Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
作者：Haidong Yan1,4,8+, Min Sun1+, Zhongren Zhang3+, Yarong Jin1+, Ailing Zhang1, Chuang Lin1, Bingchao Wu1, Min He2, Bin Xu5, Jing Wang6, Peng Qin7, John Pablo Mendieta8, Gang Nie1, Jianping Wang9, Chris S. Jones10, Guangyan Feng1, Rakesh K Srivastava11, Xinquan Zhang1, Aureliano Bombarely12, Dan Luo1, Long Jin13, Yuanying Peng14, XiaoShan Wang1, Yang Ji15, Shilin Tian3,16*, Linkai Huang1,2*
Abstract：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.