Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry
SUMMARY Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of P...
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| Veröffentlicht in: | The Plant journal : for cell and molecular biology 2023-05, Vol.114 (3), p.519-533 |
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| container_title | The Plant journal : for cell and molecular biology |
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| creator | Nie, Chaoren Zhang, Yingjie Zhang, Xiaoqin Xia, Wensheng Sun, Hongbing Zhang, Sisi Li, Na Ding, Zhaoquan Lv, Yingmin Wang, Nian |
| description | SUMMARY
Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.
Significance Statement
Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry. |
| doi_str_mv | 10.1111/tpj.16151 |
| format | Article |
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Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.
Significance Statement
Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry.</description><identifier>ISSN: 0960-7412</identifier><identifier>EISSN: 1365-313X</identifier><identifier>DOI: 10.1111/tpj.16151</identifier><identifier>PMID: 36786729</identifier><language>eng</language><publisher>England: Blackwell Publishing Ltd</publisher><subject>Chromosomes ; Color ; Cultivars ; Evolution ; flower colour variations ; Flowering ; flowering cherry ; Flowers ; Flowers - genetics ; Fruits ; Gene mapping ; Genome-Wide Association Study ; Genomes ; genome‐wide association study (GWAS) ; Genomics ; Germplasm ; high‐quality genome ; Mountains ; Origins ; origins of flowering cherry ; Phylogeny ; Prunus avium - genetics ; Prunus cerasus ; Quantitative trait loci ; subgenus Cerasus</subject><ispartof>The Plant journal : for cell and molecular biology, 2023-05, Vol.114 (3), p.519-533</ispartof><rights>2023 Society for Experimental Biology and John Wiley & Sons Ltd.</rights><rights>Copyright © 2023 Society for Experimental Biology and John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3531-fec912740849daabb1205063802b52e4204f03e23139b7f6b032deb8cee05ca03</citedby><cites>FETCH-LOGICAL-c3531-fec912740849daabb1205063802b52e4204f03e23139b7f6b032deb8cee05ca03</cites><orcidid>0000-0002-4631-3841 ; 0000-0001-9185-4199</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Ftpj.16151$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Ftpj.16151$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,1433,27924,27925,45574,45575,46409,46833</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36786729$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nie, Chaoren</creatorcontrib><creatorcontrib>Zhang, Yingjie</creatorcontrib><creatorcontrib>Zhang, Xiaoqin</creatorcontrib><creatorcontrib>Xia, Wensheng</creatorcontrib><creatorcontrib>Sun, Hongbing</creatorcontrib><creatorcontrib>Zhang, Sisi</creatorcontrib><creatorcontrib>Li, Na</creatorcontrib><creatorcontrib>Ding, Zhaoquan</creatorcontrib><creatorcontrib>Lv, Yingmin</creatorcontrib><creatorcontrib>Wang, Nian</creatorcontrib><title>Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry</title><title>The Plant journal : for cell and molecular biology</title><addtitle>Plant J</addtitle><description>SUMMARY
Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.
Significance Statement
Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry.</description><subject>Chromosomes</subject><subject>Color</subject><subject>Cultivars</subject><subject>Evolution</subject><subject>flower colour variations</subject><subject>Flowering</subject><subject>flowering cherry</subject><subject>Flowers</subject><subject>Flowers - genetics</subject><subject>Fruits</subject><subject>Gene mapping</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>genome‐wide association study (GWAS)</subject><subject>Genomics</subject><subject>Germplasm</subject><subject>high‐quality genome</subject><subject>Mountains</subject><subject>Origins</subject><subject>origins of flowering cherry</subject><subject>Phylogeny</subject><subject>Prunus avium - genetics</subject><subject>Prunus cerasus</subject><subject>Quantitative trait loci</subject><subject>subgenus Cerasus</subject><issn>0960-7412</issn><issn>1365-313X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kc1q3DAUhUVIaCbTLvoCRZBNA3GiH1u2lyW0aUKgXaTQnZHl6xkNsjSV7Bm86yP0LfJeeZJqxpMsChUCXTifDvfeg9B7Sq5oPNf9enVFBc3oEZpRLrKEU_7zGM1IKUiSp5SdorMQVoTQnIv0DTrlIi9EzsoZeroF6zrAMgToajNeYg8Bfg1glbYLLG2DF3vi-fefrW72oFNa9trZqEozBgh47d1mJ1q3AYO1DXqx7EMseof7JWDn9ULbSwwbZ4bD1wa3xm3BY-WMGzzeSD_ZBuzag7ZrQS3B-_EtOmmlCfDu8M7Rjy-fH2--Jg_fbu9uPj0kimecJi2okrI8JUVaNlLWNWUkI4IXhNUZg5SRtCUcWFxQWeetqAlnDdSFAiCZkoTP0cfJN44UtxD6qtNBgTHSghtCxfJcZLRIo8Ecnf-DruIccSWRKkjsIePxztHFRCnvQvDQVmuvO-nHipJql14V06v26UX2w8FxqDtoXsmXuCJwPQFbbWD8v1P1-P1-svwLJvyogA</recordid><startdate>202305</startdate><enddate>202305</enddate><creator>Nie, Chaoren</creator><creator>Zhang, Yingjie</creator><creator>Zhang, Xiaoqin</creator><creator>Xia, Wensheng</creator><creator>Sun, Hongbing</creator><creator>Zhang, Sisi</creator><creator>Li, Na</creator><creator>Ding, Zhaoquan</creator><creator>Lv, Yingmin</creator><creator>Wang, Nian</creator><general>Blackwell Publishing Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4631-3841</orcidid><orcidid>https://orcid.org/0000-0001-9185-4199</orcidid></search><sort><creationdate>202305</creationdate><title>Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry</title><author>Nie, Chaoren ; Zhang, Yingjie ; Zhang, Xiaoqin ; Xia, Wensheng ; Sun, Hongbing ; Zhang, Sisi ; Li, Na ; Ding, Zhaoquan ; Lv, Yingmin ; Wang, Nian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3531-fec912740849daabb1205063802b52e4204f03e23139b7f6b032deb8cee05ca03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Chromosomes</topic><topic>Color</topic><topic>Cultivars</topic><topic>Evolution</topic><topic>flower colour variations</topic><topic>Flowering</topic><topic>flowering cherry</topic><topic>Flowers</topic><topic>Flowers - genetics</topic><topic>Fruits</topic><topic>Gene mapping</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>genome‐wide association study (GWAS)</topic><topic>Genomics</topic><topic>Germplasm</topic><topic>high‐quality genome</topic><topic>Mountains</topic><topic>Origins</topic><topic>origins of flowering cherry</topic><topic>Phylogeny</topic><topic>Prunus avium - genetics</topic><topic>Prunus cerasus</topic><topic>Quantitative trait loci</topic><topic>subgenus Cerasus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nie, Chaoren</creatorcontrib><creatorcontrib>Zhang, Yingjie</creatorcontrib><creatorcontrib>Zhang, Xiaoqin</creatorcontrib><creatorcontrib>Xia, Wensheng</creatorcontrib><creatorcontrib>Sun, Hongbing</creatorcontrib><creatorcontrib>Zhang, Sisi</creatorcontrib><creatorcontrib>Li, Na</creatorcontrib><creatorcontrib>Ding, Zhaoquan</creatorcontrib><creatorcontrib>Lv, Yingmin</creatorcontrib><creatorcontrib>Wang, Nian</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The Plant journal : for cell and molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nie, Chaoren</au><au>Zhang, Yingjie</au><au>Zhang, Xiaoqin</au><au>Xia, Wensheng</au><au>Sun, Hongbing</au><au>Zhang, Sisi</au><au>Li, Na</au><au>Ding, Zhaoquan</au><au>Lv, Yingmin</au><au>Wang, Nian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry</atitle><jtitle>The Plant journal : for cell and molecular biology</jtitle><addtitle>Plant J</addtitle><date>2023-05</date><risdate>2023</risdate><volume>114</volume><issue>3</issue><spage>519</spage><epage>533</epage><pages>519-533</pages><issn>0960-7412</issn><eissn>1365-313X</eissn><abstract>SUMMARY
Flowering cherry is a very popular species around the world. High‐quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high‐quality chromosome‐scale genome of Prunus campanulata ‘Plena’ (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high‐quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome‐wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.
Significance Statement
Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry.</abstract><cop>England</cop><pub>Blackwell Publishing Ltd</pub><pmid>36786729</pmid><doi>10.1111/tpj.16151</doi><tpages>533</tpages><orcidid>https://orcid.org/0000-0002-4631-3841</orcidid><orcidid>https://orcid.org/0000-0001-9185-4199</orcidid></addata></record> |
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| subjects | Chromosomes Color Cultivars Evolution flower colour variations Flowering flowering cherry Flowers Flowers - genetics Fruits Gene mapping Genome-Wide Association Study Genomes genome‐wide association study (GWAS) Genomics Germplasm high‐quality genome Mountains Origins origins of flowering cherry Phylogeny Prunus avium - genetics Prunus cerasus Quantitative trait loci subgenus Cerasus |
| title | Genome assembly, resequencing and genome‐wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry |
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