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

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dc.contributor.authorYan, Haidongen
dc.contributor.authorSun, Minen
dc.contributor.authorZhang, Zhongrenen
dc.contributor.authorJin, Yarongen
dc.contributor.authorZhang, Ailingen
dc.contributor.authorLin, Chuangen
dc.contributor.authorWu, Bingchaoen
dc.contributor.authorHe, Minen
dc.contributor.authorXu, Binen
dc.contributor.authorWang, Jingen
dc.contributor.authorQin, Pengen
dc.contributor.authorMendieta, John Pabloen
dc.contributor.authorNie, Gangen
dc.contributor.authorWang, Jianpingen
dc.contributor.authorJones, Chris S. S.en
dc.contributor.authorFeng, Guangyanen
dc.contributor.authorSrivastava, Rakesh K. K.en
dc.contributor.authorZhang, Xinquanen
dc.contributor.authorBombarely, Aurelianoen
dc.contributor.authorLuo, Danen
dc.contributor.authorJin, Longen
dc.contributor.authorPeng, Yuanyingen
dc.contributor.authorWang, Xiaoshanen
dc.contributor.authorJi, Yangen
dc.contributor.authorTian, Shilinen
dc.contributor.authorHuang, Linkaien
dc.date.accessioned2023-10-17T12:54:20Zen
dc.date.available2023-10-17T12:54:20Zen
dc.date.issued2023-03en
dc.description.abstractPearl 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. A graph-based pan-genome constructed using de novo genome assemblies of ten pearl millet accessions adapted to different climates worldwide identifies structural variations and their contribution to heat tolerance in pearl millet.en
dc.description.notesThis 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.en
dc.description.sponsorshipModern Agricultural Industry System Sichuan Forage Innovation Team [CARS-34]; Sichuan Province Research Grant [SCCXTD-20201-16]; National Natural Science Foundation of China [2021YFYZ0013]en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41588-023-01302-4en
dc.identifier.eissn1546-1718en
dc.identifier.issn1061-4036en
dc.identifier.pmid36864101en
dc.identifier.urihttp://hdl.handle.net/10919/116489en
dc.language.isoenen
dc.publisherNature Portfolioen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectpennisetum-glaucum l.en
dc.subjectreference genomeen
dc.subjectendoplasmic-reticulumen
dc.subjecttranscription factorsen
dc.subjectexpressed genesen
dc.subjectweb serveren
dc.subjectsequenceen
dc.subjectstressen
dc.subjectpredictionen
dc.subjectresponsesen
dc.titlePangenomic analysis identifies structural variation associated with heat tolerance in pearl milleten
dc.title.serialNature Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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