O-methyltransferases (OMTs) are group of enzymes involved in the methylation of various secondary metabolites, including anthocyanins. This secondary modification, together with hydroxylation and glycosylation, affects the chromatic properties, stability and reactivity of these pigments. Meanwhile, no detailed identification or genome-wide analysis of the OMT gene family members in potato (Solanum tuberosum) has been reported. We conducted a genome-wide identification and characterization of potato OMTs, identifying 65 OMT family members. These were characterized based on gene structure, evolutionary relationships, and promoter motifs. Analysis of available gene expression profiles from public databases revealed expression patterns indicative of tissue- and temporal-specificity Finally, we further elucidated expression differences among four selected OMT-encoding genes using potato cell cultures, which represent a smart and gainful alternative for anthocyanin production and deep knowledge about these post-biosynthetic modifications.
o -甲基转移酶（OMTs）是一组参与各种次生代谢产物甲基化的酶，包括花青素。这种二级修饰，连同羟基化和糖基化，影响这些颜料的着色性能、稳定性和反应性。同时，马铃薯（Solanum tuberosum） OMT基因家族成员的详细鉴定和全基因组分析尚未见报道。我们对马铃薯OMT进行了全基因组鉴定和表征，鉴定了65个OMT家族成员。这些是基于基因结构、进化关系和启动子基序来鉴定的。通过对公共数据库中可用基因表达谱的分析，揭示了组织特异性和时间特异性的表达模式。最后，我们利用马铃薯细胞培养进一步阐明了四个选定的omt编码基因之间的表达差异，这代表了花青素生产的一个聪明而有益的选择，并深入了解了这些生物合成后修饰。
{"title":"Genome-wide characterization of the anthocyanin O-methyltransferases in the cultivated potato","authors":"Annalisa Staiti , Carmine Fruggiero , Domenico Carputo , Vincenzo D’Amelia , Nunzio D’Agostino","doi":"10.1016/j.plgene.2025.100506","DOIUrl":"10.1016/j.plgene.2025.100506","url":null,"abstract":"<div><div><em>O</em>-methyltransferases (OMTs) are group of enzymes involved in the methylation of various secondary metabolites, including anthocyanins. This secondary modification, together with hydroxylation and glycosylation, affects the chromatic properties, stability and reactivity of these pigments. Meanwhile, no detailed identification or genome-wide analysis of the OMT gene family members in potato (<em>Solanum tuberosum</em>) has been reported. We conducted a genome-wide identification and characterization of potato OMTs, identifying 65 OMT family members. These were characterized based on gene structure, evolutionary relationships, and promoter motifs. Analysis of available gene expression profiles from public databases revealed expression patterns indicative of tissue- and temporal-specificity Finally, we further elucidated expression differences among four selected OMT-encoding genes using potato cell cultures, which represent a smart and gainful alternative for anthocyanin production and deep knowledge about these post-biosynthetic modifications.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100506"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820948","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 : 2025-04-03DOI: 10.1016/j.plgene.2025.100504
Minghua Lv, Ting Deng, Jiahong Cao, Xinyu Zhang, Fangfang Cai, Jun Mei, Dongliang Yu, Yuqiang Sun
Cotton fibers are among the most important natural fibers worldwide. Developing natural colored cotton (NCC) varieties is crucial for cotton fiber utilization due to their eco-friendly properties. Manipulation of anthocyanin synthesis is an effective strategy for creating novel NCCs. Our previous research revealed enhanced anthocyanin accumulation in an empurpled Gossypium hirsutum mutant, HS2, but the regulatory mechanism has not been fully elucidated. In this study, we employed an integrated analysis of RNA sequencing, small RNA (sRNA) sequencing, and degradome sequencing to assess the expression patterns and potential roles of sRNAs in the development of the empurpled phenotype in HS2. Our findings revealed that the expression profiles of sRNAs are highly similar between the wild type and the mutant, with only 11 miRNAs and 761 siRNAs showing significant expression variation. Eight miRNAs and one siRNA exhibited inverse regulation with their targets, which were not directly involved in regulating anthocyanin biosynthesis. Notably, degradome data analysis identified interactions between miR395 and ATP sulfurylase genes (APS1 and APS3). Further assessment determined down-regulation of miR395 and up-regulation of APS genes in HS2, as well as the enhanced biosynthesis of cysteine and glutathione. These results suggest that miRNA mediated post-transcriptional regulation might not be the primary mechanism driving anthocyanin enhancement in HS2. Instead, the miR395-APS modules are possibly involved in modulating cellular processes to cope with the increased anthocyanin levels. Overall, this study deepens our understanding of the molecular mechanisms underlying the empurpled phenotype in HS2 and facilitates its future use in NCC breeding.
{"title":"Deciphering the role of small RNAs in the development of empurpled phenotypes in the Gossypium hirsutum mutant HS2","authors":"Minghua Lv, Ting Deng, Jiahong Cao, Xinyu Zhang, Fangfang Cai, Jun Mei, Dongliang Yu, Yuqiang Sun","doi":"10.1016/j.plgene.2025.100504","DOIUrl":"10.1016/j.plgene.2025.100504","url":null,"abstract":"<div><div>Cotton fibers are among the most important natural fibers worldwide. Developing natural colored cotton (NCC) varieties is crucial for cotton fiber utilization due to their eco-friendly properties. Manipulation of anthocyanin synthesis is an effective strategy for creating novel NCCs. Our previous research revealed enhanced anthocyanin accumulation in an empurpled <em>Gossypium hirsutum</em> mutant, <em>HS2</em>, but the regulatory mechanism has not been fully elucidated. In this study, we employed an integrated analysis of RNA sequencing, small RNA (sRNA) sequencing, and degradome sequencing to assess the expression patterns and potential roles of sRNAs in the development of the empurpled phenotype in <em>HS2</em>. Our findings revealed that the expression profiles of sRNAs are highly similar between the wild type and the mutant, with only 11 miRNAs and 761 siRNAs showing significant expression variation. Eight miRNAs and one siRNA exhibited inverse regulation with their targets, which were not directly involved in regulating anthocyanin biosynthesis. Notably, degradome data analysis identified interactions between miR395 and ATP sulfurylase genes (<em>APS1</em> and <em>APS3</em>). Further assessment determined down-regulation of miR395 and up-regulation of <em>APS</em> genes in <em>HS2</em>, as well as the enhanced biosynthesis of cysteine and glutathione. These results suggest that miRNA mediated post-transcriptional regulation might not be the primary mechanism driving anthocyanin enhancement in <em>HS2</em>. Instead, the miR395-<em>APS</em> modules are possibly involved in modulating cellular processes to cope with the increased anthocyanin levels. Overall, this study deepens our understanding of the molecular mechanisms underlying the empurpled phenotype in <em>HS2</em> and facilitates its future use in NCC breeding.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100504"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792513","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 : 2025-04-03DOI: 10.1016/j.plgene.2025.100511
Xiaozeng Mi , Dahe Qiao , Yanlin An , Chun Yang , Kaiqin Lin , Congling Peng , Juan Chen
As one of the most important agronomic traits of the tea plant (Camellia sinensis), the timing of bud flush (TBF) affects the sales price of tea beverages. Here, we performed specific-locus amplified fragment (SLAF) sequencing and genome-wide association study (GWAS) analysis on 200 offspring of natural hybridization from the ‘Qianmei 601’. A total of 796,294 SLAF tags and 2,324,211 single-nucleotide polymorphisms (SNPs) were obtained by sequencing. The 200 tea germplasms were clustered into four groups by population structure, principal component analysis (PCA) and phylogenetic tree analysis. GWAS identified twelve SNPs loci that were significantly associated with TBF traits. Seven candidate genes associated with TBF were subsequently identified by scanning in the regions within 1 Mb SNP loci. In addition, we found that two candidate genes (ARP and WRKY) were highly expressed in individuals with early TBF. Interestingly, cloning and sequencing of the ARP gene revealed C-G variants between the early and late TBF individuals. Our results provide a theoretical basis for early TBF breeding and functional gene analysis in tea plants.
{"title":"Genome-wide association study of tea plant based on SLAF-seq revealed SNP variations regulating timing of bud flush","authors":"Xiaozeng Mi , Dahe Qiao , Yanlin An , Chun Yang , Kaiqin Lin , Congling Peng , Juan Chen","doi":"10.1016/j.plgene.2025.100511","DOIUrl":"10.1016/j.plgene.2025.100511","url":null,"abstract":"<div><div>As one of the most important agronomic traits of the tea plant (<em>Camellia sinensis</em>), the timing of bud flush (TBF) affects the sales price of tea beverages. Here, we performed specific-locus amplified fragment (SLAF) sequencing and genome-wide association study (GWAS) analysis on 200 offspring of natural hybridization from the ‘Qianmei 601’. A total of 796,294 SLAF tags and 2,324,211 single-nucleotide polymorphisms (SNPs) were obtained by sequencing. The 200 tea germplasms were clustered into four groups by population structure, principal component analysis (PCA) and phylogenetic tree analysis. GWAS identified twelve SNPs loci that were significantly associated with TBF traits. Seven candidate genes associated with TBF were subsequently identified by scanning in the regions within 1 Mb SNP loci. In addition, we found that two candidate genes (<em>ARP</em> and <em>WRKY</em>) were highly expressed in individuals with early TBF. Interestingly, cloning and sequencing of the <em>ARP</em> gene revealed C-G variants between the early and late TBF individuals. Our results provide a theoretical basis for early TBF breeding and functional gene analysis in tea plants.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100511"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792514","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}
Located in the highest and coldest region of north-eastern Türkiye, the province of Kars boasts a remarkable floral diversity, accounting for 16 % of the country's flora with 1615 plant species identified. This region represents the Caucasian lands of Türkiye and serves as a transition point between the Iranian-Turkish, European-Siberian and Mediterranean floral regions. Despite its considerable botanical wealth of the province, the flora of Kars Province remains poorly documented in the scientific literature. The aim of this research was to provide the molecular identity of 14 endemic plant species in the province using DNA-based methods. Three universal DNA barcode genes—trnH-psbA (non-coding spacer region), ribulose-1,5-bisphosphate carboxylase large subunit (rbcL), and maturase K (matK)—were sequenced to facilitate accurate identification. The endemic plant species were correctly identified to genus and species level based on the presence of the corresponding sequence of the investigated gene regions. By submitting 36 new barcodes to the NCBI database, this study contributes valuable genetic resources for future research in plant genetic studies. The findings highlight the potential of DNA barcoding to improve our understanding of plant diversity and to inform conservation efforts in the Caucasus region. The research not only contributes to our knowledge of Türkiye's plant diversity, but also advances the global discourse on genetic, taxonomic, ecological and biodiversity research dedicated to the conservation of endemic species in their natural habitats.
{"title":"Molecular identification of endemic plant species in Kars Province based on universal barcode gene regions","authors":"Asiye Uluğ , Funda Özdemir Değirmenci , Gül Esma Akdoğan","doi":"10.1016/j.plgene.2025.100514","DOIUrl":"10.1016/j.plgene.2025.100514","url":null,"abstract":"<div><div>Located in the highest and coldest region of north-eastern Türkiye, the province of Kars boasts a remarkable floral diversity, accounting for 16 % of the country's flora with 1615 plant species identified. This region represents the Caucasian lands of Türkiye and serves as a transition point between the Iranian-Turkish, European-Siberian and Mediterranean floral regions. Despite its considerable botanical wealth of the province, the flora of Kars Province remains poorly documented in the scientific literature. The aim of this research was to provide the molecular identity of 14 endemic plant species in the province using DNA-based methods. Three universal DNA barcode genes—<em>trnH-psbA</em> (non-coding spacer region), ribulose-1,5-bisphosphate carboxylase large subunit (<em>rbcL</em>), and maturase K (<em>matK</em>)—were sequenced to facilitate accurate identification. The endemic plant species were correctly identified to genus and species level based on the presence of the corresponding sequence of the investigated gene regions. By submitting 36 new barcodes to the NCBI database, this study contributes valuable genetic resources for future research in plant genetic studies. The findings highlight the potential of DNA barcoding to improve our understanding of plant diversity and to inform conservation efforts in the Caucasus region. The research not only contributes to our knowledge of Türkiye's plant diversity, but also advances the global discourse on genetic, taxonomic, ecological and biodiversity research dedicated to the conservation of endemic species in their natural habitats.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100514"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785384","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 : 2025-04-03DOI: 10.1016/j.plgene.2025.100509
Franklin Alongi , Anja Petek-Petrik , Mohammad Mukarram , Hülya Torun , Bernhard Schuldt , Peter Petrík
Drought stress memory in plants is an adaptive mechanism that enhances resilience to future water stress through physiological and molecular modifications triggered by previous drought events. This review explores somatic drought stress memory within a plant's lifespan, with a specific focus on leaf and stomatal morphology, minimum leaf conductance, photosynthetic efficiency, water-use efficiency, antioxidant capacity, and leaf senescence. We examine how epigenetic mechanisms—such as DNA methylation, histone modifications, and non-coding RNAs—regulate gene expression in coordination with hormonal signalling pathways. Phytohormones, including abscisic acid, jasmonic acid, ethylene, salicylic acid, auxins and cytokinins, are central to these processes, influencing key morphological and physiological adaptations, such as stomatal regulation, cuticle thickness, water retention, and improved water-use efficiency. The review synthesizes current knowledge on the molecular and hormonal networks underlying these adaptations and their impact on leaf architecture and metabolism. Despite advancements, critical gaps remain in identifying the specific genes and pathways involved, understanding the longevity of epigenetic marks, and elucidating the intricate cross-talk between phytohormones during drought stress memory. This review emphasizes the need for integrated -omics approaches to map epigenetic modifications and uncover their roles in developing drought-resistant plants through targeted stress priming strategies.
{"title":"Somatic drought stress memory affects leaf morpho-physiological traits of plants via epigenetic mechanisms and phytohormonal signalling","authors":"Franklin Alongi , Anja Petek-Petrik , Mohammad Mukarram , Hülya Torun , Bernhard Schuldt , Peter Petrík","doi":"10.1016/j.plgene.2025.100509","DOIUrl":"10.1016/j.plgene.2025.100509","url":null,"abstract":"<div><div>Drought stress memory in plants is an adaptive mechanism that enhances resilience to future water stress through physiological and molecular modifications triggered by previous drought events. This review explores somatic drought stress memory within a plant's lifespan, with a specific focus on leaf and stomatal morphology, minimum leaf conductance, photosynthetic efficiency, water-use efficiency, antioxidant capacity, and leaf senescence. We examine how epigenetic mechanisms—such as DNA methylation, histone modifications, and non-coding RNAs—regulate gene expression in coordination with hormonal signalling pathways. Phytohormones, including abscisic acid, jasmonic acid, ethylene, salicylic acid, auxins and cytokinins, are central to these processes, influencing key morphological and physiological adaptations, such as stomatal regulation, cuticle thickness, water retention, and improved water-use efficiency. The review synthesizes current knowledge on the molecular and hormonal networks underlying these adaptations and their impact on leaf architecture and metabolism. Despite advancements, critical gaps remain in identifying the specific genes and pathways involved, understanding the longevity of epigenetic marks, and elucidating the intricate cross-talk between phytohormones during drought stress memory. This review emphasizes the need for integrated -omics approaches to map epigenetic modifications and uncover their roles in developing drought-resistant plants through targeted stress priming strategies.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100509"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143785385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-04-03DOI: 10.1016/j.plgene.2025.100512
Abdel Hamid A. Khedr , Mamdouh S. Serag , Haneen A. Abdulsamad , Reham M. Nada
One of the potential routes for improving the stress tolerance of crops is discovering the tolerance mechanisms of halophytes. Cakile maritima and Brassica tournefortii were collected from four sites with different salinity levels. Two populations for each species were collected from each site. The populations of C. maritima had different phenotypic traits, especially at high salinity levels. Meanwhile, the populations of B. tournefortii had approximately similar phenotypic traits at all sites. The present study aimed to compare the tolerance strategies used by C. maritima and B. tournefortii by examining the responses of different populations of each species to high salinity levels in their natural habitats. The evolutionary relationship among the populations of each species was recorded. Growth performance, pigment concentration, Rubisco protein content, ion concentration and regulation of salt-inducible genes were evaluated. At high salinity levels, the biomass of most C. maritima populations increased, but the reverse was true for B. tournefortii populations. The acclimation of B. tournefortii to salt stress depends on Na+ extrusion mechanisms. Meanwhile, C. maritima acclimated by a regulated and controlled ion uptake, regulated salt-inducible genes and efficient use of Na+ in osmotic adjustment. Hierarchical analysis revealed that the expression pattern of Na+-inducible genes was not only species-dependent but also organ-dependent. The expression pattern did not correspond to the profiles of promoter regulatory motifs of the examined genes. The study concluded that the tolerance mechanisms are not static among halophytes, but they are dependent on the species and even on the population of a species.
提高作物抗逆性的潜在途径之一是发现盐生植物的抗逆机制。从盐度不同的四个地点收集了 Cakile maritima 和 Brassica tournefortii。每个地点采集了两个种群。C. maritima 的种群具有不同的表型特征，尤其是在高盐度水平下。与此同时，B. tournefortii 种群在所有地点的表型特征大致相似。本研究旨在通过研究 C. maritima 和 B. tournefortii 的不同种群在其自然栖息地对高盐度的反应，比较它们所采用的耐盐策略。记录了每个物种种群之间的进化关系。评估了生长性能、色素浓度、Rubisco 蛋白含量、离子浓度和盐诱导基因的调控。在高盐度条件下，大多数 C. maritima 种群的生物量增加，但 B. tournefortii 种群的生物量则相反。B. tournefortii对盐胁迫的适应取决于Na+挤出机制。与此同时，C. maritima 通过调节和控制离子吸收、调节盐诱导基因以及在渗透调节中有效利用 Na+ 来适应盐胁迫。层次分析表明，Na+诱导基因的表达模式不仅与物种有关，而且与器官有关。这种表达模式与所研究基因的启动子调控基团的轮廓并不一致。研究得出的结论是，卤叶植物的耐受机制并非一成不变，而是取决于物种，甚至取决于物种的种群。
{"title":"Regulation of sodium-inducible genes and efficient use of sodium ions determine the tolerance strategies of Cakile maritima and Brassica tournefortii in natural habitats","authors":"Abdel Hamid A. Khedr , Mamdouh S. Serag , Haneen A. Abdulsamad , Reham M. Nada","doi":"10.1016/j.plgene.2025.100512","DOIUrl":"10.1016/j.plgene.2025.100512","url":null,"abstract":"<div><div>One of the potential routes for improving the stress tolerance of crops is discovering the tolerance mechanisms of halophytes. <em>Cakile maritima</em> and <em>Brassica tournefortii</em> were collected from four sites with different salinity levels. Two populations for each species were collected from each site. The populations of <em>C. maritima</em> had different phenotypic traits, especially at high salinity levels. Meanwhile, the populations of <em>B. tournefortii</em> had approximately similar phenotypic traits at all sites. The present study aimed to compare the tolerance strategies used by <em>C. maritima</em> and <em>B. tournefortii</em> by examining the responses of different populations of each species to high salinity levels in their natural habitats. The evolutionary relationship among the populations of each species was recorded. Growth performance, pigment concentration, Rubisco protein content, ion concentration and regulation of salt-inducible genes were evaluated. At high salinity levels, the biomass of most <em>C. maritima</em> populations increased, but the reverse was true for <em>B. tournefortii</em> populations. The acclimation of <em>B. tournefortii</em> to salt stress depends on Na<sup>+</sup> extrusion mechanisms. Meanwhile, <em>C. maritima</em> acclimated by a regulated and controlled ion uptake, regulated salt-inducible genes and efficient use of Na<sup>+</sup> in osmotic adjustment. Hierarchical analysis revealed that the expression pattern of Na<sup>+</sup>-inducible genes was not only species-dependent but also organ-dependent. The expression pattern did not correspond to the profiles of promoter regulatory motifs of the examined genes. The study concluded that the tolerance mechanisms are not static among halophytes, but they are dependent on the species and even on the population of a species.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100512"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835255","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}
Baccaurea ramiflora Lour. (Burmese grape), a wild fruit tree with edible, ornamental, and medicinal qualities. The mechanism behind the color accumulation in its fruit pulp, which can be either pink or milky-white, remains unclear. This study investigates the metabolome and transcriptome of two B. ramiflora pulp types—LR (milky-white at maturity) and BR (pink at maturity)—to elucidate their coloration processes. We identified 35 flavonoids, including nine involved in the anthocyanin synthesis pathway, confirming cyanidin as the pivotal pigment for the pink pulp coloration. An examination of the flavonoid and anthocyanin biosynthetic pathways in B. ramiflora pulp uncovered 39 differentially expressed genes associated with structural genes. The genes F3′5′H and UFGT exhibited high expression levels in the first two developmental stages of BR, significantly more than in LR, and were almost non-existent in later stages, signifying their crucial role in the differential color accumulation between BR and LR pulps. Additionally, the expression levels of CHI and FLS, early-stage structural genes in the anthocyanin synthesis pathway, correlated with the concentrations of naringenin and quercetin, indicating their importance in the anthocyanin biosynthesis pathway of B. ramiflora pulp. These discoveries provide new insights that could facilitate the breeding of B. ramiflora varieties with diverse pulp colors.
{"title":"Integrated metabolomic and transcriptomic insights into the role of anthocyanin and flavonoid biosynthesis in the pulp coloration mechanisms of Baccaurea ramiflora Lour. (Burmese grape)","authors":"Jianjian Huang , Jie Chen , Hui Zhu , Yuzhong Zheng , Xueying Wen , Suying Cai , Yingchun Zhu , Mo Ding , Qinghan Wu , Zikai Chen , Fengnian Wu","doi":"10.1016/j.plgene.2025.100510","DOIUrl":"10.1016/j.plgene.2025.100510","url":null,"abstract":"<div><div><em>Baccaurea ramiflora</em> Lour. (Burmese grape), a wild fruit tree with edible, ornamental, and medicinal qualities. The mechanism behind the color accumulation in its fruit pulp, which can be either pink or milky-white, remains unclear. This study investigates the metabolome and transcriptome of two <em>B. ramiflora</em> pulp types—LR (milky-white at maturity) and BR (pink at maturity)—to elucidate their coloration processes. We identified 35 flavonoids, including nine involved in the anthocyanin synthesis pathway, confirming cyanidin as the pivotal pigment for the pink pulp coloration. An examination of the flavonoid and anthocyanin biosynthetic pathways in <em>B. ramiflora</em> pulp uncovered 39 differentially expressed genes associated with structural genes. The genes <em>F3′5′H</em> and <em>UFGT</em> exhibited high expression levels in the first two developmental stages of BR, significantly more than in LR, and were almost non-existent in later stages, signifying their crucial role in the differential color accumulation between BR and LR pulps. Additionally, the expression levels of <em>CHI</em> and <em>FLS</em>, early-stage structural genes in the anthocyanin synthesis pathway, correlated with the concentrations of naringenin and quercetin, indicating their importance in the anthocyanin biosynthesis pathway of <em>B. ramiflora</em> pulp. These discoveries provide new insights that could facilitate the breeding of <em>B. ramiflora</em> varieties with diverse pulp colors.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100510"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143800256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-26DOI: 10.1016/j.plgene.2025.100502
Sandip Pal , Dip Pal , Rup Kumar Kar , Debasish Panda , Pradip Chandra Dey , Narottam Dey
Despite the availability of flood-tolerant genotypes with Sub1a-mediated elongation, SK has been depicted as the primary gene responsible for elongation under prolonged submergence. However, the combined role of both loci (Sub1a and SK) are prerequisites for the survival of rice plants under flash floods followed by stagnant floods that are yet to be revealed. The combinatorial action of Sub1a and SK in a selected group of lowland rice with the simultaneous presence of both loci were studied for their physio-biochemical performance under induced flash flood followed by water stagnation for 21 days. Among the lines, var. Ganga Sali showed elongation and Kalapatia showed quiescence growth with varied degrees of aerenchyma formation. Further, it was endorsed that var. Ganga Sali showed the highest enzymatic activity of ADH and minimal for PDC under submerged conditions. RT PCR-based expression analysis of Sub1a, SK1, SK2, adh1, pdc1, and susy1 genetic loci under differential submergence showed a mixed response to the depth and duration of the induced flood, among which Sub1a and SK2 showed distinct differences between normal and test plant tissue. From expression analysis, the differential activity of Sub1a and SK2 was recorded, which showed that during the onset of flood, Sub1a starts to express in both the var. Ganga Sali and var. Kalapatia, but as the flood prevails for a longer period, the expression of Sub1a is masked by both SK1 and SK2. Overall, the study demonstrates the combinatorial role of both the genes in two studied rice lines under different flood regimes and their effect on phenotype. The present work may be the first report on the combinatorial expression of Sub1a and SK under differentially induced submergence on a mixed rice population.
尽管存在具有sub1a介导的伸长的耐洪水基因型，但SK已被描述为在长时间淹没下负责伸长的主要基因。然而，这两个基因座（Sub1a和SK）的联合作用是水稻在山洪暴发后的滞洪中存活的先决条件，这一点尚未被揭示。选取同时存在Sub1a和SK基因座的水稻为研究对象，研究了这两个基因座在山洪诱导下的生理生化性能。其中Ganga Sali品种表现为伸长，Kalapatia品种表现为静止生长，并形成不同程度的通气组织。此外，在淹没条件下，var. Ganga Sali的ADH酶活性最高，而PDC酶活性最低。基于RT - pcr的差异淹水条件下Sub1a、SK1、SK2、adh1、pdc1和susy1基因位点的表达分析显示，不同淹水条件下，Sub1a、pdc1和susy1基因位点的表达对诱导淹水的深度和持续时间有不同的响应，其中Sub1a和SK2基因位点在正常和受试植物组织中表现出明显差异。从表达分析来看，记录了Sub1a和SK2的差异活性，表明在洪水开始时，Sub1a在Ganga Sali和Kalapatia中都开始表达，但随着洪水持续时间的延长，Sub1a的表达被SK1和SK2掩盖。总之，本研究证明了这两个基因在不同洪水条件下的组合作用及其对表型的影响。本研究可能是首次报道了Sub1a和SK在不同诱导淹没条件下在混合水稻群体上的组合表达。
{"title":"Coetaneous activity of Sub1a and SK for maintenance of underwater growth in rice genotypes","authors":"Sandip Pal , Dip Pal , Rup Kumar Kar , Debasish Panda , Pradip Chandra Dey , Narottam Dey","doi":"10.1016/j.plgene.2025.100502","DOIUrl":"10.1016/j.plgene.2025.100502","url":null,"abstract":"<div><div>Despite the availability of flood-tolerant genotypes with <em>Sub1a-</em>mediated elongation, <em>SK</em> has been depicted as the primary gene responsible for elongation under prolonged submergence. However, the combined role of both loci (<em>Sub1a</em> and <em>SK</em>) are prerequisites for the survival of rice plants under flash floods followed by stagnant floods that are yet to be revealed. The combinatorial action of <em>Sub1a</em> and <em>SK</em> in a selected group of lowland rice with the simultaneous presence of both loci were studied for their physio-biochemical performance under induced flash flood followed by water stagnation for 21 days. Among the lines, var. Ganga Sali showed elongation and Kalapatia showed quiescence growth with varied degrees of aerenchyma formation. Further, it was endorsed that var. Ganga Sali showed the highest enzymatic activity of ADH and minimal for PDC under submerged conditions. RT PCR-based expression analysis of <em>Sub1a, SK1, SK2, adh1, pdc1, and susy1</em> genetic loci under differential submergence showed a mixed response to the depth and duration of the induced flood, among which <em>Sub1a</em> and <em>SK2</em> showed distinct differences between normal and test plant tissue. From expression analysis, the differential activity of <em>Sub1a</em> and <em>SK2</em> was recorded, which showed that during the onset of flood, <em>Sub1a</em> starts to express in both the var. Ganga Sali and var. Kalapatia, but as the flood prevails for a longer period, the expression of <em>Sub1a</em> is masked by both <em>SK1</em> and <em>SK2</em>. Overall, the study demonstrates the combinatorial role of both the genes in two studied rice lines under different flood regimes and their effect on phenotype. The present work may be the first report on the combinatorial expression of <em>Sub1a</em> and <em>SK</em> under differentially induced submergence on a mixed rice population.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100502"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143760245","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}
Sorghum (Sorghum bicolor (L.) Moench) is a climate-resilient cereal vital for food security, especially in arid and semi-arid regions. Understanding the molecular characterization of sorghum mutant genotypes is crucial for crop improvement, yet their genetic diversity and population structure remain poorly understood. This study assessed 190 randomly selected mutant genotypes from 2000 M2 lines generated via Ethyl Methanesulfonate (EMS) treatment, alongside two parental lines, using 10 Simple Sequence Repeat (SSR) markers. Key diversity metrics, including polymorphic information content (PIC), genetic diversity (GD), and allelic richness (Ar), were analyzed. The SSR analysis revealed significant polymorphism, with mean values of 0.84 (PIC), 0.83 (GD), and 6.41 (Ar), indicating substantial genetic variation. Analysis of Molecular Variance (AMOVA) showed that 97 % of genetic variation occurred among individuals, with only 2 % and 1 % attributed to population and within-individual variations, respectively. The high within-population variation suggests extensive genetic diversity due to mutagenesis and selection. Despite this, moderate population divergence was observed, indicating genetic relatedness among groups. Cluster analysis identified two distinct genetic groups, with most clusters containing mutants from both parental lines, reflecting shared ancestry. Several mutants with high genetic diversity were identified as promising candidates for multi-location agronomic trials, particularly for drought resilience and yield stability. These findings highlight the potential of these genotypes for breeding programs aimed at enhancing sorghum resilience and productivity.
{"title":"Genetic Diversity and Population Structure of Sorghum mutant genotypes revealed through genetic Characterization","authors":"Abera Takele , Tesfaye Disasa , Tileye Feyissa , Alemu Lencho , Chemeda Birhanu","doi":"10.1016/j.plgene.2025.100501","DOIUrl":"10.1016/j.plgene.2025.100501","url":null,"abstract":"<div><div>Sorghum (<em>Sorghum bicolor</em> (L.) Moench) is a climate-resilient cereal vital for food security, especially in arid and semi-arid regions. Understanding the molecular characterization of sorghum mutant genotypes is crucial for crop improvement, yet their genetic diversity and population structure remain poorly understood. This study assessed 190 randomly selected mutant genotypes from 2000 M<sub>2</sub> lines generated via Ethyl Methanesulfonate (EMS) treatment, alongside two parental lines, using 10 Simple Sequence Repeat (SSR) markers. Key diversity metrics, including polymorphic information content (PIC), genetic diversity (GD), and allelic richness (Ar), were analyzed. The SSR analysis revealed significant polymorphism, with mean values of 0.84 (PIC), 0.83 (GD), and 6.41 (Ar), indicating substantial genetic variation. Analysis of Molecular Variance (AMOVA) showed that 97 % of genetic variation occurred among individuals, with only 2 % and 1 % attributed to population and within-individual variations, respectively. The high within-population variation suggests extensive genetic diversity due to mutagenesis and selection. Despite this, moderate population divergence was observed, indicating genetic relatedness among groups. Cluster analysis identified two distinct genetic groups, with most clusters containing mutants from both parental lines, reflecting shared ancestry. Several mutants with high genetic diversity were identified as promising candidates for multi-location agronomic trials, particularly for drought resilience and yield stability. These findings highlight the potential of these genotypes for breeding programs aimed at enhancing sorghum resilience and productivity.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100501"},"PeriodicalIF":2.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143704785","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 : 2025-03-17DOI: 10.1016/j.plgene.2025.100500
Lei-Ming Liu , Chuan-Bo Jiang , Yi-Lin Yang , Tian-Run Mei , Ruo-Fei Liu , Hai-Liang Liu , Xian-Zhong Huang
Flowering is a critical plant growth stage coordinated by internal and external factors. Changes to endogenous sugar levels can promote or inhibit flowering, but research on the regulation of flowering-related genes associated with the sugar pathway in cotton is limited. Here, a genome-wide study identified 165 flowering and sugar pathway-related genes in five cotton species: Gossypium herbaceum, G. arboreum, G. hirsutum, G. barbadense, and G. raimondii. The genes were phylogenetically classified into nine subfamilies and showed a high degree of conservation. Notably, no homologs of INDETERMINATE DOMAIN 8 (IDD8), SUCROSE-PROTON SYMPORTER 9 (SUC9), or AGP GALACTOSYLTRANSFERASE 2 (GALT2) were identified. A synteny analysis provided evidence of varying degrees of gene expansion, and a selection pressure analysis indicated that the genes had undergone purifying selection, with Ka/Ks ratios of <1. The similarity among the genes identified in G. herbaceum, G. arboreum, and G. raimondii was higher than between these species and the allopolyploid cotton species, indicating the earlier divergence of these genes. A network analysis of protein interaction revealed G. hirsutum proteins to be associated primarily with sugar synthesis, transport, and metabolism. Yeast two-hybrid assays demonstrated that GhTPS1–1 and GhHXK1–1 can interact with GhPGI1–1. RNA-sequencing data for 46 genes from eight tissue-types in G. hirsutum revealed that most were highly expressed in stems and flowers. This study provides a comprehensive phylogenetic and network analysis of flowering-related genes in the sugar pathway across five Gossypium species, laying a foundation for future in-depth research on the functional mechanisms of these genes.
{"title":"Identification and comparative analysis of flowering genes in the Sugar pathway from five Gossypium species","authors":"Lei-Ming Liu , Chuan-Bo Jiang , Yi-Lin Yang , Tian-Run Mei , Ruo-Fei Liu , Hai-Liang Liu , Xian-Zhong Huang","doi":"10.1016/j.plgene.2025.100500","DOIUrl":"10.1016/j.plgene.2025.100500","url":null,"abstract":"<div><div>Flowering is a critical plant growth stage coordinated by internal and external factors. Changes to endogenous sugar levels can promote or inhibit flowering, but research on the regulation of flowering-related genes associated with the sugar pathway in cotton is limited. Here, a genome-wide study identified 165 flowering and sugar pathway-related genes in five cotton species: <em>Gossypium herbaceum</em>, <em>G. arboreum</em>, <em>G. hirsutum</em>, <em>G. barbadense</em>, and <em>G. raimondii</em>. The genes were phylogenetically classified into nine subfamilies and showed a high degree of conservation. Notably, no homologs of <em>INDETERMINATE DOMAIN 8</em> (<em>IDD8</em>), <em>SUCROSE-PROTON SYMPORTER 9</em> (<em>SUC9</em>), or <em>AGP GALACTOSYLTRANSFERASE 2</em> (<em>GALT2</em>) were identified. A synteny analysis provided evidence of varying degrees of gene expansion, and a selection pressure analysis indicated that the genes had undergone purifying selection, with <em>Ka</em>/<em>Ks</em> ratios of <1. The similarity among the genes identified in <em>G. herbaceum</em>, <em>G. arboreum</em>, and <em>G. raimondii</em> was higher than between these species and the allopolyploid cotton species, indicating the earlier divergence of these genes. A network analysis of protein interaction revealed <em>G. hirsutum</em> proteins to be associated primarily with sugar synthesis, transport, and metabolism. Yeast two-hybrid assays demonstrated that GhTPS1–1 and GhHXK1–1 can interact with GhPGI1–1. RNA-sequencing data for 46 genes from eight tissue-types in <em>G. hirsutum</em> revealed that most were highly expressed in stems and flowers. This study provides a comprehensive phylogenetic and network analysis of flowering-related genes in the sugar pathway across five <em>Gossypium</em> species, laying a foundation for future in-depth research on the functional mechanisms of these genes.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"42 ","pages":"Article 100500"},"PeriodicalIF":2.2,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143644510","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号