Pub Date : 2024-12-12DOI: 10.1038/s41477-024-01873-y
Xiangbo Zhang, Chaochen Tang, Bingzhi Jiang, Rong Zhang, Ming Li, Yaoyao Wu, Zhufang Yao, Lifei Huang, Zhongxia Luo, Hongda Zou, Yiling Yang, Minyi Wu, Ao Chen, Shan Wu, Xingliang Hou, Xu Liu, Zhangjun Fei, Junjie Fu, Zhangying Wang
Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices. Deep genome sequencing and comprehensive phenotyping of 294 hexaploid sweet potato accessions reveal the effect of allele dosage on phenotypic variation, offering valuable insights into the breeding history of sweet potato.
{"title":"Refining polyploid breeding in sweet potato through allele dosage enhancement","authors":"Xiangbo Zhang, Chaochen Tang, Bingzhi Jiang, Rong Zhang, Ming Li, Yaoyao Wu, Zhufang Yao, Lifei Huang, Zhongxia Luo, Hongda Zou, Yiling Yang, Minyi Wu, Ao Chen, Shan Wu, Xingliang Hou, Xu Liu, Zhangjun Fei, Junjie Fu, Zhangying Wang","doi":"10.1038/s41477-024-01873-y","DOIUrl":"10.1038/s41477-024-01873-y","url":null,"abstract":"Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices. Deep genome sequencing and comprehensive phenotyping of 294 hexaploid sweet potato accessions reveal the effect of allele dosage on phenotypic variation, offering valuable insights into the breeding history of sweet potato.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 1","pages":"36-48"},"PeriodicalIF":15.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809650","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}
Pub Date : 2024-12-12DOI: 10.1038/s41477-024-01854-1
Zhi-Cheng Hu, Mateusz Majda, Hao-Ran Sun, Yao Zhang, Yi-Ning Ding, Quan Yuan, Tong-Bing Su, Tian-Feng Lü, Feng Gao, Gui-Xia Xu, Richard S. Smith, Lars Østergaard, Yang Dong
In animals and plants, organ shape is primarily determined during primordium development by carefully coordinated growth and cell division1–3. Rare examples of post-primordial change in morphology (reshaping) exist that offer tractable systems for the study of mechanisms required for organ shape determination and diversification. One such example is morphogenesis in Capsella fruits whose heart-shaped appearance emerges by reshaping of the ovate spheroid gynoecium upon fertilization4. Here we use whole-organ live-cell imaging and single-cell RNA sequencing (scRNA-seq) analysis to show that Capsella fruit shape determination is based on dynamic changes in cell growth and cell division coupled with local maintenance of meristematic identity. At the molecular level, we reveal an auxin-induced mechanism that is required for morphological alteration and ultimately determined by a single cis-regulatory element. This element resides in the promoter of the Capsella rubella SHOOTMERISTEMLESS5 (CrSTM) gene. The CrSTM meristem identity factor positively regulates its own expression through binding to this element, thereby providing a feed-forward loop at the position and time of protrusion emergence to form the heart. Independent evolution of the STM-binding element in STM promoters across Brassicaceae species correlates with those undergoing a gynoecium-to-fruit shape change. Accordingly, genetic and phenotypic studies show that the STM-binding element is required to facilitate the shape transition and suggest a conserved molecular mechanism for organ morphogenesis. This study identifies a molecular mechanism promoting fruit shape variation. Local meristem identity is maintained through autoregulatory activation of the STM gene to allow post-fertilization changes in fruit morphology.
{"title":"Evolution of a SHOOTMERISTEMLESS transcription factor binding site promotes fruit shape determination","authors":"Zhi-Cheng Hu, Mateusz Majda, Hao-Ran Sun, Yao Zhang, Yi-Ning Ding, Quan Yuan, Tong-Bing Su, Tian-Feng Lü, Feng Gao, Gui-Xia Xu, Richard S. Smith, Lars Østergaard, Yang Dong","doi":"10.1038/s41477-024-01854-1","DOIUrl":"10.1038/s41477-024-01854-1","url":null,"abstract":"In animals and plants, organ shape is primarily determined during primordium development by carefully coordinated growth and cell division1–3. Rare examples of post-primordial change in morphology (reshaping) exist that offer tractable systems for the study of mechanisms required for organ shape determination and diversification. One such example is morphogenesis in Capsella fruits whose heart-shaped appearance emerges by reshaping of the ovate spheroid gynoecium upon fertilization4. Here we use whole-organ live-cell imaging and single-cell RNA sequencing (scRNA-seq) analysis to show that Capsella fruit shape determination is based on dynamic changes in cell growth and cell division coupled with local maintenance of meristematic identity. At the molecular level, we reveal an auxin-induced mechanism that is required for morphological alteration and ultimately determined by a single cis-regulatory element. This element resides in the promoter of the Capsella rubella SHOOTMERISTEMLESS5 (CrSTM) gene. The CrSTM meristem identity factor positively regulates its own expression through binding to this element, thereby providing a feed-forward loop at the position and time of protrusion emergence to form the heart. Independent evolution of the STM-binding element in STM promoters across Brassicaceae species correlates with those undergoing a gynoecium-to-fruit shape change. Accordingly, genetic and phenotypic studies show that the STM-binding element is required to facilitate the shape transition and suggest a conserved molecular mechanism for organ morphogenesis. This study identifies a molecular mechanism promoting fruit shape variation. Local meristem identity is maintained through autoregulatory activation of the STM gene to allow post-fertilization changes in fruit morphology.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 1","pages":"23-35"},"PeriodicalIF":15.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01854-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809838","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}
Pub Date : 2024-12-05DOI: 10.1038/s41477-024-01842-5
Yi-Qun Gao, Yu Su, Dai-Yin Chao
Plant roots serve as the primary interface between the plant and the soil, encountering numerous challenges ranging from water balance to nutrient uptake. One of the central mechanisms enabling plants to thrive in diverse ecosystems is the building of apoplastic diffusion barriers. These barriers control the flow of solutes into and out of the roots, maintaining water and nutrient homeostasis. In this Review, we summarize recent advances in understanding the establishment, function and ecological significance of root apoplastic diffusion barriers. We highlight the plasticity of apoplastic diffusion barriers under various abiotic stresses such as drought, salinity and nutrient deficiency. We also propose new frontiers by discussing the current bottlenecks in the study of plant apoplastic diffusion barriers. This Review summarizes recent progress in the understanding of plant apoplastic diffusion barriers, their formation and their function in an environmental context. Open questions and promising research directions in this field are addressed.
{"title":"Exploring the function of plant root diffusion barriers in sealing and shielding for environmental adaptation","authors":"Yi-Qun Gao, Yu Su, Dai-Yin Chao","doi":"10.1038/s41477-024-01842-5","DOIUrl":"10.1038/s41477-024-01842-5","url":null,"abstract":"Plant roots serve as the primary interface between the plant and the soil, encountering numerous challenges ranging from water balance to nutrient uptake. One of the central mechanisms enabling plants to thrive in diverse ecosystems is the building of apoplastic diffusion barriers. These barriers control the flow of solutes into and out of the roots, maintaining water and nutrient homeostasis. In this Review, we summarize recent advances in understanding the establishment, function and ecological significance of root apoplastic diffusion barriers. We highlight the plasticity of apoplastic diffusion barriers under various abiotic stresses such as drought, salinity and nutrient deficiency. We also propose new frontiers by discussing the current bottlenecks in the study of plant apoplastic diffusion barriers. This Review summarizes recent progress in the understanding of plant apoplastic diffusion barriers, their formation and their function in an environmental context. Open questions and promising research directions in this field are addressed.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 12","pages":"1865-1874"},"PeriodicalIF":15.8,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142777003","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}
Pub Date : 2024-12-03DOI: 10.1038/s41477-024-01856-z
Andreas Keppler, Michelle Roulier, Sebastian Pfeilmeier, Gabriella C. Petti, Anna Sintsova, Benjamin A. Maier, Miriam Bortfeld-Miller, Shinichi Sunagawa, Cyril Zipfel, Julia A. Vorholt
The ability of plants to perceive and react to biotic and abiotic stresses is critical for their health. We recently identified a core set of genes consistently induced by members of the leaf microbiota, termed general non-self response (GNSR) genes. Here we show that GNSR components conversely impact leaf microbiota composition. Specific strains that benefited from this altered assembly triggered strong plant responses, suggesting that the GNSR is a dynamic system that modulates colonization by certain strains. Examination of the GNSR to live and inactivated bacteria revealed that bacterial abundance, cellular composition and exposure time collectively determine the extent of the host response. We link the GNSR to pattern-triggered immunity, as diverse microbe- or danger-associated molecular patterns cause dynamic GNSR gene expression. Our findings suggest that the GNSR is the result of a dose-responsive perception and signalling system that feeds back to the leaf microbiota and contributes to the intricate balance of plant–microbiome interactions. The plant general non-self response system is triggered by leaf microbiota members and, in turn, impacts their colonization.
{"title":"Plant microbiota feedbacks through dose-responsive expression of general non-self response genes","authors":"Andreas Keppler, Michelle Roulier, Sebastian Pfeilmeier, Gabriella C. Petti, Anna Sintsova, Benjamin A. Maier, Miriam Bortfeld-Miller, Shinichi Sunagawa, Cyril Zipfel, Julia A. Vorholt","doi":"10.1038/s41477-024-01856-z","DOIUrl":"10.1038/s41477-024-01856-z","url":null,"abstract":"The ability of plants to perceive and react to biotic and abiotic stresses is critical for their health. We recently identified a core set of genes consistently induced by members of the leaf microbiota, termed general non-self response (GNSR) genes. Here we show that GNSR components conversely impact leaf microbiota composition. Specific strains that benefited from this altered assembly triggered strong plant responses, suggesting that the GNSR is a dynamic system that modulates colonization by certain strains. Examination of the GNSR to live and inactivated bacteria revealed that bacterial abundance, cellular composition and exposure time collectively determine the extent of the host response. We link the GNSR to pattern-triggered immunity, as diverse microbe- or danger-associated molecular patterns cause dynamic GNSR gene expression. Our findings suggest that the GNSR is the result of a dose-responsive perception and signalling system that feeds back to the leaf microbiota and contributes to the intricate balance of plant–microbiome interactions. The plant general non-self response system is triggered by leaf microbiota members and, in turn, impacts their colonization.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 1","pages":"74-89"},"PeriodicalIF":15.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01856-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760709","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}
Avena sterilis, the ancestral species of cultivated oats, is a valuable genetic resource for oat improvement. Here we generated a near-complete 10.99 Gb A. sterilis genome and a high-quality 10.89 Gb cultivated oat genome. Genome evolution analysis revealed the centromeres dynamic and structural variations landscape associated with domestication between wild and cultivated oats. Population genetic analysis of 117 wild and cultivated oat accessions worldwide detected many candidate genes associated with important agronomic traits for oat domestication and improvement. Remarkably, a large fragment duplication from chromosomes 4A to 4D harbouring many agronomically important genes was detected during oat domestication and was fixed in almost all cultivated oats from around the world. The genes in the duplication region from 4A showed significantly higher expression levels and lower methylation levels than the orthologous genes located on 4D in A. sterilis. This study provides valuable resources for evolutionary and functional genomics and genetic improvement of oat. The near-complete genome of hexaploid wild oat, along with 117 global wild and cultivated accessions, reveals genome divergence between wild and cultivated oats and a large fragment duplication event from chromosomes 4A to 4D during oat domestication.
{"title":"The near-complete genome assembly of hexaploid wild oat reveals its genome evolution and divergence with cultivated oats","authors":"Qiang He, Wei Li, Yuqing Miao, Yu Wang, Ningkun Liu, Jianan Liu, Tao Li, Yao Xiao, Hongyu Zhang, Yaru Wang, Hanfei Liang, Yange Yun, Shuhui Wang, Qingbin Sun, Hongru Wang, Zhizhong Gong, Huilong Du","doi":"10.1038/s41477-024-01866-x","DOIUrl":"10.1038/s41477-024-01866-x","url":null,"abstract":"Avena sterilis, the ancestral species of cultivated oats, is a valuable genetic resource for oat improvement. Here we generated a near-complete 10.99 Gb A. sterilis genome and a high-quality 10.89 Gb cultivated oat genome. Genome evolution analysis revealed the centromeres dynamic and structural variations landscape associated with domestication between wild and cultivated oats. Population genetic analysis of 117 wild and cultivated oat accessions worldwide detected many candidate genes associated with important agronomic traits for oat domestication and improvement. Remarkably, a large fragment duplication from chromosomes 4A to 4D harbouring many agronomically important genes was detected during oat domestication and was fixed in almost all cultivated oats from around the world. The genes in the duplication region from 4A showed significantly higher expression levels and lower methylation levels than the orthologous genes located on 4D in A. sterilis. This study provides valuable resources for evolutionary and functional genomics and genetic improvement of oat. The near-complete genome of hexaploid wild oat, along with 117 global wild and cultivated accessions, reveals genome divergence between wild and cultivated oats and a large fragment duplication event from chromosomes 4A to 4D during oat domestication.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 12","pages":"2062-2078"},"PeriodicalIF":15.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142760710","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}
Pub Date : 2024-12-02DOI: 10.1038/s41477-024-01864-z
Concepcion Manzano, Kevin W. Morimoto, Lidor Shaar-Moshe, G. Alex Mason, Alex Cantó-Pastor, Mona Gouran, Damien De Bellis, Robertas Ursache, Kaisa Kajala, Neelima Sinha, Julia Bailey-Serres, Niko Geldner, J. Carlos del Pozo, Siobhan M. Brady
Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli. In tomato roots, the exodermis forms a genetically distinct polar lignin cap (PLC) barrier from the Casparian strip. SlSCZ and SlEXO1 repress PLC deposition in inner layers. The PLC cannot fully compensate for the CS as a mineral ion barrier.
{"title":"Regulation and function of a polarly localized lignin barrier in the exodermis","authors":"Concepcion Manzano, Kevin W. Morimoto, Lidor Shaar-Moshe, G. Alex Mason, Alex Cantó-Pastor, Mona Gouran, Damien De Bellis, Robertas Ursache, Kaisa Kajala, Neelima Sinha, Julia Bailey-Serres, Niko Geldner, J. Carlos del Pozo, Siobhan M. Brady","doi":"10.1038/s41477-024-01864-z","DOIUrl":"10.1038/s41477-024-01864-z","url":null,"abstract":"Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli. In tomato roots, the exodermis forms a genetically distinct polar lignin cap (PLC) barrier from the Casparian strip. SlSCZ and SlEXO1 repress PLC deposition in inner layers. The PLC cannot fully compensate for the CS as a mineral ion barrier.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 1","pages":"118-130"},"PeriodicalIF":15.8,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01864-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758278","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}
Pub Date : 2024-11-29DOI: 10.1038/s41477-024-01867-w
Jeffrey E. Herrick, Cary Fowler, Lindiwe Majele Sibanda, Rattan Lal, Anna M. Nelson
The Vision for Adapted Crops and Soils (VACS) is a global movement, launched in 2023, to improve human nutrition in the face of a changing climate and degraded lands. VACS emphasizes an integrated approach to investments in crops and soils, concentrating on the potential of traditional and indigenous ‘opportunity crops’. VACS also addresses priorities, including climate change and drought, biodiversity, soil fertility, gender equality and women’s empowerment, water, sanitation and health.
{"title":"The vision for adapted crops and soils: how to prioritize investments to achieve sustainable nutrition for all","authors":"Jeffrey E. Herrick, Cary Fowler, Lindiwe Majele Sibanda, Rattan Lal, Anna M. Nelson","doi":"10.1038/s41477-024-01867-w","DOIUrl":"10.1038/s41477-024-01867-w","url":null,"abstract":"The Vision for Adapted Crops and Soils (VACS) is a global movement, launched in 2023, to improve human nutrition in the face of a changing climate and degraded lands. VACS emphasizes an integrated approach to investments in crops and soils, concentrating on the potential of traditional and indigenous ‘opportunity crops’. VACS also addresses priorities, including climate change and drought, biodiversity, soil fertility, gender equality and women’s empowerment, water, sanitation and health.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 12","pages":"1840-1846"},"PeriodicalIF":15.8,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142753752","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}
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