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

Autor: Yan H; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.; School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.; Department of Genetics, University of Georgia, Athens, GA, USA., Sun M; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Zhang Z; Novogene Bioinformatics Institute, Beijing, China., Jin Y; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Zhang A; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Lin C; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Wu B; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., He M; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China., Xu B; College of Grassland Science, Nanjing Agricultural University, Nanjing, China., Wang J; Key Laboratory of Bio-Source and Environmental Conservation, School of Life Science, Sichuan University, Chengdu, China., Qin P; Rice Research Institute, Sichuan Agricultural University, Chengdu, China., Mendieta JP; Department of Genetics, University of Georgia, Athens, GA, USA., Nie G; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Wang J; Agronomy Department, University of Florida, Gainesville, FL, USA., Jones CS; Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya., Feng G; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Srivastava RK; International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India., Zhang X; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Bombarely A; Instituto de Biologia Molecular y Celular de Plantas, UPV-CSIC, Valencia, Spain., Luo D; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Jin L; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China., Peng Y; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China., Wang X; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China., Ji Y; Sichuan Animal Science Academy, Chengdu, China., Tian S; Novogene Bioinformatics Institute, Beijing, China. tianshilin@novogene.com.; Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China. tianshilin@novogene.com., Huang L; College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China. huanglinkai@sicau.edu.cn.; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China. huanglinkai@sicau.edu.cn.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2023 Mar; Vol. 55 (3), pp. 507-518. Date of Electronic Publication: 2023 Mar 02.
DOI: 10.1038/s41588-023-01302-4
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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