Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.
{"title":"Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation.","authors":"Wei Tong, Yanli Wang, Fangdong Li, Fei Zhai, Jingjing Su, Didi Wu, Lianghui Yi, Qijuan Gao, Qiong Wu, Enhua Xia","doi":"10.1111/jipb.13737","DOIUrl":"https://doi.org/10.1111/jipb.13737","url":null,"abstract":"<p><p>Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaolian Wang, Yanfang Yuan, Laurence Charrier, Zhaoguo Deng, Markus Geisler, Xing Wang Deng, Haodong Chen
Light and gravity coordinately regulate the directional growth of plants. Arabidopsis Gravitropic in the Light 1 (GIL1) inhibits the negative gravitropism of hypocotyls in red and far-red light, but the underlying molecular mechanisms remain elusive. Our study found that GIL1 is a plasma membrane-localized protein. In endodermal cells of the upper part of hypocotyls, GIL1 controls the negative gravitropism of hypocotyls. GIL1 directly interacts with PIN3 and inhibits the auxin transport activity of PIN3. Mutation of PIN3 suppresses the abnormal gravitropic response of gil1 mutant. The GIL1 protein is unstable in darkness but it is stabilized by red and far-red light. Together, our data suggest that light-stabilized GIL1 inhibits the negative gravitropism of hypocotyls by suppressing the activity of the auxin transporter PIN3, thereby enhancing the emergence of young seedlings from the soil.
{"title":"Light-stabilized GIL1 suppresses PIN3 activity to inhibit hypocotyl gravitropism","authors":"Xiaolian Wang, Yanfang Yuan, Laurence Charrier, Zhaoguo Deng, Markus Geisler, Xing Wang Deng, Haodong Chen","doi":"10.1111/jipb.13736","DOIUrl":"10.1111/jipb.13736","url":null,"abstract":"<p>Light and gravity coordinately regulate the directional growth of plants. Arabidopsis Gravitropic in the Light 1 (GIL1) inhibits the negative gravitropism of hypocotyls in red and far-red light, but the underlying molecular mechanisms remain elusive. Our study found that GIL1 is a plasma membrane-localized protein. In endodermal cells of the upper part of hypocotyls, GIL1 controls the negative gravitropism of hypocotyls. GIL1 directly interacts with PIN3 and inhibits the auxin transport activity of PIN3. Mutation of <i>PIN3</i> suppresses the abnormal gravitropic response of <i>gil1</i> mutant. The GIL1 protein is unstable in darkness but it is stabilized by red and far-red light. Together, our data suggest that light-stabilized GIL1 inhibits the negative gravitropism of hypocotyls by suppressing the activity of the auxin transporter PIN3, thereby enhancing the emergence of young seedlings from the soil.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13736","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141578385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Prime editing is a versatile CRISPR/Cas-based precise genome-editing technique for crop breeding. Four new types of prime editors (PEs) named PE6a–d were recently generated using evolved and engineered reverse transcriptase (RT) variants from three different sources. In this study, we tested the editing efficiencies of four PE6 variants and two additional PE6 constructs with double-RT modules in transgenic rice (Oryza sativa) plants. PE6c, with an evolved and engineered RT variant from the yeast Tf1 retrotransposon, yielded the highest prime-editing efficiency. The average fold change in the editing efficiency of PE6c compared with PEmax exceeded 3.5 across 18 agronomically important target sites from 15 genes. We also demonstrated the feasibility of using two RT modules to improve prime-editing efficiency. Our results suggest that PE6c or its derivatives would be an excellent choice for prime editing in monocot plants. In addition, our findings have laid a foundation for prime-editing-based breeding of rice varieties with enhanced agronomically important traits.
{"title":"PE6c greatly enhances prime editing in transgenic rice plants","authors":"Zhenghong Cao, Wei Sun, Dexin Qiao, Junya Wang, Siyun Li, Xiaohan Liu, Cuiping Xin, Yu Lu, Syeda Leeda Gul, Xue-Chen Wang, Qi-Jun Chen","doi":"10.1111/jipb.13738","DOIUrl":"10.1111/jipb.13738","url":null,"abstract":"<p>Prime editing is a versatile CRISPR/Cas-based precise genome-editing technique for crop breeding. Four new types of prime editors (PEs) named PE6a–d were recently generated using evolved and engineered reverse transcriptase (RT) variants from three different sources. In this study, we tested the editing efficiencies of four PE6 variants and two additional PE6 constructs with double-RT modules in transgenic rice (<i>Oryza sativa</i>) plants. PE6c, with an evolved and engineered RT variant from the yeast Tf1 retrotransposon, yielded the highest prime-editing efficiency. The average fold change in the editing efficiency of PE6c compared with PEmax exceeded 3.5 across 18 agronomically important target sites from 15 genes. We also demonstrated the feasibility of using two RT modules to improve prime-editing efficiency. Our results suggest that PE6c or its derivatives would be an excellent choice for prime editing in monocot plants. In addition, our findings have laid a foundation for prime-editing-based breeding of rice varieties with enhanced agronomically important traits.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13738","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141557655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Weizhi He, Hang Liu, Zhangkuanyu Wu, Qing Miao, Xinyi Hu, Xin Yan, Hangyu Wen, Yaojie Zhang, Xueqing Fu, Li Ren, Kexuan Tang, Ling Li
The sesquiterpene lactone artemisinin is an important anti-malarial component produced by the glandular secretory trichomes of sweet wormwood (Artemisia annua L.). Light was previously shown to promote artemisinin production, but the underlying regulatory mechanism remains elusive. In this study, we demonstrate that ELONGATED HYPOCOTYL 5 (HY5), a central transcription factor in the light signaling pathway, cannot promote artemisinin biosynthesis on its own, as the binding of AaHY5 to the promoters of artemisinin biosynthetic genes failed to activate their transcription. Transcriptome analysis and yeast two-hybrid screening revealed the B-box transcription factor AaBBX21 as a potential interactor with AaHY5. AaBBX21 showed a trichome-specific expression pattern. Additionally, the AaBBX21–AaHY5 complex cooperatively activated transcription from the promoters of the downstream genes AaGSW1, AaMYB108, and AaORA, encoding positive regulators of artemisinin biosynthesis. Moreover, AaHY5 and AaBBX21 physically interacted with the A. annua E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). In the dark, AaCOP1 decreased the accumulation of AaHY5 and AaBBX21 and repressed the activation of genes downstream of the AaHY5–AaBBX21 complex, explaining the enhanced production of artemisinin upon light exposure. Our study provides insights into the central regulatory mechanism by which light governs terpenoid biosynthesis in the plant kingdom.
{"title":"The AaBBX21–AaHY5 module mediates light-regulated artemisinin biosynthesis in Artemisia annua L.","authors":"Weizhi He, Hang Liu, Zhangkuanyu Wu, Qing Miao, Xinyi Hu, Xin Yan, Hangyu Wen, Yaojie Zhang, Xueqing Fu, Li Ren, Kexuan Tang, Ling Li","doi":"10.1111/jipb.13708","DOIUrl":"10.1111/jipb.13708","url":null,"abstract":"<p>The sesquiterpene lactone artemisinin is an important anti-malarial component produced by the glandular secretory trichomes of sweet wormwood (<i>Artemisia annua</i> L.). Light was previously shown to promote artemisinin production, but the underlying regulatory mechanism remains elusive. In this study, we demonstrate that ELONGATED HYPOCOTYL 5 (HY5), a central transcription factor in the light signaling pathway, cannot promote artemisinin biosynthesis on its own, as the binding of AaHY5 to the promoters of artemisinin biosynthetic genes failed to activate their transcription. Transcriptome analysis and yeast two-hybrid screening revealed the B-box transcription factor AaBBX21 as a potential interactor with AaHY5. <i>AaBBX21</i> showed a trichome-specific expression pattern. Additionally, the AaBBX21–AaHY5 complex cooperatively activated transcription from the promoters of the downstream genes <i>AaGSW1</i>, <i>AaMYB108</i>, and <i>AaORA</i>, encoding positive regulators of artemisinin biosynthesis. Moreover, AaHY5 and AaBBX21 physically interacted with the <i>A. annua</i> E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). In the dark, AaCOP1 decreased the accumulation of AaHY5 and AaBBX21 and repressed the activation of genes downstream of the AaHY5–AaBBX21 complex, explaining the enhanced production of artemisinin upon light exposure. Our study provides insights into the central regulatory mechanism by which light governs terpenoid biosynthesis in the plant kingdom.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13708","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141557656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}