷类作物，具有较强的耐热性。在这里，我们通过组装十个染色体基因组并结合一个适应不同气候的现有基因组，开发了基于图的泛基因组，捕获了 424085 个基因组结构变异（SVs）。比较基因组学和转录组学分析揭示了 RWP-RK 转录因子家族的扩张以及内质网（ER）相关基因在耐热性中的参与。一个 RWP-RK 基因的过表达导致植物耐热性增强，并且快速反式激活 ER 相关基因，支持 RWP-RK 转录因子和 ER 系统在耐热性中的重要作用。此外，我们发现一些 SVs 影响与耐热性相关的基因表达，并且 ER 相关基因周围的 SVs 在群体驯化过程中塑造了对耐热性的适应。我们的研究提供了一个全面的基因组资源，揭示了耐热性的机制，并为在气候变化下培育更健壮的作物奠定了基础。
