Pub Date : 2024-09-19DOI: 10.1101/2024.09.16.613234
Lea Jacquier, Celeste Fiorenza, Kevin Robe, Jian-Pu Han, Fabienne Cleard, Christelle Fuchs, Priya Ramakrishna, Sylvain Loubery, Linnka Lefebvre-Legendre, Marie Barberon
Cell-to-cell communication is critical for multicellular organisms. In plants, plasmodesmata - cytoplasmic channels - enable molecular transport between adjacent cells. In roots, this transport is predicted to be essential in nutrient acquisition and delivery to the vasculature. We demonstrate that plasmodesmatal transport persists in differentiated roots, despite apoplastic barriers such as Casparian strips and suberin lamellae in the endodermis, suggesting plasmodesmata as the sole pathway for water and nutrient flow at this stage. We also reveal a developmental switch in plasmodesmata function resulting in an unidirectional transport in differentiated roots. A genetic screen identified mutations that disrupt this directionality, leading to bidirectional transport. These mutations correlate with larger plasmodesmatal apertures, linked to defects in pectin composition and cell wall organization. This discovery underscores the role of plasmodesmatal aperture regulation and pectin in controlling directional transport. Our findings provide insights into plasmodesmata function and their regulation in roots.
{"title":"Directional Cell-to-cell Transport in Plant Roots","authors":"Lea Jacquier, Celeste Fiorenza, Kevin Robe, Jian-Pu Han, Fabienne Cleard, Christelle Fuchs, Priya Ramakrishna, Sylvain Loubery, Linnka Lefebvre-Legendre, Marie Barberon","doi":"10.1101/2024.09.16.613234","DOIUrl":"https://doi.org/10.1101/2024.09.16.613234","url":null,"abstract":"Cell-to-cell communication is critical for multicellular organisms. In plants, plasmodesmata - cytoplasmic channels - enable molecular transport between adjacent cells. In roots, this transport is predicted to be essential in nutrient acquisition and delivery to the vasculature. We demonstrate that plasmodesmatal transport persists in differentiated roots, despite apoplastic barriers such as Casparian strips and suberin lamellae in the endodermis, suggesting plasmodesmata as the sole pathway for water and nutrient flow at this stage. We also reveal a developmental switch in plasmodesmata function resulting in an unidirectional transport in differentiated roots. A genetic screen identified mutations that disrupt this directionality, leading to bidirectional transport. These mutations correlate with larger plasmodesmatal apertures, linked to defects in pectin composition and cell wall organization. This discovery underscores the role of plasmodesmatal aperture regulation and pectin in controlling directional transport. Our findings provide insights into plasmodesmata function and their regulation in roots.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cystopteris chinensis is an endangered fern endemic to China, which only has a small wild population due to its poor reproductive ability. However, we recently found that it can produce bulbils on its pinnule to generate new plants but the molecular mechanism underlying this unique phenomenon remained unknown. In this study, we have identified four distinct stages in the initiation and development of bulbils based on morphological and anatomical observation. We performed transcriptome and metabolome analyses on the collected samples at each stage. Through KEGG enrichment analysis, it was found that the phytohormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways play a significant role in regulating bulbil initiation and development. Specifically, the involvement of three phytohormones and sugar substances was identified in the process of bulbil initiation. Our study provides the first detailed observation of the bulbils in C. chinensis and explains their initiation and development at the molecular level. However, more in-depth studies are needed to discover the functions of key genes controlling the formation of bulbils to conserve the endangered C. chinensis population.
{"title":"Integrated Transcriptome and Metabolome Analyses Reveal the Mechanism Regulating Bulbil Initiation and Development in Cystopteris chinensis","authors":"An Yu, Xiaohong Chen, Wenkai Xi, Xia Zhao, Yazhu Wang, Zhihong Gong, Xiaofeng Zhou","doi":"10.1101/2024.09.18.613657","DOIUrl":"https://doi.org/10.1101/2024.09.18.613657","url":null,"abstract":"Cystopteris chinensis is an endangered fern endemic to China, which only has a small wild population due to its poor reproductive ability. However, we recently found that it can produce bulbils on its pinnule to generate new plants but the molecular mechanism underlying this unique phenomenon remained unknown. In this study, we have identified four distinct stages in the initiation and development of bulbils based on morphological and anatomical observation. We performed transcriptome and metabolome analyses on the collected samples at each stage. Through KEGG enrichment analysis, it was found that the phytohormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways play a significant role in regulating bulbil initiation and development. Specifically, the involvement of three phytohormones and sugar substances was identified in the process of bulbil initiation. Our study provides the first detailed observation of the bulbils in C. chinensis and explains their initiation and development at the molecular level. However, more in-depth studies are needed to discover the functions of key genes controlling the formation of bulbils to conserve the endangered C. chinensis population.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.13.612789
Marina Millan-Blanquez, James Simmonds, Nicholas Bird, Yann Manes, Cristobal Uauy, Scott Andrew Boden
Hybrids offer a promising approach to improve crop performance because the progeny are often superior to their parent lines and they outyield inbred varieties. A major challenge in producing hybrid progeny in wheat, however, lies in the low outcrossing rates of the maternal parent. This is often attributed to suboptimal synchronisation of male and female flowering as delayed pollination can result in reproductive failure due to female stigma deterioration. To test this accepted dogma, we examined the seed set capacity of six male sterile (MS) cultivars, each varying in the onset of stigma deterioration. To mimic a hybrid seed production scenario, MS cultivars were grown during two consecutive field seasons, and open pollination was allowed up to 15 days after flowering of the female parent using a blend of seven male fertile cultivars with varying flowering times. Detailed analysis of the temporal and spatial distribution of hybrid seed set along the spike across the six MS cultivars showed that grain production remained remarkably stable during the pollination window tested. These findings suggest sustained receptivity of stigma to pollen across all tested MS cultivars throughout the entire time course. We therefore conclude that stigma longevity does not represent a limiting factor in hybrid wheat seed production, and that breeding efforts should prioritise the study of other female traits, such as enhanced access to airborne pollen.
杂交种为提高作物产量提供了一种很有前景的方法，因为其后代往往优于其亲本品系，而且产量超过近交品种。然而，生产小麦杂交后代的一个主要挑战在于母本亲本的低杂交率。这通常归因于雌雄花期的不同步，因为授粉延迟会导致雌花柱头退化而导致繁殖失败。为了验证这一公认的理论，我们研究了六种雄性不育（MS）栽培品种的结实能力，每种栽培品种的柱头退化程度各不相同。为了模拟杂交种子的生产情况，我们在连续两个田间季节种植了 MS 栽培品种，并在雌性亲本开花后 15 天内，利用开花时间不同的七个雄性可育栽培品种混合进行开放授粉。对 6 个 MS 栽培品种沿穗杂交结籽的时间和空间分布进行的详细分析显示，在测试的授粉窗口期间，谷物产量保持了显著的稳定性。这些发现表明，在整个时间过程中，所有测试的 MS 栽培品种的柱头都能持续接受花粉。因此，我们得出结论，柱头寿命并不是杂交小麦种子生产的限制因素，育种工作应优先研究其他雌性性状，如增强对空气传播花粉的获取能力。
{"title":"Stigma longevity is not a major limiting factor in hybrid wheat seed production","authors":"Marina Millan-Blanquez, James Simmonds, Nicholas Bird, Yann Manes, Cristobal Uauy, Scott Andrew Boden","doi":"10.1101/2024.09.13.612789","DOIUrl":"https://doi.org/10.1101/2024.09.13.612789","url":null,"abstract":"Hybrids offer a promising approach to improve crop performance because the progeny are often superior to their parent lines and they outyield inbred varieties. A major challenge in producing hybrid progeny in wheat, however, lies in the low outcrossing rates of the maternal parent. This is often attributed to suboptimal synchronisation of male and female flowering as delayed pollination can result in reproductive failure due to female stigma deterioration. To test this accepted dogma, we examined the seed set capacity of six male sterile (MS) cultivars, each varying in the onset of stigma deterioration. To mimic a hybrid seed production scenario, MS cultivars were grown during two consecutive field seasons, and open pollination was allowed up to 15 days after flowering of the female parent using a blend of seven male fertile cultivars with varying flowering times. Detailed analysis of the temporal and spatial distribution of hybrid seed set along the spike across the six MS cultivars showed that grain production remained remarkably stable during the pollination window tested. These findings suggest sustained receptivity of stigma to pollen across all tested MS cultivars throughout the entire time course. We therefore conclude that stigma longevity does not represent a limiting factor in hybrid wheat seed production, and that breeding efforts should prioritise the study of other female traits, such as enhanced access to airborne pollen.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.1101/2024.09.13.612856
Yuta Kato, Takao Oi, Yoshikatsu Sato, Mitsutaka Taniguchi
In C4 plants, mesophyll (M) chloroplasts aggregate toward bundle sheath (BS) cells in response to environmental stress, which would contribute to C4 photosynthetic cycle adjustment between M and BS cells. However, it remains unclear whether mesophyll chloroplast movement is an intercellular response mediated by BS cells. One major challenge to resolving this is the difficulty in observing how M chloroplasts aggregate toward adjacent BS cells due to scattering and absorption of observation light in live-leaf tissues. We established a live leaf-section imaging technique that enables the long-term observation of sections of chemically unfixed leaf blades, with which we quantitatively analyzed M chloroplast movements. Another challenge in clarifying the contribution of BS cells to M chloroplast movement is the selective ablation of BS cells without impairing their function of M cells. To investigate the necessity of BS cells for M chloroplast movement, we developed a method to remove BS cells only based on differences in shape and size between M and BS cells. We also found that chloroplasts in M cells without adjacent BS cell contents did not show typical aggregative movement but showed a light-avoidance response. This indicates that the M chloroplast aggregative movement occurs during communication with BS cells.
在 C4 植物中，中叶（M）叶绿体在环境胁迫下向束鞘细胞聚集，这将有助于 M 细胞和 BS 细胞之间的 C4 光合周期调整。然而，叶绿体中间体的移动是否是由 BS 细胞介导的细胞间反应，目前仍不清楚。解决这一问题的一个主要挑战是，由于观察光在活叶片组织中的散射和吸收，很难观察到 M 叶绿体如何向相邻的 BS 细胞聚集。我们建立了一种活体叶片切片成像技术，可以长期观察未经化学固定的叶片切片，并利用这种技术定量分析了中叶叶绿体的运动。要弄清 BS 细胞对 M 叶绿体运动的贡献，另一个挑战是选择性地消融 BS 细胞而不损害其作为 M 细胞的功能。为了研究 BS 细胞对 M 叶绿体运动的必要性，我们开发了一种方法，仅根据 M 细胞和 BS 细胞在形状和大小上的差异去除 BS 细胞。我们还发现，没有邻近 BS 细胞内容物的 M 细胞中的叶绿体没有表现出典型的聚集运动，而是表现出避光反应。这表明，M 叶绿体的聚集运动发生在与 BS 细胞交流的过程中。
{"title":"Bundle sheath cell-dependent chloroplast movement in mesophyll cells of C4 plants analyzed using live leaf-section imaging","authors":"Yuta Kato, Takao Oi, Yoshikatsu Sato, Mitsutaka Taniguchi","doi":"10.1101/2024.09.13.612856","DOIUrl":"https://doi.org/10.1101/2024.09.13.612856","url":null,"abstract":"In C4 plants, mesophyll (M) chloroplasts aggregate toward bundle sheath (BS) cells in response to environmental stress, which would contribute to C4 photosynthetic cycle adjustment between M and BS cells. However, it remains unclear whether mesophyll chloroplast movement is an intercellular response mediated by BS cells. One major challenge to resolving this is the difficulty in observing how M chloroplasts aggregate toward adjacent BS cells due to scattering and absorption of observation light in live-leaf tissues. We established a live leaf-section imaging technique that enables the long-term observation of sections of chemically unfixed leaf blades, with which we quantitatively analyzed M chloroplast movements. Another challenge in clarifying the contribution of BS cells to M chloroplast movement is the selective ablation of BS cells without impairing their function of M cells. To investigate the necessity of BS cells for M chloroplast movement, we developed a method to remove BS cells only based on differences in shape and size between M and BS cells. We also found that chloroplasts in M cells without adjacent BS cell contents did not show typical aggregative movement but showed a light-avoidance response. This indicates that the M chloroplast aggregative movement occurs during communication with BS cells.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.1101/2024.06.17.597683
Jie Yun, Angela C Burnett, Alistair Rogers, David L Des Marais
Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called GxE. Understanding the mechanisms driving GxE is fundamental for ensuring stable crop performance across environments and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, yet the interactions between genotype and environment on genome-wide regulatory networks are rarely considered. In this study, we model genome-scale gene expression variation between two natural accessions of the model grass Brachypodium distachyon and their response to soil drying. We identified genotypic, environmental, and GxE responses in physiological, metabolic, and gene expression traits. We then identified gene regulation conservation and variation among conditions and genotypes, simplified as co-expression clusters in each combination of genotype and environmental treatment. Putative gene regulatory interactions are inferred as network edges with a graphical modelling approach, resulting in hypotheses about gene-gene interactions specific to -- or with higher affinity in -- one genotype, one treatment, or in one genotype under treatment. We further find that some gene-gene interactions are conserved across conditions such that differential expression of one gene is apparently transmitted to a target gene. These variably detected edges cluster together in co-expression modules, suggestive of different constraints or selection strength acting on specific pathways. These variable features of gene regulatory networks may represent candidates modulate environmental response via genome editing, and suggest possible targets of evolutionary change in gene regulatory networks associated with phenotypic plasticity.
{"title":"Genotype by environment interactions in gene regulation underlie the response to soil drying in the model grass Brachypodium distachyon","authors":"Jie Yun, Angela C Burnett, Alistair Rogers, David L Des Marais","doi":"10.1101/2024.06.17.597683","DOIUrl":"https://doi.org/10.1101/2024.06.17.597683","url":null,"abstract":"Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called GxE. Understanding the mechanisms driving GxE is fundamental for ensuring stable crop performance across environments and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, yet the interactions between genotype and environment on genome-wide regulatory networks are rarely considered. In this study, we model genome-scale gene expression variation between two natural accessions of the model grass <em>Brachypodium distachyon</em> and their response to soil drying. We identified genotypic, environmental, and GxE responses in physiological, metabolic, and gene expression traits. We then identified gene regulation conservation and variation among conditions and genotypes, simplified as co-expression clusters in each combination of genotype and environmental treatment. Putative gene regulatory interactions are inferred as network edges with a graphical modelling approach, resulting in hypotheses about gene-gene interactions specific to -- or with higher affinity in -- one genotype, one treatment, or in one genotype under treatment. We further find that some gene-gene interactions are conserved across conditions such that differential expression of one gene is apparently transmitted to a target gene. These variably detected edges cluster together in co-expression modules, suggestive of different constraints or selection strength acting on specific pathways. These variable features of gene regulatory networks may represent candidates modulate environmental response via genome editing, and suggest possible targets of evolutionary change in gene regulatory networks associated with phenotypic plasticity.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.12.612679
Karel Raabe, Alena Náprstková, Janto Pieters, Elnura Torutaeva, Veronika Jirásková, Zahra Kahrizi, Christos Michailidis, David Honys
Translation is a fundamental process for every living organism. In plants, the rate of translation is tightly modulated during development and in response to environmental cues. However, it is difficult to measure the actual translation state of the tissues in vivo. Here, we report the implementation of an in vivo translation marker based on bimolecular fluorescence complementation, the Ribo-BiFC. We combined method originally developed for fruit-fly with an improved low background split-mVenus BiFC system previously described in plants. We labelled Arabidopsis thaliana small subunit ribosomal protein (RPS) and large subunit ribosomal protein (RPL) with fragments of the mVenus fluorescent protein. Upon the assembly of the 80S ribosome, the mVenus fragments complemented and were detected by fluorescent microscopy. We show that these recombinant proteins are in close proximity in the tobacco epidermal cells, although the signal is reduced when compared to BiFC signal from known interactors. This Ribo-BiFC method system can be used in stable transgenic lines to enable visualisation of translational rate in plant tissues and could be used to study translation dynamics and its changes during plant development, under abiotic stress or in different genetic backgrounds.
{"title":"Implementation of Ribo-BiFC method to plant systems using a split mVenus approach","authors":"Karel Raabe, Alena Náprstková, Janto Pieters, Elnura Torutaeva, Veronika Jirásková, Zahra Kahrizi, Christos Michailidis, David Honys","doi":"10.1101/2024.09.12.612679","DOIUrl":"https://doi.org/10.1101/2024.09.12.612679","url":null,"abstract":"Translation is a fundamental process for every living organism. In plants, the rate of translation is tightly modulated during development and in response to environmental cues. However, it is difficult to measure the actual translation state of the tissues in vivo. Here, we report the implementation of an in vivo translation marker based on bimolecular fluorescence complementation, the Ribo-BiFC. We combined method originally developed for fruit-fly with an improved low background split-mVenus BiFC system previously described in plants. We labelled Arabidopsis thaliana small subunit ribosomal protein (RPS) and large subunit ribosomal protein (RPL) with fragments of the mVenus fluorescent protein. Upon the assembly of the 80S ribosome, the mVenus fragments complemented and were detected by fluorescent microscopy. We show that these recombinant proteins are in close proximity in the tobacco epidermal cells, although the signal is reduced when compared to BiFC signal from known interactors. This Ribo-BiFC method system can be used in stable transgenic lines to enable visualisation of translational rate in plant tissues and could be used to study translation dynamics and its changes during plant development, under abiotic stress or in different genetic backgrounds.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-17DOI: 10.1101/2024.09.12.612642
Linhao Xu, Yafei Wang, Xueying Li, Qin Hu, Vanda Adamkova, Junjie Xu, C. Jake Harris, Israel Ausin
The H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes. The SWR1 chromatin remodeling complex deposits H2A.Z. How SWR1 is directed to gene bodies is largely unknown. Here, we show that ALFIN-LIKE (AL) proteins are responsible for H2A.Z gene body patterning in Arabidopsis. AL proteins encode H3K4me3-binding PHD domains, and by ChIP-seq, we confirm preferential binding of AL5 to H3K4me3 over H3K4me1/2 in planta. We observe a global reduction in H2A.Z in al septuple mutants (al7m), especially of over H3K4me3-enriched genic regions. While MBD9 recruits SWR1 to nucleosome-free regions, ALs act non-redundantly with MBD9 for deposition of H2A.Z. Notably, al7m mutants show severe developmental abnormalities and upregulation of H2A.Z gene body-enriched responsive genes. Therefore, we propose a model whereby AL proteins direct gene body enrichment of H2A.Z by recruiting SWR1 to H3K4me3-containing responsive genes.
{"title":"The H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z","authors":"Linhao Xu, Yafei Wang, Xueying Li, Qin Hu, Vanda Adamkova, Junjie Xu, C. Jake Harris, Israel Ausin","doi":"10.1101/2024.09.12.612642","DOIUrl":"https://doi.org/10.1101/2024.09.12.612642","url":null,"abstract":"The H2A.Z histone variant is highly enriched over gene bodies, playing an essential role in several genome-templated processes, including transcriptional regulation and epigenetic patterning across eukaryotes. The SWR1 chromatin remodeling complex deposits H2A.Z. How SWR1 is directed to gene bodies is largely unknown. Here, we show that ALFIN-LIKE (AL) proteins are responsible for H2A.Z gene body patterning in Arabidopsis. AL proteins encode H3K4me3-binding PHD domains, and by ChIP-seq, we confirm preferential binding of AL5 to H3K4me3 over H3K4me1/2 in planta. We observe a global reduction in H2A.Z in al septuple mutants (al7m), especially of over H3K4me3-enriched genic regions. While MBD9 recruits SWR1 to nucleosome-free regions, ALs act non-redundantly with MBD9 for deposition of H2A.Z. Notably, al7m mutants show severe developmental abnormalities and upregulation of H2A.Z gene body-enriched responsive genes. Therefore, we propose a model whereby AL proteins direct gene body enrichment of H2A.Z by recruiting SWR1 to H3K4me3-containing responsive genes.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-16DOI: 10.1101/2024.09.13.612952
Miaomiao Li, Tao Yao, Mary Galli, Wanru Lin, Yilin Zhou, Jin-Gui Chen, Andrea Gallavotti, Shao-shan Carol Huang
SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors in Arabidopsis thaliana, providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins. Comparative analysis between the paralogs AtSPL9 and AtSPL15 revealed differences in their binding motifs, suggesting divergent regulatory functions. Additionally, we expanded our investigation to homologs of AtSPL9/15 in Zea mays (ZmSBP8/30) and Triticum aestivum (TaSPL7/13), identifying conserved and unique DNA-binding patterns across species. These findings provide key resources for understanding the molecular mechanisms of SPL transcription factors in regulating plant development and evolution across different species.
SQUAMOSA Promoter-Binding Protein-Like（SPL）转录因子在植物发育和胁迫反应中发挥着重要作用。在这项研究中，我们报告了对拟南芥中 16 个 SPL 转录因子中的 14 个进行的全面 DNA 亲和纯化测序（DAP-seq）分析，为了解它们的 DNA 结合特异性提供了宝贵的信息。我们对目标基因进行了基因本体（GO）分析，以揭示 SPL 家族蛋白之间趋同而多样的生物学功能。AtSPL9和AtSPL15同源物之间的比较分析表明，它们的结合基序存在差异，这表明它们具有不同的调控功能。此外，我们还对玉米（Zea mays）和小麦（Triticum aestivum）中 AtSPL9/15 的同源物（ZmSBP8/30 和 TaSPL7/13）进行了研究，发现了跨物种的保守和独特 DNA 结合模式。这些发现为了解 SPL 转录因子调控不同物种植物发育和进化的分子机制提供了关键资源。
{"title":"Diversification and conservation of DNA binding specificities of SPL family of transcription factors","authors":"Miaomiao Li, Tao Yao, Mary Galli, Wanru Lin, Yilin Zhou, Jin-Gui Chen, Andrea Gallavotti, Shao-shan Carol Huang","doi":"10.1101/2024.09.13.612952","DOIUrl":"https://doi.org/10.1101/2024.09.13.612952","url":null,"abstract":"SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors in <em>Arabidopsis thaliana</em>, providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins. Comparative analysis between the paralogs AtSPL9 and AtSPL15 revealed differences in their binding motifs, suggesting divergent regulatory functions. Additionally, we expanded our investigation to homologs of AtSPL9/15 in <em>Zea mays</em> (ZmSBP8/30) and <em>Triticum aestivum</em> (TaSPL7/13), identifying conserved and unique DNA-binding patterns across species. These findings provide key resources for understanding the molecular mechanisms of SPL transcription factors in regulating plant development and evolution across different species.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Selecting both high-yield and low-kernel-moisture varieties is essential for modern maize production, but relevant breeding efforts are hindered by a lack of valuable regulatory genes. Here, we demonstrate that the transcription factor (TF) basic leucine zipper 75 (ZmbZIP75) promotes grain yield and reduces kernel moisture in maize. Knockout of ZmbZIP75 results in defective grain filling and kernel dehydration, whereas ZmbZIP75 overexpression confers increased grain yield per plant and decreased kernel moisture without altering plant architecture. Mechanistically, during the grain filling stage, ZmbZIP75 is transcriptionally induced by maternal-derived basal abscisic acid (ABA) and directly activates multiple core starch synthesis-related genes and key TFs, thereby promoting grain filling and final yield. In the late stage of kernel development, high concentrations of zygotic ABA enhance ZmbZIP75 phosphorylation through SnRK2.10. The phosphorylated ZmbZIP75 subsequently transactivates and interacts with TF VP1 to synergistically promote kernel dehydration. This study thus highlights the potential of ZmbZIP75 for engineering both high-yield and low-kernel-moisture varieties to meet the demands of high-efficient maize production.
{"title":"The transcription factor ZmbZIP75 promotes both grain filling and kernel dehydration in maize","authors":"Tiandan Long, Yayun Wang, Jin Yang, Zhou Liu, Changqing Mao, Yufeng Hu, Junjie Zhang, Hanmei Liu, Yinghong Liu, Xiujun Fan, Lei Gao, Huanhuan Huang, Ying Xie, Daqiu Zhao, Yubi Huang, Yangping Li","doi":"10.1101/2024.09.11.612493","DOIUrl":"https://doi.org/10.1101/2024.09.11.612493","url":null,"abstract":"Selecting both high-yield and low-kernel-moisture varieties is essential for modern maize production, but relevant breeding efforts are hindered by a lack of valuable regulatory genes. Here, we demonstrate that the transcription factor (TF) basic leucine zipper 75 (ZmbZIP75) promotes grain yield and reduces kernel moisture in maize. Knockout of ZmbZIP75 results in defective grain filling and kernel dehydration, whereas ZmbZIP75 overexpression confers increased grain yield per plant and decreased kernel moisture without altering plant architecture. Mechanistically, during the grain filling stage, ZmbZIP75 is transcriptionally induced by maternal-derived basal abscisic acid (ABA) and directly activates multiple core starch synthesis-related genes and key TFs, thereby promoting grain filling and final yield. In the late stage of kernel development, high concentrations of zygotic ABA enhance ZmbZIP75 phosphorylation through SnRK2.10. The phosphorylated ZmbZIP75 subsequently transactivates and interacts with TF VP1 to synergistically promote kernel dehydration. This study thus highlights the potential of ZmbZIP75 for engineering both high-yield and low-kernel-moisture varieties to meet the demands of high-efficient maize production.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-16DOI: 10.1101/2024.09.11.612578
Harihar Jaishree Subrahmaniam, F. Xavier Pico, Thomas Bataillon, Camilla Lind Salomonsen, Marianne Glasius, Bodil K. Ehlers
Plant root exudates are involved in nutrient acquisition, microbial partnerships, and inter-organism signaling. Yet, little is known about the genetic and environmental drivers of root exudate variation at large geographical scales, which may help understand evolutionary trajectories of plants in heterogeneous environments. We quantified natural variation in chemical composition of Arabidopsis thaliana root exudates in 105 Iberian accessions. We identified up to 373 putative compounds using ultra high performance liquid chromatography coupled with mass spectrometry. We estimated broad-sense heritability of compounds and conducted a genome-wide association (GWA) study. We associated variation in root exudates to variation in geographic, environmental, life history, and genetic attributes of Iberian accessions. Only 25 of 373 compounds exhibited broad-sense heritability values significantly different from zero. GWA analysis identified polymorphisms associated to 12 root exudate compounds and 26 known genes involved in metabolism, defense, signaling, and nutrient transport. The genetic structure influenced root exudate composition involving terpenoids. We detected five terpenoids related to plant defense significantly varying in mean abundances in two genetic clusters. Our study provides first insights into the extent of root exudate natural variation at a regional scale depicting a diversified evolutionary trajectory among A. thaliana genetic clusters chiefly mediated by terpenoid composition.
{"title":"Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula","authors":"Harihar Jaishree Subrahmaniam, F. Xavier Pico, Thomas Bataillon, Camilla Lind Salomonsen, Marianne Glasius, Bodil K. Ehlers","doi":"10.1101/2024.09.11.612578","DOIUrl":"https://doi.org/10.1101/2024.09.11.612578","url":null,"abstract":"Plant root exudates are involved in nutrient acquisition, microbial partnerships, and inter-organism signaling. Yet, little is known about the genetic and environmental drivers of root exudate variation at large geographical scales, which may help understand evolutionary trajectories of plants in heterogeneous environments. We quantified natural variation in chemical composition of Arabidopsis thaliana root exudates in 105 Iberian accessions. We identified up to 373 putative compounds using ultra high performance liquid chromatography coupled with mass spectrometry. We estimated broad-sense heritability of compounds and conducted a genome-wide association (GWA) study. We associated variation in root exudates to variation in geographic, environmental, life history, and genetic attributes of Iberian accessions. Only 25 of 373 compounds exhibited broad-sense heritability values significantly different from zero. GWA analysis identified polymorphisms associated to 12 root exudate compounds and 26 known genes involved in metabolism, defense, signaling, and nutrient transport. The genetic structure influenced root exudate composition involving terpenoids. We detected five terpenoids related to plant defense significantly varying in mean abundances in two genetic clusters. Our study provides first insights into the extent of root exudate natural variation at a regional scale depicting a diversified evolutionary trajectory among A. thaliana genetic clusters chiefly mediated by terpenoid composition.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142268369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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