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Mutation of strigolactone biosynthetic gene DWARF 17 impairs the responses of rice tillering to N supply
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-04-01 DOI: 10.1111/tpj.70124
Xin Huang, Zhiming Kuang, Rui Zhou, Tiantian Liu, Li Tang, Zhipeng Gao, Tao Liu, Xiaorong Fan, Wei Xuan, Le Luo, Guohua Xu
{"title":"Mutation of strigolactone biosynthetic gene DWARF 17 impairs the responses of rice tillering to N supply","authors":"Xin Huang,&nbsp;Zhiming Kuang,&nbsp;Rui Zhou,&nbsp;Tiantian Liu,&nbsp;Li Tang,&nbsp;Zhipeng Gao,&nbsp;Tao Liu,&nbsp;Xiaorong Fan,&nbsp;Wei Xuan,&nbsp;Le Luo,&nbsp;Guohua Xu","doi":"10.1111/tpj.70124","DOIUrl":"https://doi.org/10.1111/tpj.70124","url":null,"abstract":"<div>\u0000 \u0000 <p>Tiller number is one important parameter for rice yield and is influenced by both strigolactone (SL) and nitrogen (N). However, how SL and N interact to regulate the tiller outgrowth in rice is unclear. In this study, we isolated a multi-tillering mutant, <i>tin</i>, from an ethyl methanesulfonate (EMS)-mutagenized population of Wuyunjing 7, a japonica cultivar. The <i>tin</i> mutant exhibited low sensitivity to varying N concentrations during the tiller development. Through bulk segregation analysis (BSA), we identified a missense mutation located in the exon of <i>DWARF 17</i> (<i>D17</i>), a key gene involved in SL biosynthesis. Complementation experiments confirmed that <i>D17</i> is responsible for the <i>tin</i> tiller phenotype, and exogenous application of the SL analogue GR24 restored the tiller response of <i>tin</i> to N. Transcriptome analysis further revealed that D17 and SL regulate the tiller response to N by modulating the expression of <i>SQUAMOSA PROMOTER BINDING PROTEIN-LIKE</i> (<i>SPL</i>) genes and ammonium transporter genes. These findings elucidate the mechanism by which SL and N coordinate to regulate rice tillering growth, providing valuable insights for optimizing rice plant architecture to enhance yield potential.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749755","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}
引用次数: 0
Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70122
Deying Zeng, Jiayu Peng, Lan Zhang, Mathew J. Hayden, Tina M. Rathjen, Xiaoqing Li, Wenfang Jiang, Emmanuel Delhaize
{"title":"Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures","authors":"Deying Zeng,&nbsp;Jiayu Peng,&nbsp;Lan Zhang,&nbsp;Mathew J. Hayden,&nbsp;Tina M. Rathjen,&nbsp;Xiaoqing Li,&nbsp;Wenfang Jiang,&nbsp;Emmanuel Delhaize","doi":"10.1111/tpj.70122","DOIUrl":"https://doi.org/10.1111/tpj.70122","url":null,"abstract":"<div>\u0000 \u0000 <p>We identified a mutant of hexaploid wheat (<i>Triticum aestivum</i>) with impaired responses to gravity. The mutant, named <i>Twisted Sister1</i> (<i>TS1</i>), had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of <i>TS1</i> were insensitive to externally applied auxin, with the genetics and physiology suggestive of a mutated <i>AUX/IAA</i> transcription factor gene. Hexaploid wheat possesses over 80 <i>AUX/IAA</i> genes, and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F<sub>2</sub> population mapped the mutation to chromosome 5A, and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the <i>TraesCS5A03G0149800</i> gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed <i>TraesCS5A03G0149800</i> as underlying the mutant phenotype by generating transgenic <i>Arabidopsis thaliana</i>. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of <i>AUX/IAA</i> genes in gravity responses, although there were marked differences. Here we show that the sequenced wheat genome, along with previous knowledge of the physiology of gravity responses from other plant species, gene mapping, RNA-seq, and expression in Arabidopsis have enabled the cloning of a key wheat gene that defines plant architecture.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741629","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}
引用次数: 0
A space for time. Exploring temporal regulation of plant development across spatial scales
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70130
Yadhusankar Sasidharan, Vijayalakshmi Suryavanshi, Margot E. Smit
{"title":"A space for time. Exploring temporal regulation of plant development across spatial scales","authors":"Yadhusankar Sasidharan,&nbsp;Vijayalakshmi Suryavanshi,&nbsp;Margot E. Smit","doi":"10.1111/tpj.70130","DOIUrl":"https://doi.org/10.1111/tpj.70130","url":null,"abstract":"<p>Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment and progression of cell fates. The relative timing of developmental events is tightly controlled and involves integration of environmental, spatial, and relative age-related signals and actors. While plant phase transitions have been studied extensively and many of their regulators have been described, less is known about temporal regulation on a smaller, cell-level scale. Here, using examples from both plant and animal systems, we outline time-dependent changes. Looking at systemic scale changes, we discuss the timing of germination, juvenile-to-adult transition, flowering, and senescence, together with regeneration timing. Switching to temporal regulation on a cellular level, we discuss several instances from the animal field in which temporal control has been examined extensively at this scale. Then, we switch back to plants and summarize examples where plant cell-level changes are temporally regulated. As time cannot easily be separated from signaling derived from the environment and tissue context, we next discuss factors that have been implicated in controlling the timing of developmental events, reviewing temperature, photoperiod, nutrient availability, as well as tissue context and mechanical cues on the cellular scale. Afterwards, we provide an overview of mechanisms that have been shown or implicated in the temporal control of development, considering metabolism, division control, mobile signals, epigenetic regulation, and the action of transcription factors. Lastly, we look at remaining questions for the future study of developmental timing in plants and how recent technical advancement can enable these efforts.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741560","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}
引用次数: 0
The cysteine protease RD19C suppresses plant immunity to Phytophthora by modulating copper chaperone ATX1 stability
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70120
Jingwen Dong, Weiwei Li, Yang Yang, Song Liu, Yilin Li, Yuling Meng, Weixing Shan
{"title":"The cysteine protease RD19C suppresses plant immunity to Phytophthora by modulating copper chaperone ATX1 stability","authors":"Jingwen Dong,&nbsp;Weiwei Li,&nbsp;Yang Yang,&nbsp;Song Liu,&nbsp;Yilin Li,&nbsp;Yuling Meng,&nbsp;Weixing Shan","doi":"10.1111/tpj.70120","DOIUrl":"https://doi.org/10.1111/tpj.70120","url":null,"abstract":"<div>\u0000 \u0000 <p>Papain-like cysteine proteases (PLCPs) are pivotal in plant development and immunity, though their specific regulatory mechanisms in immune responses remain largely unexplored. In this study, we identify AtRD19C, a vacuole-localized PLCP, and demonstrate its role in negatively regulating plant immunity to <i>Phytophthora parasitica</i>. We show that AtRD19C suppresses the ethylene (ET) signaling pathway by destabilizing the copper chaperone AtATX1, which is essential for activating ET signaling through the ethylene receptor ETR1. Genetic and biochemical analyses reveal that AtATX1 and the ET signaling pathway positively regulate immunity against <i>Phytophthora</i>. Given the conserved roles of <i>RD19C</i> and <i>ATX1</i> in <i>Solanum tuberosum</i>, our findings suggest a conserved mechanism by which RD19C and ATX1 regulate resistance to <i>Phytophthora</i> across plant species.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741559","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}
引用次数: 0
Heritable virus-induced germline editing in tomato
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70115
Youngbin Oh, Ugrappa Nagalakshmi, Douglas Dahlbeck, Naio Koehler, Myeong-Je Cho, Savithramma P. Dinesh-Kumar, Brian J. Staskawicz
{"title":"Heritable virus-induced germline editing in tomato","authors":"Youngbin Oh,&nbsp;Ugrappa Nagalakshmi,&nbsp;Douglas Dahlbeck,&nbsp;Naio Koehler,&nbsp;Myeong-Je Cho,&nbsp;Savithramma P. Dinesh-Kumar,&nbsp;Brian J. Staskawicz","doi":"10.1111/tpj.70115","DOIUrl":"https://doi.org/10.1111/tpj.70115","url":null,"abstract":"<p>Here, we report the successful implementation of heritable virus-induced genome editing (VIGE) in tomato (<i>Solanum lycopersicum</i>). We generated three transgenic tomato lines expressing <i>Streptococcus pyogenes Cas9</i> (SpCas9) under the control of Cauliflower mosaic virus 35S (35S), <i>S. lycopersicum</i> ribosomal protein S5A (<i>Sl</i>RPS5A), or <i>S. lycopersicum</i> YAO promoters (<i>Sl</i>YAO). These three lines were tested for somatic and heritable editing using the tobacco rattle virus (TRV)-based system carrying guide RNAs (gRNAs) fused with mobile RNA sequences. TRV with gRNA targeted to <i>Phytoene desaturase</i> (<i>SlPDS</i>) and <i>Downy mildew resistance 6</i> (<i>SlDMR6</i>) genes fused to mobile RNA sequences showed significant somatic editing efficiency in all three tomato lines expressing SpCas9. However, the progenies from the <i>Sl</i>YAO promoter-driven SpCas9 tomato infected with TRV with gRNA targeted to <i>SlDMR6</i> fused to the mobile RNA sequence resulted in monoallelic mutations with a frequency of 3%. Optimization of environmental conditions, such as reduced light intensity, significantly increased heritable editing frequencies, from 0% to 86% at the <i>SlPDS</i> and from 3% to 100% at the <i>SlDMR6</i>, including biallelic mutations. These findings underscore the use of appropriate promoters to express Cas nucleases and optimized environmental conditions to enhance heritable genome editing efficiency in tomato using VIGE. Furthermore, our method enables the generation of mutants without additional tissue culture or transformation once a SpCas9-expressing tomato line is established.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741561","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}
引用次数: 0
LTD1 plays a key role in rice tillering regulation through cooperation with CycH1;1 and TFB2 subunits of the TFIIH complex
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70119
Xiaorong Yang, Chun Hu, Xiangyu Zhang, Xiaolan Wang, Longfei Chen, Hongshan Zhang, Xinxin Ma, Ke Liang, Congping Chen, Jia Guo, Chun Li, Bin Yang, Changhui Sun, Xiaojian Deng, Pingrong Wang
{"title":"LTD1 plays a key role in rice tillering regulation through cooperation with CycH1;1 and TFB2 subunits of the TFIIH complex","authors":"Xiaorong Yang,&nbsp;Chun Hu,&nbsp;Xiangyu Zhang,&nbsp;Xiaolan Wang,&nbsp;Longfei Chen,&nbsp;Hongshan Zhang,&nbsp;Xinxin Ma,&nbsp;Ke Liang,&nbsp;Congping Chen,&nbsp;Jia Guo,&nbsp;Chun Li,&nbsp;Bin Yang,&nbsp;Changhui Sun,&nbsp;Xiaojian Deng,&nbsp;Pingrong Wang","doi":"10.1111/tpj.70119","DOIUrl":"https://doi.org/10.1111/tpj.70119","url":null,"abstract":"<div>\u0000 \u0000 <p>Tillering contributes greatly to grain yield in rice (<i>Oryza sativa</i>). At present, many genes involved in rice tillering regulation have been cloned and characterized. However, the identification of more novel genes is still necessary to fully understand the molecular mechanisms regulating rice tillering. In this study, we isolated a <i>low</i>-<i>tillering and dwarf 1</i> (<i>ltd1</i>) mutant in <i>indica</i> rice. Map-based cloning and MutMap analysis showed that the candidate gene <i>LTD1</i> (<i>LOC_Os01g19760</i>) encodes a putative FAM91A1 protein with an unknown function in plants. <i>LTD1</i>-complementation and -RNAi confirmed that <i>LTD1</i> is responsible for the mutant phenotype of <i>ltd1</i>. The LTD1 protein is localized to the plasma membrane, endoplasmic reticulum, and multi-vesicular bodies. Furthermore, protein interaction and colocalization assays showed that LTD1 interacts with both the TFB2 subunit of the core subcomplex and the CycH1;1 subunit of the cyclin-dependent kinase-activating kinase (CAK) subcomplex of the TFIIH complex, and TFB2 also interacts with CycH1;1. qRT-PCR demonstrated that the expression levels of most genes related to the cell cycle are changed significantly in the <i>ltd1</i> tiller buds, and flow cytometry assays revealed that there are more polyploid nuclei in the <i>ltd1</i> leaves and roots, suggesting that LTD1 could be involved in cell cycle regulation. Taken together, our findings indicated that <i>LTD1</i> plays a key role in rice tillering regulation by involvement in the cell cycle through cooperation with CycH1;1 and TFB2 subunits of TFIIH. This work also sheds light on the biological function of FAM91A1 in regulating important agronomic traits of rice.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741618","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}
引用次数: 0
Differential methylation of a retrotransposon upstream of a MYB gene causes variegation of lettuce leaves, which is abolished by the presence of an (AT)5 repeat in the promoter
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70123
Rong Tao, Jiaojiao Ma, Jinlong Qian, Yali Liu, Weiyi Zhang, Dean Lavelle, Xin Wang, Wenhao Yan, Richard W. Michelmore, Jiongjiong Chen, Hanhui Kuang
{"title":"Differential methylation of a retrotransposon upstream of a MYB gene causes variegation of lettuce leaves, which is abolished by the presence of an (AT)5 repeat in the promoter","authors":"Rong Tao,&nbsp;Jiaojiao Ma,&nbsp;Jinlong Qian,&nbsp;Yali Liu,&nbsp;Weiyi Zhang,&nbsp;Dean Lavelle,&nbsp;Xin Wang,&nbsp;Wenhao Yan,&nbsp;Richard W. Michelmore,&nbsp;Jiongjiong Chen,&nbsp;Hanhui Kuang","doi":"10.1111/tpj.70123","DOIUrl":"https://doi.org/10.1111/tpj.70123","url":null,"abstract":"<div>\u0000 \u0000 <p>Variegation, a common phenomenon in plants, can be the result of several genetic, developmental, and physiological factors. Leaves of some lettuce cultivars exhibit dramatic red variegation; however, the genetic mechanisms underlying this variegation remain unknown. In this study, we cloned the causal gene for variegation on lettuce leaves and elucidated the underlying molecular mechanisms. Genetic analysis revealed that the polymorphism of variegated versus uniformly red leaves is caused by an “AT” repeat in the promoter of the <i>RLL2A</i> gene encoding a MYB transcription factor. Complementation tests demonstrated that the <i>RLL2A</i> allele (<i>RLL2A</i><sup><i>V</i></sup>) with (AT)<sub>n</sub> repeat numbers other than five led to variegated leaves. <i>RLL2A</i><sup><i>V</i></sup> was expressed in the red spots but not in neighboring green regions. This expression pattern was in concert with a relatively low level of methylation in a retrotransposon inserted in −761 bp of the gene in the red spots compared to high methylation of the retrotransposon in the green region. The presence of (AT)<sub>5</sub> in the promoter region, however, stabilized the expression of <i>RLL2A</i>, resulting in uniformly red leaves. In summary, we identified a novel promoter mechanism controlling variegation through inconsistent levels of methylation and showed that the presence of a simple sequence repeat of specific size could stabilize gene expression.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741630","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}
引用次数: 0
Anther-specific expression of MsMYB35 transcription factor in alfalfa (Medicago sativa L.) and its crucial role in pollen development
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70126
Huicai Cai, Shuhe Zhang, Yingzhe Wang, Zhenning Yang, Lin Zhang, Jiahao Zhang, Minmin Zhang, Bo Xu
{"title":"Anther-specific expression of MsMYB35 transcription factor in alfalfa (Medicago sativa L.) and its crucial role in pollen development","authors":"Huicai Cai,&nbsp;Shuhe Zhang,&nbsp;Yingzhe Wang,&nbsp;Zhenning Yang,&nbsp;Lin Zhang,&nbsp;Jiahao Zhang,&nbsp;Minmin Zhang,&nbsp;Bo Xu","doi":"10.1111/tpj.70126","DOIUrl":"https://doi.org/10.1111/tpj.70126","url":null,"abstract":"<div>\u0000 \u0000 <p>Alfalfa (<i>Medicago sativa</i> L.) is a high-quality forage crop and an essential resource for livestock. Understanding the molecular mechanisms underlying male sterility in alfalfa is pivotal for the development of superior forage varieties. Despite the critical role of anther development in plant reproduction, its molecular regulation—particularly the involvement of transcription factors in <i>M. sativa</i>—remains insufficiently explored. This study bridges this gap by isolating and characterizing an R2R3-MYB transcription factor, <i>MsMYB35</i>, and unveiling its regulatory role in anther development. Quantitative RT-PCR (qRT-PCR) revealed that <i>MsMYB35</i> is predominantly expressed during early anther development and is homologous to <i>AtMYB35</i>. <i>MsMYB35</i> was found to localize in both the cytoplasm and nucleus. DNA affinity purification sequencing (DAP-seq) identified 3647 target genes of <i>MsMYB35</i>, with enrichment analysis uncovering three recognition motifs. Integrated DAP-seq and RNA-seq analyses revealed that <i>MsMYB35</i> directly regulates two key anther development-related genes. Functional analyses showed that overexpression of <i>MsMYB35</i> promotes anther development, while silencing <i>MsMYB35</i> leads to defective anther sacs and wrinkled pollen grains. Proper <i>MsMYB35</i> expression ensures the formation of viable and fertile pollen grains, solidifying its role as a critical regulator of anther development. These findings provide a novel perspective on the molecular mechanisms regulating anther development in <i>M. sativa</i> and offer valuable insights for improving molecular breeding and hybrid seed production strategies. By advancing the fundamental understanding of transcriptional regulation in anther development, this study sets the stage for innovative approaches to alfalfa crop improvement.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741642","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}
引用次数: 0
Integrated multi-omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70113
Hengzhao Liu, Huijuan Zhou, Hang Ye, Mengdi Li, Jiayu Ma, Ruimin Xi, Xiaozhou He, Peng Zhao
{"title":"Integrated multi-omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp","authors":"Hengzhao Liu,&nbsp;Huijuan Zhou,&nbsp;Hang Ye,&nbsp;Mengdi Li,&nbsp;Jiayu Ma,&nbsp;Ruimin Xi,&nbsp;Xiaozhou He,&nbsp;Peng Zhao","doi":"10.1111/tpj.70113","DOIUrl":"https://doi.org/10.1111/tpj.70113","url":null,"abstract":"<div>\u0000 \u0000 <p>Persian walnut (<i>Juglans regia</i>) is an economically important nut oil tree; the fruit has a hard endocarp/shell to protect seeds, thus playing a key role in its evolution, and the shell thickness is an important trait for walnut breeding. However, the genomic landscape and the gene regulatory networks associated with walnut shell development remain to be systematically elucidated. Here, we report a high-quality genome assembly of the walnut cultivar ‘Xiangling’ and construct a graphic structure pan-genome of eight <i>Juglans</i> species to reveal the genetic variations at the genome level. We re-sequence 285 accessions to characterize the genomic variation landscape. Through genome-wide association studies (GWAS), we identified 19 loci associated with more than 268 loci that underwent selection during walnut domestication and improvement. Multi-omics analyses, including transcriptomics, metabolomics, DNA methylation, and spatial transcriptomics across eleven developmental stages, revealed several candidate genes related to secondary cell biosynthesis and lignin accumulation. This integrated multi-omics approach revealed several candidate genes associated with secondary cell biosynthesis and lignin accumulation, such as <i>UGP</i>, <i>MYB308, MYB83</i>, <i>NAC043</i>, <i>NAC073</i>, <i>CCoAOMT1</i>, <i>CCoAOMT7</i>, <i>CHS2</i>, <i>CESA7</i>, <i>LAC7</i>, <i>COBL4</i>, and <i>IRX12</i>. Overexpression of <i>JrUGP</i> and <i>JrMYB308</i> in <i>Arabidopsis thaliana</i> confirmed their roles in lignin biosynthesis and cell wall thickening. Consequently, our comprehensive multi-omics findings offer novel insights into walnut genetic variation and network regulation of endocarp development and shell thickness, which enable further genome-informed breeding strategies for walnut cultivar improvement.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741613","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}
引用次数: 0
Autophagy positively regulates ethylene-induced colouration in citrus fruits
IF 6.2 1区 生物学
The Plant Journal Pub Date : 2025-03-31 DOI: 10.1111/tpj.70114
Ye Guo, Jinli Gong, Ran Hu, Meiyan Shi, Zhiru Bao, Saiyu Cao, Kaijie Zhu, Xiuxin Deng, Yunjiang Cheng, Pengwei Wang
{"title":"Autophagy positively regulates ethylene-induced colouration in citrus fruits","authors":"Ye Guo,&nbsp;Jinli Gong,&nbsp;Ran Hu,&nbsp;Meiyan Shi,&nbsp;Zhiru Bao,&nbsp;Saiyu Cao,&nbsp;Kaijie Zhu,&nbsp;Xiuxin Deng,&nbsp;Yunjiang Cheng,&nbsp;Pengwei Wang","doi":"10.1111/tpj.70114","DOIUrl":"https://doi.org/10.1111/tpj.70114","url":null,"abstract":"<div>\u0000 \u0000 <p>Autophagy is an evolutionarily conserved process in eukaryotes that regulates metabolic reprogramming and organelle recycling in response to various environmental signals and developmental cues. However, little is known about its regulatory mechanism during fruit colouration and ripening, which also undergo dramatic metabolic and cellular alterations. Here, we demonstrate that the autophagy pathway is activated during citrus fruit colouration, and the colour transition of citrus fruit is significantly delayed when autophagy is blocked. Furthermore, we revealed that ethylene, a plant hormone crucial for citrus fruit colouration, activates the autophagy pathway through the ethylene-responsive factor, CsERF061. Further analysis revealed that CsERF061 directly binds to the promoter of <i>CsATG8h</i> and activates its expression, thereby promoting autophagy and fruit colouration, suggesting autophagy is a key determinant of citrus fruit colouration in response to ethylene. These findings enhance our understanding of fruit colouration and offer a potential method to improve citrus fruit colour and quality for future applications.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741614","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}
引用次数: 0
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