Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
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). Compara...
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| Veröffentlicht in: | Nature genetics 2023-03, Vol.55 (3), p.507-518 |
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| creator | Yan, Haidong Sun, Min Zhang, Zhongren Jin, Yarong Zhang, Ailing Lin, Chuang Wu, Bingchao He, Min Xu, Bin Wang, Jing Qin, Peng Mendieta, John Pablo Nie, Gang Wang, Jianping Jones, Chris S. Feng, Guangyan Srivastava, Rakesh K. Zhang, Xinquan Bombarely, Aureliano Luo, Dan Jin, Long Peng, Yuanying Wang, Xiaoshan Ji, Yang Tian, Shilin Huang, Linkai |
| description | 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.
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. |
| doi_str_mv | 10.1038/s41588-023-01302-4 |
| format | Article |
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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.</description><identifier>ISSN: 1061-4036</identifier><identifier>EISSN: 1546-1718</identifier><identifier>DOI: 10.1038/s41588-023-01302-4</identifier><identifier>PMID: 36864101</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>13/106 ; 13/109 ; 38 ; 38/44 ; 38/77 ; 38/91 ; 42 ; 45 ; 45/22 ; 45/23 ; 45/43 ; 631/208/212 ; 631/449/2491 ; Adaptation ; Adaptation, Physiological - genetics ; Agricultural production ; Agriculture ; Animal Genetics and Genomics ; Assembling ; Biomedical and Life Sciences ; Biomedicine ; Cancer Research ; Cereal crops ; Climate change ; Crops ; Domestication ; Endoplasmic reticulum ; Food ; Gene expression ; Gene Expression Profiling ; Gene Function ; Genes ; Genomes ; Genomics ; Heat ; Heat tolerance ; Human Genetics ; Millet ; Pennisetum - genetics ; Population studies ; Thermotolerance - genetics ; Transcription factors ; Transcriptomics</subject><ispartof>Nature genetics, 2023-03, Vol.55 (3), p.507-518</ispartof><rights>The Author(s) 2023</rights><rights>2023. The Author(s).</rights><rights>Copyright Nature Publishing Group Mar 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c475t-30c2ae70d4d56be2aaa03ec0d3de49b2b213d6d7048e804d0d9bc160199a019b3</citedby><cites>FETCH-LOGICAL-c475t-30c2ae70d4d56be2aaa03ec0d3de49b2b213d6d7048e804d0d9bc160199a019b3</cites><orcidid>0000-0001-7810-4852 ; 0000-0002-3304-3301 ; 0000-0001-5623-5974 ; 0000-0002-4996-7912 ; 0000-0002-0259-1508 ; 0000-0001-6257-8914 ; 0000-0002-3793-3264 ; 0000-0001-8958-1806 ; 0000-0001-7113-2973 ; 0000-0002-6055-4692 ; 0000-0002-9701-7583 ; 0000-0001-9096-9728 ; 0000-0002-1433-9510</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41588-023-01302-4$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41588-023-01302-4$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36864101$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yan, Haidong</creatorcontrib><creatorcontrib>Sun, Min</creatorcontrib><creatorcontrib>Zhang, Zhongren</creatorcontrib><creatorcontrib>Jin, Yarong</creatorcontrib><creatorcontrib>Zhang, Ailing</creatorcontrib><creatorcontrib>Lin, Chuang</creatorcontrib><creatorcontrib>Wu, Bingchao</creatorcontrib><creatorcontrib>He, Min</creatorcontrib><creatorcontrib>Xu, Bin</creatorcontrib><creatorcontrib>Wang, Jing</creatorcontrib><creatorcontrib>Qin, Peng</creatorcontrib><creatorcontrib>Mendieta, John Pablo</creatorcontrib><creatorcontrib>Nie, Gang</creatorcontrib><creatorcontrib>Wang, Jianping</creatorcontrib><creatorcontrib>Jones, Chris S.</creatorcontrib><creatorcontrib>Feng, Guangyan</creatorcontrib><creatorcontrib>Srivastava, Rakesh K.</creatorcontrib><creatorcontrib>Zhang, Xinquan</creatorcontrib><creatorcontrib>Bombarely, Aureliano</creatorcontrib><creatorcontrib>Luo, Dan</creatorcontrib><creatorcontrib>Jin, Long</creatorcontrib><creatorcontrib>Peng, Yuanying</creatorcontrib><creatorcontrib>Wang, Xiaoshan</creatorcontrib><creatorcontrib>Ji, Yang</creatorcontrib><creatorcontrib>Tian, Shilin</creatorcontrib><creatorcontrib>Huang, Linkai</creatorcontrib><title>Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet</title><title>Nature genetics</title><addtitle>Nat Genet</addtitle><addtitle>Nat Genet</addtitle><description>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.
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.</description><subject>13/106</subject><subject>13/109</subject><subject>38</subject><subject>38/44</subject><subject>38/77</subject><subject>38/91</subject><subject>42</subject><subject>45</subject><subject>45/22</subject><subject>45/23</subject><subject>45/43</subject><subject>631/208/212</subject><subject>631/449/2491</subject><subject>Adaptation</subject><subject>Adaptation, Physiological - genetics</subject><subject>Agricultural production</subject><subject>Agriculture</subject><subject>Animal Genetics and Genomics</subject><subject>Assembling</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cancer Research</subject><subject>Cereal crops</subject><subject>Climate 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Linkai</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet</atitle><jtitle>Nature genetics</jtitle><stitle>Nat Genet</stitle><addtitle>Nat Genet</addtitle><date>2023-03-01</date><risdate>2023</risdate><volume>55</volume><issue>3</issue><spage>507</spage><epage>518</epage><pages>507-518</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><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.
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.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>36864101</pmid><doi>10.1038/s41588-023-01302-4</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0001-7810-4852</orcidid><orcidid>https://orcid.org/0000-0002-3304-3301</orcidid><orcidid>https://orcid.org/0000-0001-5623-5974</orcidid><orcidid>https://orcid.org/0000-0002-4996-7912</orcidid><orcidid>https://orcid.org/0000-0002-0259-1508</orcidid><orcidid>https://orcid.org/0000-0001-6257-8914</orcidid><orcidid>https://orcid.org/0000-0002-3793-3264</orcidid><orcidid>https://orcid.org/0000-0001-8958-1806</orcidid><orcidid>https://orcid.org/0000-0001-7113-2973</orcidid><orcidid>https://orcid.org/0000-0002-6055-4692</orcidid><orcidid>https://orcid.org/0000-0002-9701-7583</orcidid><orcidid>https://orcid.org/0000-0001-9096-9728</orcidid><orcidid>https://orcid.org/0000-0002-1433-9510</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1061-4036 |
| ispartof | Nature genetics, 2023-03, Vol.55 (3), p.507-518 |
| issn | 1061-4036 1546-1718 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10011142 |
| source | MEDLINE; Nature Journals Online; SpringerLink Journals - AutoHoldings |
| subjects | 13/106 13/109 38 38/44 38/77 38/91 42 45 45/22 45/23 45/43 631/208/212 631/449/2491 Adaptation Adaptation, Physiological - genetics Agricultural production Agriculture Animal Genetics and Genomics Assembling Biomedical and Life Sciences Biomedicine Cancer Research Cereal crops Climate change Crops Domestication Endoplasmic reticulum Food Gene expression Gene Expression Profiling Gene Function Genes Genomes Genomics Heat Heat tolerance Human Genetics Millet Pennisetum - genetics Population studies Thermotolerance - genetics Transcription factors Transcriptomics |
| title | Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-05T12%3A53%3A43IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Pangenomic%20analysis%20identifies%20structural%20variation%20associated%20with%20heat%20tolerance%20in%20pearl%20millet&rft.jtitle=Nature%20genetics&rft.au=Yan,%20Haidong&rft.date=2023-03-01&rft.volume=55&rft.issue=3&rft.spage=507&rft.epage=518&rft.pages=507-518&rft.issn=1061-4036&rft.eissn=1546-1718&rft_id=info:doi/10.1038/s41588-023-01302-4&rft_dat=%3Cproquest_pubme%3E2783497112%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2787280102&rft_id=info:pmid/36864101&rfr_iscdi=true |