Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet

Yan, H and Sun, M and Zhang, Z and Jin, Y and Zhang, A and Lin, C and Wu, B and He, M and Xu, B and Wang, J and Qin, P and Mendieta, J P and Nie, G and Wang, J and Jones, C S and Feng, G and Srivastava, R K and Zhang, X and Bombarely, A and Luo, D and Jin, L and Peng, Y and Wang, X and Ji, Y and Tian, S and Huang, L (2023) Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nature Genetics, 55. pp. 507-518. ISSN 1546-1718

[img] PDF - Published Version
Available under License ["licenses_description_cc_attribution" not defined].

Download (21MB)


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.

Item Type: Article
Divisions: Global Research Program - Accelerated Crop Improvement
Uncontrolled Keywords: Genomics, Plant genetics
Subjects: Others > Plant Genetics
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 09 Nov 2023 04:36
Last Modified: 09 Nov 2023 04:36
Official URL:
Acknowledgement: This work was supported by the earmarked fund for CARS (CARS-34 to L.H.), the Modern Agricultural Industry System Sichuan Forage Innovation Team (no. SCCXTD-20201-16 to L.H.), the Sichuan Province Research Grant (no. 2021YFYZ0013 to L.H.) and the National Natural Science Foundation of China (nos. 31771866 and 32071867 to L.H.). We thank X. Chen (State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University), R. J. Schmitz (Department of Genetics, University of Georgia) and Q. Tang (College of Animal Science and Technology, Sichuan Agricultural University) for providing valuable suggestions on early versions of the manuscript. We thank G. Vellidis (The Georgia Coastal Plain Experiment Station) for providing some material resources.
View Statistics

Actions (login required)

View Item View Item