Plant Science最新文献_第3页

Genetic variations in FAD3 and its influence on agronomic traits and fatty acid composition in perilla germplasm 紫苏种质中 FAD3 的遗传变异及其对农艺性状和脂肪酸组成的影响

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-03-01 DOI: 10.1016/j.plantsci.2025.112452

Eunae Yoo , Eun-Gyeong Kim , Jae-Eun Lee , Sookyeong Lee , Dongho Lee , Gi-An Lee

In this study, we explored the relationship between agronomic characteristics and fatty acid composition in perilla germplasm and examined the potential effects of genetic variations in the FAD3 gene on these traits. Our analysis involved correlation, principal component analysis (PCA), hierarchical clustering, and path analysis. We discovered the days to flowering (DTF), days to maturing (DTM) number of branches (NB), and stearic acid (SA) content were positively correlated with each other. Conversely, oleic acid (OA), linoleic acid (LA), and alpha-linolenic acid (ALA) showed negative correlations among themselves. We observed significant differences in agronomic traits and fatty acid composition based on the color of the perilla seed hull, indicating the influence of genetic factors on these traits. A single nucleotide polymorphism (SNP) variation at the 182 bp position in the FAD3 gene, characterized by a homozygous G base, was significantly associated with a decrease in LA proportion. This is in line with the known biochemical role of FAD3 in fatty acid desaturation. Interestingly, this SNP was also correlated with an increase in NB, suggesting that FAD3 may have pleiotropic effects on both agronomic traits and fatty acid composition. However, SNPs at the 596 bp and 599 bp positions in the FAD3 gene did not show clear patterns, suggesting potential influences from other genetic or environmental factors. These findings offer valuable insights into the genetic and phenotypic interactions in perilla, highlighting the importance of FAD3 variation. This knowledge can aid in the development of targeted breeding and selection strategies for perilla cultivars, optimizing both agronomic performance and nutritional quality. Further research is required to clarify the precise mechanisms of FAD3 and its impact on perilla traits.

{"title":"Genetic variations in FAD3 and its influence on agronomic traits and fatty acid composition in perilla germplasm","authors":"Eunae Yoo , Eun-Gyeong Kim , Jae-Eun Lee , Sookyeong Lee , Dongho Lee , Gi-An Lee","doi":"10.1016/j.plantsci.2025.112452","DOIUrl":"10.1016/j.plantsci.2025.112452","url":null,"abstract":"<div><div>In this study, we explored the relationship between agronomic characteristics and fatty acid composition in perilla germplasm and examined the potential effects of genetic variations in the <em>FAD3</em> gene on these traits. Our analysis involved correlation, principal component analysis (PCA), hierarchical clustering, and path analysis. We discovered the days to flowering (DTF), days to maturing (DTM) number of branches (NB), and stearic acid (SA) content were positively correlated with each other. Conversely, oleic acid (OA), linoleic acid (LA), and alpha-linolenic acid (ALA) showed negative correlations among themselves. We observed significant differences in agronomic traits and fatty acid composition based on the color of the perilla seed hull, indicating the influence of genetic factors on these traits. A single nucleotide polymorphism (SNP) variation at the 182 bp position in the <em>FAD3</em> gene, characterized by a homozygous G base, was significantly associated with a decrease in LA proportion. This is in line with the known biochemical role of <em>FAD3</em> in fatty acid desaturation. Interestingly, this SNP was also correlated with an increase in NB, suggesting that <em>FAD3</em> may have pleiotropic effects on both agronomic traits and fatty acid composition. However, SNPs at the 596 bp and 599 bp positions in the <em>FAD3</em> gene did not show clear patterns, suggesting potential influences from other genetic or environmental factors. These findings offer valuable insights into the genetic and phenotypic interactions in perilla, highlighting the importance of <em>FAD3</em> variation. This knowledge can aid in the development of targeted breeding and selection strategies for perilla cultivars, optimizing both agronomic performance and nutritional quality. Further research is required to clarify the precise mechanisms of <em>FAD3</em> and its impact on perilla traits.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"355 ","pages":"Article 112452"},"PeriodicalIF":4.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143543077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Cytological observation and transcriptome analysis reveal that NTFR1 is a new tetraploid rice fertility gene using the tetraploid fertility-directed lines

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-28 DOI: 10.1016/j.plantsci.2025.112437

Hao Fan , Kai Li , Mengzhu Hu , Zijuan Huang , Haibin Guo , Xiang Li , Zhixiong Chen , Lan Wang , Muhammad Qasim Shahid , Xiangdong Liu , Jinwen Wu

Neo-tetraploid rice, a type of high-fertility tetraploid rice, is thought to be a useful material for utilizing its heterosis. However, the mechanism of its high fertility remains little known. Here, two tetraploid fertility-directed lines were generated and used to evaluate their variation on fertility charts. Cytological observations indicated that the low tetraploid fertility-directed lines (LFDL) exhibited a lower seed-setting ratio (12.64 %), pollen fertility (53.28 %), embryo sac fertility (85.71 %) while compared with the high tetraploid fertility-directed lines (HFDL). In addition, approximately 31.44 % and 48.13 % of chromosome lagging at Metaphase I and Metaphase II, and 33.33 % and 53.47 % of chromosome straggling at Anaphase I and Anaphase II were detected in the LFDL, respectively. Transcriptome analysis identified 911 differentially expressed genes (DEGs) in the HFDL compared with the LFDL. Among these DEGs, 202 meiosis-related or stage-specific genes exhibited significant down-regulation in HFDL compared with LFDL. Further, we selected NTFR1 as the candidate gene and verified its fertility phenotype in knock-out mutants, and detected a significant decrease in the seed-setting ratio, pollen viability, pollen fertility, and embryo sac fertility. This study provided a new fertility gene for tetraploid rice, and it may offer the fertility regulatory mechanisms in neo-tetraploid rice.

{"title":"Cytological observation and transcriptome analysis reveal that NTFR1 is a new tetraploid rice fertility gene using the tetraploid fertility-directed lines","authors":"Hao Fan , Kai Li , Mengzhu Hu , Zijuan Huang , Haibin Guo , Xiang Li , Zhixiong Chen , Lan Wang , Muhammad Qasim Shahid , Xiangdong Liu , Jinwen Wu","doi":"10.1016/j.plantsci.2025.112437","DOIUrl":"10.1016/j.plantsci.2025.112437","url":null,"abstract":"<div><div>Neo-tetraploid rice, a type of high-fertility tetraploid rice, is thought to be a useful material for utilizing its heterosis. However, the mechanism of its high fertility remains little known. Here, two tetraploid fertility-directed lines were generated and used to evaluate their variation on fertility charts. Cytological observations indicated that the low tetraploid fertility-directed lines (LFDL) exhibited a lower seed-setting ratio (12.64 %), pollen fertility (53.28 %), embryo sac fertility (85.71 %) while compared with the high tetraploid fertility-directed lines (HFDL). In addition, approximately 31.44 % and 48.13 % of chromosome lagging at Metaphase I and Metaphase II, and 33.33 % and 53.47 % of chromosome straggling at Anaphase I and Anaphase II were detected in the LFDL, respectively. Transcriptome analysis identified 911 differentially expressed genes (DEGs) in the HFDL compared with the LFDL. Among these DEGs, 202 meiosis-related or stage-specific genes exhibited significant down-regulation in HFDL compared with LFDL. Further, we selected <em>NTFR1</em> as the candidate gene and verified its fertility phenotype in knock-out mutants, and detected a significant decrease in the seed-setting ratio, pollen viability, pollen fertility, and embryo sac fertility. This study provided a new fertility gene for tetraploid rice, and it may offer the fertility regulatory mechanisms in neo-tetraploid rice.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"355 ","pages":"Article 112437"},"PeriodicalIF":4.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Genome-wide analysis of apple histone acetyltransferases reveals the regulatory roles of MdHAG1 and MdHAM1 in response to abiotic stresses

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-28 DOI: 10.1016/j.plantsci.2025.112441

Weiyu Jiang , Furong Hong , Bolin Niu , Hongzhen Zhu , Mengyao Yang , Jinjiao Yan , Jiangbo Wang , Xiaolin Song , Fengwang Ma , Qingmei Guan , Qianming Zheng , Jidi Xu

It is known that histone acetyltransferases (HATs) are involved in a wide range of biological processes by activating gene expression. However, the regulatory role of HATs in apple remains to be elucidated. This study identified 58 HATs from the apple genome (named MdHATs) and performed comprehensive analyses of these MdHATs, given their involvements in plant development and stress response. Firstly, we classified 58 predicted MdHATs into four different categories based on the phylogenetic analyses. Then, the intron/exon structures, conserved motifs, and structural domain organization of MdHAT genes and predicted proteins were further analyzed. Next, we investigated the expression patterns of MdHATs during apple plants' development process and stress responses. Moreover, according to these findings, we selected two candidate genes, MdHAG1 and MdHAM1, and ectopically expressed them in tobacco to investigate their function in response to drought and low-temperature stress, respectively. The results showed that overexpression of MdHAG1 in tobacco negatively regulated drought tolerance and cold tolerance of transgenic tobacco, and overexpression of MdHAM1 in tobacco improved drought tolerance and cold tolerance of transgenic tobacco. In summary, our study provides a comprehensive analysis of the MdHAT family and insights into the epigenetic mechanisms of histone acetylases under abiotic stress.

{"title":"Genome-wide analysis of apple histone acetyltransferases reveals the regulatory roles of MdHAG1 and MdHAM1 in response to abiotic stresses","authors":"Weiyu Jiang , Furong Hong , Bolin Niu , Hongzhen Zhu , Mengyao Yang , Jinjiao Yan , Jiangbo Wang , Xiaolin Song , Fengwang Ma , Qingmei Guan , Qianming Zheng , Jidi Xu","doi":"10.1016/j.plantsci.2025.112441","DOIUrl":"10.1016/j.plantsci.2025.112441","url":null,"abstract":"<div><div>It is known that histone acetyltransferases (HATs) are involved in a wide range of biological processes by activating gene expression. However, the regulatory role of HATs in apple remains to be elucidated. This study identified 58 <em>HATs</em> from the apple genome (named <em>MdHATs</em>) and performed comprehensive analyses of these <em>MdHATs</em>, given their involvements in plant development and stress response. Firstly, we classified 58 predicted <em>MdHATs</em> into four different categories based on the phylogenetic analyses. Then, the intron/exon structures, conserved motifs, and structural domain organization of <em>MdHAT</em> genes and predicted proteins were further analyzed. Next, we investigated the expression patterns of <em>MdHATs</em> during apple plants' development process and stress responses. Moreover, according to these findings, we selected two candidate genes, <em>MdHAG1</em> and <em>MdHAM1</em>, and ectopically expressed them in tobacco to investigate their function in response to drought and low-temperature stress, respectively. The results showed that overexpression of <em>MdHAG1</em> in tobacco negatively regulated drought tolerance and cold tolerance of transgenic tobacco, and overexpression of <em>MdHAM1</em> in tobacco improved drought tolerance and cold tolerance of transgenic tobacco. In summary, our study provides a comprehensive analysis of the <em>MdHAT</em> family and insights into the epigenetic mechanisms of histone acetylases under abiotic stress.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"355 ","pages":"Article 112441"},"PeriodicalIF":4.2,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Over-expression of XA21 binding protein 3 enhances rice survival under water-deficit stress

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-28 DOI: 10.1016/j.plantsci.2025.112454

Xiaoen Huang , Xiuhua Chen , Satyam Vergish , Xiaodong Ding , Xiaofei Liang , Sixue Chen , Karen Koch , Wen-Yuan Song

E3 ubiquitin ligases have been positively or negatively implicated in the response to water-deficit stress. Here we demonstrate that rice XA21 binding protein 3 (XB3), the founder member of an E3 ubiquitin ligase gene family, is induced by drought stress and, when over-expressed, enhances survival of rice plants under water deficit. Down-regulation of XB3 increases rice sensitivity to drought. The E3 ubiquitin ligase is localized to both the plasma membrane and the nucleus. XB3 interacts with OsDIS1, a nuclear-localized rice ubiquitin ligase playing a negative role in responding to water-deficit stress. Co-expression of XB3 and OsDIS1 in Nicotiana benthamiana leads to a reduced accumulation of OsDIS1. Our data, together with the discoveries made by others, indicate that some members of the XB3 ubiquitin ligase family are positively involved in regulating the response to water deficit possibly through directly or indirectly destabilizing their substrates (e.g., OsDIS1) in the nucleus. Genes in this family could be used for engineering drought tolerance in major food crops.

E3 泛素连接酶与缺水胁迫的反应有积极或消极的联系。在这里，我们证明了水稻 XA21 结合蛋白 3（XB3）是 E3 泛素连接酶基因家族的创始成员，会被干旱胁迫诱导，当其过度表达时，会提高水稻植株在缺水胁迫下的存活率。下调 XB3 可提高水稻对干旱的敏感性。该 E3 泛素连接酶定位于质膜和细胞核。XB3与核定位的水稻泛素连接酶OsDIS1相互作用，OsDIS1在响应缺水胁迫中起负作用。在烟草中共同表达 XB3 和 OsDIS1 会导致 OsDIS1 的积累减少。我们的数据以及其他人的发现表明，XB3 泛素连接酶家族的一些成员可能通过直接或间接地破坏其底物（如 OsDIS1）在细胞核中的稳定性，积极地参与了缺水反应的调节。该家族的基因可用于主要粮食作物的抗旱工程。

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引用次数: 0

The molecular mechanism of transcription factor regulation of grain size in rice

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-27 DOI: 10.1016/j.plantsci.2025.112434

Yanxiu Du, Chun Ye, Peijie Han, Yile Sheng, Fei Li, Hongzheng Sun, Jing Zhang, Junzhou Li

Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.

{"title":"The molecular mechanism of transcription factor regulation of grain size in rice","authors":"Yanxiu Du, Chun Ye, Peijie Han, Yile Sheng, Fei Li, Hongzheng Sun, Jing Zhang, Junzhou Li","doi":"10.1016/j.plantsci.2025.112434","DOIUrl":"10.1016/j.plantsci.2025.112434","url":null,"abstract":"<div><div>Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"354 ","pages":"Article 112434"},"PeriodicalIF":4.2,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Advances in research on the control of pollen tube growth by calcium in higher plants

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-26 DOI: 10.1016/j.plantsci.2025.112436

Yi Hua Lin , Mei Zhen Lin , Hui Qiao Tian , Dong Xiao Li

The function of the pollen tube in higher plants is to deliver two male gametes to the embryo sac to ensure successful double fertilization. During this process, many interactions occur among pollen tubes and pistil cells and tissues. Calcium ion (Ca^2 +) dynamics mediate these interactions to ensure that the pollen tube grows with correct polarity and orientation to reach its target, the embryo sac. The pistil tissue, which contains abundant Ca²⁺, attracts the growing pollen tube via changes in Ca²⁺. Recent studies have shed light on the mechanisms of vacuole biogenesis and the Ca²⁺ action pathway in the growing pollen tube. This successfully explains the distribution characteristics of high Ca²⁺ at the tip of the pollen tube and the physiological mechanism of Ca²⁺ controlling pollen tube growth. In last stage of pollen tube growth, some studies indicated that the cessation of pollen tube growth and breaking of the tube in embryo sac maybe related to Ca²⁺ dynamic, which finishes its complex journey of pollen tube in vivo.

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引用次数: 0

Root-derived small peptides: Key regulators of plant development, stress resilience, and nutrient acquisition

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-26 DOI: 10.1016/j.plantsci.2025.112433

Krishnamurthi Keerthana , Muthusamy Ramakrishnan , Zishan Ahmad , P Amali , Venkatesan Vijayakanth , Qiang Wei

Small peptides (SPs), emerging as crucial signaling molecules in plants, regulate diverse processes such as plant development, stress tolerance, and nutrient acquisition. Consisting of fewer than 100 amino acids, SPs are classified into two main groups: precursor-derived SPs and small open reading frame (sORF)-encoded SPs, including miRNA-encoded SPs. SPs are secreted from various plant parts, with root-derived SPs playing particularly significant roles in stress tolerance and nutrient uptake. Even at low concentrations, root-derived SPs are highly effective signaling molecules that influence the distribution and effects of phytohormones, particularly auxin. For instance, under low phosphorus conditions, CLAVATA3/Embryo-Surrounding Region-Related (CLE/CLV), a root-derived SP, enhances root apical meristem differentiation and root architecture to improve phosphate acquisition. By interacting with CLV2 and PEPR2 receptors, it modulates auxin-related pathways, directing root morphology changes to optimize nutrient uptake. During nitrogen (N) starvation, root-derived SPs are transported to the shoot, where they interact with leucine-rich repeat receptor kinases (LRR-RKs) to alleviate nitrogen deficiency. Similarly, C-terminally Encoded Peptides (CEPs) are involved in primary root growth and N-acquisition responses. Despite the identification of many SPs, countless others remain to be discovered, and the functions of those identified so far remain elusive. This review focuses on the functions of root-derived SPs, such as CLE, CEP, RALF, RGF, PSK, PSY, and DVL, and discusses the receptor-mediated signaling pathways involved. Additionally, it explores the roles of SPs in root architecture, plant development, and their metabolic functions in nutrient signaling.

{"title":"Root-derived small peptides: Key regulators of plant development, stress resilience, and nutrient acquisition","authors":"Krishnamurthi Keerthana , Muthusamy Ramakrishnan , Zishan Ahmad , P Amali , Venkatesan Vijayakanth , Qiang Wei","doi":"10.1016/j.plantsci.2025.112433","DOIUrl":"10.1016/j.plantsci.2025.112433","url":null,"abstract":"<div><div>Small peptides (SPs), emerging as crucial signaling molecules in plants, regulate diverse processes such as plant development, stress tolerance, and nutrient acquisition. Consisting of fewer than 100 amino acids, SPs are classified into two main groups: precursor-derived SPs and small open reading frame (sORF)-encoded SPs, including miRNA-encoded SPs. SPs are secreted from various plant parts, with root-derived SPs playing particularly significant roles in stress tolerance and nutrient uptake. Even at low concentrations, root-derived SPs are highly effective signaling molecules that influence the distribution and effects of phytohormones, particularly auxin. For instance, under low phosphorus conditions, CLAVATA3/Embryo-Surrounding Region-Related (CLE/CLV), a root-derived SP, enhances root apical meristem differentiation and root architecture to improve phosphate acquisition. By interacting with CLV2 and PEPR2 receptors, it modulates auxin-related pathways, directing root morphology changes to optimize nutrient uptake. During nitrogen (N) starvation, root-derived SPs are transported to the shoot, where they interact with leucine-rich repeat receptor kinases (LRR-RKs) to alleviate nitrogen deficiency. Similarly, C-terminally Encoded Peptides (CEPs) are involved in primary root growth and N-acquisition responses. Despite the identification of many SPs, countless others remain to be discovered, and the functions of those identified so far remain elusive. This review focuses on the functions of root-derived SPs, such as CLE, CEP, RALF, RGF, PSK, PSY, and DVL, and discusses the receptor-mediated signaling pathways involved. Additionally, it explores the roles of SPs in root architecture, plant development, and their metabolic functions in nutrient signaling.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"354 ","pages":"Article 112433"},"PeriodicalIF":4.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Intronic alternative polyadenylation in MdMYB1 regulates fruit coloration in apple

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-25 DOI: 10.1016/j.plantsci.2025.112450

Kaixuan Yu , Yaxiao Song , Xiaohu Gao , Yingying Yang , Liya Huang , Jianghong Fu , Huijuan Yang , Xiaofei Wang , Yazhou Yang

MdMYB1 gene plays a crucial role in anthocyanin synthesis in apple, with truncated MdMYB1 transcripts observed in the initial stage of coloration. However, the mechanism underlying the abnormal transcription of MdMYB1 and its role in fruit coloration remains unclear. Two transcript forms, MdMYB1-S and MdMYB1-L were identified through RNA-Seq and qRT-PCR analysis. The non-functional MdMYB1-S exhibited high expression in the initial coloration stage, while MdMYB1-L was predominantly expressed in the late coloration stage. 3′ RACE confirmed that MdMYB1-S transcripts terminated with poly(A) in intron-2nd. Additionally, three transposable elements (TEs) in intron-2nd were highly methylated, and the polyadenylation signal region in this intron demonstrated increasing methylation during fruit development. We hypothesize that intronic alternative polyadenylation (APA) in conjunction with DNA methylation, regulates the transition from MdMYB1-S to MdMYB1-L, thereby promoting fruit coloration.

MdMYB1 基因在苹果花青素合成中起着关键作用，在着色初期可观察到截短的 MdMYB1 转录本。然而，MdMYB1 的异常转录及其在果实着色中的作用的机制仍不清楚。通过 RNA-Seq 和 qRT-PCR 分析，确定了两种转录形式，即 MdMYB1-S 和 MdMYB1-L。无功能的 MdMYB1-S 在着色初期高表达，而 MdMYB1-L 则主要在着色后期表达。3' RACE证实，MdMYB1-S转录本在第2内含子中以poly(A)终止。此外，内含子-2nd 中的三个转座元件（TEs）被高度甲基化，该内含子中的多聚腺苷酸化信号区在果实发育过程中甲基化程度不断增加。我们推测，内含子替代多腺苷酸化（APA）与DNA甲基化相结合，调节了MdMYB1-S向MdMYB1-L的转变，从而促进了果实着色。

{"title":"Intronic alternative polyadenylation in MdMYB1 regulates fruit coloration in apple","authors":"Kaixuan Yu , Yaxiao Song , Xiaohu Gao , Yingying Yang , Liya Huang , Jianghong Fu , Huijuan Yang , Xiaofei Wang , Yazhou Yang","doi":"10.1016/j.plantsci.2025.112450","DOIUrl":"10.1016/j.plantsci.2025.112450","url":null,"abstract":"<div><div><em>MdMYB1</em> gene plays a crucial role in anthocyanin synthesis in apple, with truncated <em>MdMYB1</em> transcripts observed in the initial stage of coloration. However, the mechanism underlying the abnormal transcription of <em>MdMYB1</em> and its role in fruit coloration remains unclear. Two transcript forms, <em>MdMYB1-S</em> and <em>MdMYB1-L</em> were identified through RNA-Seq and qRT-PCR analysis. The non-functional <em>MdMYB1-S</em> exhibited high expression in the initial coloration stage, while <em>MdMYB1-L</em> was predominantly expressed in the late coloration stage. 3′ RACE confirmed that <em>MdMYB1-S</em> transcripts terminated with poly(A) in intron-2nd. Additionally, three transposable elements (TEs) in intron-2nd were highly methylated, and the polyadenylation signal region in this intron demonstrated increasing methylation during fruit development. We hypothesize that intronic alternative polyadenylation (APA) in conjunction with DNA methylation, regulates the transition from <em>MdMYB1-S</em> to <em>MdMYB1-L</em>, thereby promoting fruit coloration.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"354 ","pages":"Article 112450"},"PeriodicalIF":4.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143523960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

CRISPR/dCas9-KRAB mediated transcriptional suppression of NtbHLH47 enhances tolerance to iron stress and modulates iron content in tobacco

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-25 DOI: 10.1016/j.plantsci.2025.112449

Anshu Alok , Hanny Chauhan , Biswaranjan Rout , Ashutosh Pandey , Kashmir Singh

Iron homeostasis is a multifaceted regulatory process that needs to be studied to elucidate iron distribution, uptake, and storage in plants. NtbHLH47, a homologue to AtbHLH47, is a negative regulator of iron. The current study deploys CRISPR interference-dCas9-KRAB (Krüppel-associated box) in the transcriptional suppression of NtbHLH47 and its effect on iron uptake by plants. The pHSN6I01 harbouring dCas9-KRAB and gRNA targeting NtbHHLH47 was constructed. Four gRNAs were designed, G1, G2, G3, and G4, located at + 19, + 111, + 232, and + 335 bp upstream from the ATG start codon in the promoter region of NtbHLH47. The NtbHLH47 was repressed in the developed transgenic lines of tobacco and the qRT-PCR analysis showed that target sites G1 and G2 suppressed NtbHLH47 effectively. The transgenic pHSN6I01 +G1 plants were tolerant to the elevated levels of iron, copper, zinc, and magnesium. The root Ferric chelate reductase activity of pHSN6I01 +G1 lines was reduced against wild type. The Perl staining showed high iron content in the roots of the pHSN6I01 +G1 plants. ICP-MS analysis showed increased Fe content in the roots of pHSN6I01 +G1 line suggesting that NtbHLH47 modulates it. The expression of NtbHLH38, NtbHLH100, NtbHLH101, and NtFIT was found to be upregulated in the pHSN6I01 +G1 line. This is the first report of using CRISPRi based on dCas9-KRAB in tobacco and its application in the functional validation of a gene. Using this, NtbHLH47 was transcriptionally suppressed and the generated lines expressed increased levels of iron in the roots of N. tabacum and gave insight in the iron homeostasis.

{"title":"CRISPR/dCas9-KRAB mediated transcriptional suppression of NtbHLH47 enhances tolerance to iron stress and modulates iron content in tobacco","authors":"Anshu Alok , Hanny Chauhan , Biswaranjan Rout , Ashutosh Pandey , Kashmir Singh","doi":"10.1016/j.plantsci.2025.112449","DOIUrl":"10.1016/j.plantsci.2025.112449","url":null,"abstract":"<div><div>Iron homeostasis is a multifaceted regulatory process that needs to be studied to elucidate iron distribution, uptake, and storage in plants. <em>NtbHLH47,</em> a homologue to <em>AtbHLH47</em>, is a negative regulator of iron. The current study deploys CRISPR interference-dCas9-KRAB (Krüppel-associated box) in the transcriptional suppression of <em>NtbHLH47</em> and its effect on iron uptake by plants. The pHSN6I01 harbouring dCas9-KRAB and gRNA targeting <em>NtbHHLH47</em> was constructed. Four gRNAs were designed, G1, G2, G3, and G4, located at + 19, + 111, + 232, and + 335 bp upstream from the ATG start codon in the promoter region of <em>NtbHLH47</em>. The <em>NtbHLH47</em> was repressed in the developed transgenic lines of tobacco and the qRT-PCR analysis showed that target sites G1 and G2 suppressed <em>NtbHLH47</em> effectively. The transgenic pHSN6I01 +G1 plants were tolerant to the elevated levels of iron, copper, zinc, and magnesium. The root Ferric chelate reductase activity of pHSN6I01 +G1 lines was reduced against wild type. The Perl staining showed high iron content in the roots of the pHSN6I01 +G1 plants. ICP-MS analysis showed increased Fe content in the roots of pHSN6I01 +G1 line suggesting that <em>NtbHLH47</em> modulates it. The expression of <em>NtbHLH38, NtbHLH100, NtbHLH101,</em> and <em>NtFIT</em> was found to be upregulated in the pHSN6I01 +G1 line. This is the first report of using CRISPRi based on dCas9-KRAB in tobacco and its application in the functional validation of a gene. Using this, <em>NtbHLH47</em> was transcriptionally suppressed and the generated lines expressed increased levels of iron in the roots of <em>N. tabacum</em> and gave insight in the iron homeostasis.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"354 ","pages":"Article 112449"},"PeriodicalIF":4.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

SmGRAS5 acts as a positive regulator in GA-induced biosynthesis of tanshinones in Salvia miltiorrhiza hairy roots

IF 4.2 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Plant Science

Pub Date : 2025-02-24 DOI: 10.1016/j.plantsci.2025.112440

Wenrui Li , Suyu Lin , Ruihong Wang , Chen Chen , Qiliang Huang , Feng Ling , Zongsuo Liang

GA is an important phytohormone that regulates root growth and secondary metabolism. GRAS family transcription factors (TFs) are the key regulators of GA signaling. Here, we found that SmGRAS5 was co-expressed in the root periderm with tanshinones in Salvia miltiorrhiza. Overexpression (OE) of SmGRAS5 increased tanshinones accumulation and upregulated the biosynthetic genes. Antisense expression (AE) of SmGRAS5 reduced tanshinones accumulation and downregulated the biosynthetic genes. Yeast one-hybrid (Y1H), dual-luciferase (Dual-LUC), and electrophoretic mobility shift assays (EMSA) showed that SmGRAS5 promoted tanshinones biosynthesis by directly binding to the GARE motif in the promoter of SmKSL1 to induce its expression. However, overexpressing SmGRAS5 reduced GA content through downregulating the biosynthetic genes and also reduced root biomass. GA treatment further increased tanshinones accumulation and restored the root growth inhibited by overexpressing SmGRAS5. SmGRAS5 could not directly bind to the GA biosynthetic genes. Transcriptome analysis revealed the potential functions of SmGRAS5 in regulating secondary metabolism. Taken together, SmGRAS5 is involved in the regulation of GA-promoted tanshinones biosynthesis by directly activating the expression of SmKSL1, which suggests that SmGRAS5 may be a potential target for further metabolic engineering of tanshinones biosynthesis in S. miltiorrhiza.

{"title":"SmGRAS5 acts as a positive regulator in GA-induced biosynthesis of tanshinones in Salvia miltiorrhiza hairy roots","authors":"Wenrui Li , Suyu Lin , Ruihong Wang , Chen Chen , Qiliang Huang , Feng Ling , Zongsuo Liang","doi":"10.1016/j.plantsci.2025.112440","DOIUrl":"10.1016/j.plantsci.2025.112440","url":null,"abstract":"<div><div>GA is an important phytohormone that regulates root growth and secondary metabolism. GRAS family transcription factors (TFs) are the key regulators of GA signaling. Here, we found that <em>SmGRAS5</em> was co-expressed in the root periderm with tanshinones in <em>Salvia miltiorrhiza</em>. Overexpression (OE) of <em>SmGRAS5</em> increased tanshinones accumulation and upregulated the biosynthetic genes. Antisense expression (AE) of <em>SmGRAS5</em> reduced tanshinones accumulation and downregulated the biosynthetic genes. Yeast one-hybrid (Y1H), dual-luciferase (Dual-LUC), and electrophoretic mobility shift assays (EMSA) showed that SmGRAS5 promoted tanshinones biosynthesis by directly binding to the GARE motif in the promoter of <em>SmKSL1</em> to induce its expression. However, overexpressing <em>SmGRAS5</em> reduced GA content through downregulating the biosynthetic genes and also reduced root biomass. GA treatment further increased tanshinones accumulation and restored the root growth inhibited by overexpressing <em>SmGRAS5</em>. SmGRAS5 could not directly bind to the GA biosynthetic genes. Transcriptome analysis revealed the potential functions of SmGRAS5 in regulating secondary metabolism. Taken together, SmGRAS5 is involved in the regulation of GA-promoted tanshinones biosynthesis by directly activating the expression of <em>SmKSL1</em>, which suggests that SmGRAS5 may be a potential target for further metabolic engineering of tanshinones biosynthesis in <em>S. miltiorrhiza</em>.</div></div>","PeriodicalId":20273,"journal":{"name":"Plant Science","volume":"354 ","pages":"Article 112440"},"PeriodicalIF":4.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143512308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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