{"title":"Identification of key pathways and associated transcription factor-miRNA-gene regulatory networks driving heterosis in cotton (<i>Gossypium</i> spp.).","authors":"Rasmieh Hamid, Bahman Panahi, Feba Jacob","doi":"10.1071/FP25041","DOIUrl":"https://doi.org/10.1071/FP25041","url":null,"abstract":"<p><p>Heterosis, or hybrid vigor, represents a pivotal phenomenon in cotton (Gossypium spp.) breeding, enabling substantial advancements in yield, stress tolerance, and fiber quality. However, the underlying molecular mechanisms of this phenomenon are still largely unexplored. To address this issue, we performed RNA-seq meta-analysis using a P -value combination approach to identify key molecular signaling pathways associated with heterosis in root and bud tissues of hybrid and parental lines. In addition, the regulatory miRNA-transcription factor (TF) gene interactions associated with heterosis were further constructed and dissected. This comprehensive analysis identified 591 differentially expressed genes (DEGs) that were consistently observed in all datasets. In particular, 435 root-specific, 130 bud-specific, and 159 shared meta-DEGs were identified, revealing the intricate interplay between tissue-specific and shared molecular pathways. Functional enrichment analysis of identified meta-DEGs highlighted critical roles of specific biological processes, including circadian rhythm regulation and water transport, alongside essential metabolic pathways such as glutathione metabolism, and starch and sucrose metabolism in the heterosis phenomenon. Genes pivotal to growth and development, such as GhFT (flowering regulation), GhXTH9 (cell wall modification), and GhSUS4 (energy storage), were identified as key players in the heterosis phenomenon in cotton. The associations between several miRNA-TF-gene interaction networks such as Ghi -miR164-NAC and Ghi -miR166-HD-ZIP as heterosis driving regulatory interactions were highlighted by systems level analysis. This study provides a comprehensive framework for dissection of transcriptional regulatory mechanisms underlying heterosis in cotton and offers new insights for targeted breeding strategies to improve the performance of hybrids in modern cotton breeding programs.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Md Mezanur Rahman, Sanjida Sultana Keya, Mallesham Bulle, S M Ahsan, Md Abiar Rahman, Md Shyduzzaman Roni, Md Mahmud Al Noor, Mehedi Hasan
{"title":"Past trauma, better future: how stress memory shapes plant adaptation to drought.","authors":"Md Mezanur Rahman, Sanjida Sultana Keya, Mallesham Bulle, S M Ahsan, Md Abiar Rahman, Md Shyduzzaman Roni, Md Mahmud Al Noor, Mehedi Hasan","doi":"10.1071/FP24355","DOIUrl":"https://doi.org/10.1071/FP24355","url":null,"abstract":"<p><p>Can plants remember drought? Emerging evidence suggests that prior stress exposure leaves an epigenetic imprint, reprogramming plants for enhanced resilience. However, the stability and functional relevance of drought memory remain unresolved. This review synthesizes recent advances in epigenetic modifications, transcriptional reprogramming, and metabolic priming, critically assessing their roles in plant stress adaptation. DNA methylation dynamically reshapes chromatin landscapes, yet its transient nature questions its long-term inheritance. Histone modifications, particularly H3K9ac and H2Bub1, may encode stress signatures, enabling rapid transcriptional responses, whereas small RNAs fine-tune chromatin states to reinforce memory. Beyond epigenetics, physiological priming, including osmotic adjustments, antioxidant defenses, and hormonal crosstalk, introduces further complexity, yet its evolutionary advantage remains unclear. Root system plasticity may enhance drought resilience, but its metabolic trade-offs and epigenetic underpinnings are largely unexplored. A critical challenge is disentangling stable adaptive mechanisms from transient acclimatory shifts. We propose a framework for evaluating drought memory across temporal and generational scales and highlight the potential of precision genome editing to establish causality. By integrating multi-omics, gene editing, and field-based validation, this review aims to unlock the molecular blueprint of drought memory. Understanding these mechanisms is key to engineering climate-resilient crops, ensuring global food security in an era of increasing environmental uncertainty.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aayushree Kharel, Mark Ziemann, James Rookes, David Cahill
{"title":"Modulation of key sterol-related genes of <i>Nicotiana benthamiana</i> by phosphite treatment during infection with <i>Phytophthora cinnamomi</i>.","authors":"Aayushree Kharel, Mark Ziemann, James Rookes, David Cahill","doi":"10.1071/FP24251","DOIUrl":"https://doi.org/10.1071/FP24251","url":null,"abstract":"<p><p>Phytophthora cinnamomi is a globally destructive pathogen causing disease in over 5000 plant species. As sterol auxotrophs, Phytophthora species rely on host-derived phytosterols for reproduction, yet the effects of pathogen infection on plant sterol biosynthesis remains unclear. We utilised a soil-free plant growth system to analyze the impacts of P. cinnamomi on Nicotiana benthamiana roots, a new model for studying P. cinnamomi -plant root interactions. Our results show that P. cinnamomi successfully infected all ecotypes tested, but infection was inhibited by the systemic chemical, phosphite. While phosphite is traditionally associated with the activation of plant defence mechanisms, we show that phosphite also modulates plant immune receptors and phytosterol biosynthesis. qPCR analyses revealed a two-fold upregulation of the N. benthamiana elicitin receptor, Responsive to Elicitins (REL ), and its co-receptor, suppressor of BIR1-1 (SOBIR ) during P. cinnamomi infection when compared with infected, phosphite-treated plants. Furthermore, key genes related to plant sterol biosynthesis were upregulated in their expression during pathogen infection but were suppressed in phosphite-treated and infected plants. Notably, the cytochrome P450 family 710 (CYP710A ) gene encoding a C22-sterol desaturase, involved in stigmasterol production, a phytosterol known to be linked to plant susceptibility to pathogens, was downregulated in phosphite-treated plants, independent of infection status. These findings reveal novel insights into the role of phosphite in modulating plant immune responses and sterol metabolism, with potential in managing diseases caused by P. cinnamomi .</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144077249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Angelia Tanu, Allan Rattey, Andrew Fletcher, Sarah Rich, Alexandra Taylor, Erik Veneklaas
{"title":"Enhancing deep sowing success: genetic diversity in mesocotyl and coleoptile length, and field establishment of oats (<i>Avena sativa</i>).","authors":"Angelia Tanu, Allan Rattey, Andrew Fletcher, Sarah Rich, Alexandra Taylor, Erik Veneklaas","doi":"10.1071/FP24321","DOIUrl":"https://doi.org/10.1071/FP24321","url":null,"abstract":"<p><p>Early and deep sowing practices have revolutionised Australian winter cropping. Oats (Avena sativa ) are the only winter-cereal with a mesocotyl, potentially allowing them to successfully emerge from deep sowing. This study examined the genetic differences in mesocotyl and coleoptile length, the effect of temperature on these traits, and undertook a field validation of deep-sown oats compared to selected wheat (Triticum aestivum ) and barley (Hordeum vulgare ) genotypes. A controlled environment experiment on 195 oat genotypes revealed long combined mesocotyl and coleoptile lengths (112-219 mm) with significant genotypic variation. A further controlled environment study compared the mesocotyl and coleoptile lengths of 42 genotypes across four temperatures (15-30°C). This revealed that temperatures exceeding 20°C reduced coleoptile and mesocotyl length by 3.7mm and 1.1mm per °C. Five field experiments compared the emergence of 19 oat, four wheat, and two barley genotypes from deep (110mm) and shallow sowing (40mm). Oats had greater emergence at depth compared to wheat and barley genotypes. The results indicate that oats are highly suited to early and deep sowing conditions due to their long mesocotyl and combined mesocotyl and coleoptile length.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emily R R Mackie, Mirrin V McKay, Andrew S Barrow, Tatiana P Soares da Costa
{"title":"Inhibitors of lysine biosynthesis enzymes as potential new herbicides.","authors":"Emily R R Mackie, Mirrin V McKay, Andrew S Barrow, Tatiana P Soares da Costa","doi":"10.1071/FP25030","DOIUrl":"https://doi.org/10.1071/FP25030","url":null,"abstract":"<p><p>Lysine is an amino acid that is essential for the growth and development of all organisms owing to its role in a plethora of critical biological functions and reactions. In plants, lysine is synthesised via five sequential enzyme-catalysed reactions collectively known as the diaminopimelate (DAP) pathway, whereas animals are reliant on their plant dietary intake to obtain lysine. Given that lysine is one of the most nutritionally limiting amino acids, several studies have focused on developing strategies to modulate the activity of DAP pathway enzymes to improve the nutritional value of crops. More recently, research has emerged on the potential of inhibiting DAP pathway enzymes for the development of herbicides with a novel mode of action. Over reliance on a small number of modes of action has led to a herbicide resistance crisis, necessitating the development of new modes of action to which no resistance exists. As such, the first herbicidal inhibitors of the DAP pathway have been developed, which target the first three enzymes in lysine biosynthesis. This review explores the structure, function, and inhibition of these enzymes, as well as highlighting promising avenues for the future development of new plant lysine biosynthesis inhibitors.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143961663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Functional analysis of the <i>CCoAOMT</i> gene in <i>Populus deltoides</i> for enhancing tolerance to <i>Alternaria burnsii</i>.","authors":"Ankit Yadav, Amar Sakure, Sushil Kumar, Akarsh Parihar, Dimple Gor, Vidyut Balar","doi":"10.1071/FP25064","DOIUrl":"https://doi.org/10.1071/FP25064","url":null,"abstract":"<p><p>Alternaria blight (Alternaria burnsii ) causes significant economic losses due to defoliation, reduced yields, and poor-quality produce in various crops. Consequently, effective strategies for managing this disease are critical. In this study, the caffeoyl-CoA O-methyltransferase (PdCCoAOMT ) gene, which plays a key role in lignin biosynthesis and plant defense, was isolated from Populus deltoides and investigated for its potential to enhance resistance against A. burnsii , the causal agent of blight of various crop species. The PdCCoAOMT gene (741bp) was cloned, characterised, and expressed in the model plant Nicotiana tabacum via Agrobacterium -mediated transformation. Sequencing of the amplicon followed by BLAST analysis revealed 100% query coverage and 98.52% identity of CCoAOMT with the Populus tomentosa and Populus trichocarpa mRNA. Histochemical GUS staining of the putative transformed leaves displayed a distinct blue colour, predominantly in the veins. Gene expression analysis via real time quantitative PCR of 11 T1 plants showed the highest expression in T1 -6 plant. Overexpression of PdCCoAOMT gene showed a positive correlation with lignin deposition in the transformed plants compared to the control plants. A detached leaf assay for A. burnsii resistance demonstrated a significant negative correlation between lignin deposition and disease severity, suggesting that higher lignin accumulation in the leaf was associated with reduced disease symptoms. This highlights the effectiveness of the gene in mitigating the disease in the transformed tobacco plants. These findings suggest that PdCCoAOMT could be a valuable tool in developing crop varieties resistant to Alternaria blight, providing a promising strategy to combat this economically devastating pathogen.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Boris N Ivanov, Marina A Kozuleva, Natalia N Rudenko, Lyudmila K Ignatova, Elena M Nadeeva, Ilya A Naydov, Daria V Vetoshkina, Daria V Vilyanen, Maria M Borisova-Mubarakshina
{"title":"Effect of CO<sub>2</sub> content in air on functioning of <i>Arabidopsis thaliana</i> photosynthetic electron transport chain.","authors":"Boris N Ivanov, Marina A Kozuleva, Natalia N Rudenko, Lyudmila K Ignatova, Elena M Nadeeva, Ilya A Naydov, Daria V Vetoshkina, Daria V Vilyanen, Maria M Borisova-Mubarakshina","doi":"10.1071/FP24308","DOIUrl":"https://doi.org/10.1071/FP24308","url":null,"abstract":"<p><p>The functioning of the photosynthetic electron transport chain and the proceeding of accompanying processes were studied in Arabidopsis thaliana plants acclimated during 2weeks to reduced (150ppm) or elevated (1000ppm) CO2 concentrations in air. Measured at ambient CO2 , the quantum yields of both photosystems were lower in plants acclimated to these CO2 concentrations as compared with control plants grown at ambient CO2 . The difference was more pronounced at the beginning of the illumination. It is discussed that this difference resulted from the difference in Rubisco content, which at both reduced and elevated CO2 in air was lower than in control plants. The quantum yield of regulated non-photochemical energy loss in photosystem II under both reduced and elevated CO2 was lower than in control plants. This correlated with reduced expression of the PsbS protein gene. H2 O2 content in the leaves increased during the first days of plant adaptation to 150ppm CO2 , but then decreased. The increase resulted from enhanced rates of both photorespiration and Mehler reaction, while the following decrease resulted from enhancing contents of ascorbate peroxidases in all cell compartments.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143978594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lorena Guardia-Velarde, Jonathan E Cope, Holger Metzler, Anna Westerbergh, Martin Weih
{"title":"Same with less: a method to reduce destructive sampling to estimate nitrogen use efficiency components using allometric relationships in spring wheat (<i>Triticum aestivum</i>).","authors":"Lorena Guardia-Velarde, Jonathan E Cope, Holger Metzler, Anna Westerbergh, Martin Weih","doi":"10.1071/FP24201","DOIUrl":"https://doi.org/10.1071/FP24201","url":null,"abstract":"<p><p>Enhancing nitrogen (N) use efficiency is important for a sustainable food production. Measuring shoot biomass and N pool across growth stages is critical to calculate N use efficiency, but relies on slow, costly and destructive sampling. This paper presents a non-destructive allometric approach developed for cereals; in this study, we assessed wheat (Triticum aestivum ) for crop shoot biomass and N pool. Our methodology considered tiller height and number, and the estimates of leaf chlorophyll content (SPAD) as non-destructive measures to predict shoot biomass and N pool by using a multiple linear and a non-linear regression (R 2 =0.71 and R 2 =0.89, respectively) on the data from 72 samples of 16 recombinant inbred spring wheat lines (RILs) field-grown in central Sweden during 2years with contrasting weather. Model parameters are estimated separately for different years to accommodate environmental variations between them. The regressions obtained were applied to estimate critical N use efficiency traits of 80 randomly selected wheat lines from the same RIL population. The method developed here provides a promising novel tool for the cost-effective estimation of critical N use efficiency parameters in cereals, with reduced destructive sampling, and a first step toward automated phenotyping for rapid N use efficiency assessment in cereal breeding populations.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zunaira Farooq, Ahmad Ali, Hongjie Wang, Muhammad Zeeshan Mola Bakhsh, Shipeng Li, Ying Liu, Shuo Wu, Aisha Almakas, Shouping Yang, Yi Bin
{"title":"An overview of cytoplasmic male sterility in <i>Brassica napus</i>.","authors":"Zunaira Farooq, Ahmad Ali, Hongjie Wang, Muhammad Zeeshan Mola Bakhsh, Shipeng Li, Ying Liu, Shuo Wu, Aisha Almakas, Shouping Yang, Yi Bin","doi":"10.1071/FP24337","DOIUrl":"https://doi.org/10.1071/FP24337","url":null,"abstract":"<p><p>Rapeseed (Brassica napus ) is one of the world's most important oilseed crops, supplying humans with oil products, nutritious feed for livestock, and natural resources for industrial applications. Due to immense population pressure, more seed production is needed for human consumption due to its high quality of food products. As a vital genetic resource, male sterility provides ease in hybrid seed production and heterosis breeding. Better utilization of male sterility requires understanding its mechanisms, mode of action, and genes involved to be characterized in detail. Cytoplasmic male sterility (CMS) has been reported in many plant species and is a maternally inherited trait that restricts viable pollen development and production. The mitochondrial genome is involved in the induction of male sterility, while the nuclear genome plays its role in the restoration. Presently, rapeseed has more than 10 CMS systems. Pol-CMS and Shaan2A are autoplasmic resources that arose via natural mutation, while Nap-CMS and Nsa-CMS are alloplasmic and were created by intergeneric hybridisation. In this review, we discuss the types of male sterility systems in rapeseed and provide comprehensive information on CMS in rapeseed with a particular focus and emphasis the types of CMS in rapeseed.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phytochrome A in etiolated wild-type and <i>albino</i> barley seedlings: a far-red pulse induces interconversion between the two physicochemically and functionally distinct phyA types - phyA' into phyA″.","authors":"V Sineshchekov, L Koppel","doi":"10.1071/FP25012","DOIUrl":"https://doi.org/10.1071/FP25012","url":null,"abstract":"<p><p>The phytochrome (phy) photoreceptors, comprising a small family of species, regulate plant development, being most active under red (R) and far-red (FR) light. One of the major phytochromes, phyA, is unique among the others: it mediates distinct photoreactions - the very low fluence responses (VLFR), the high irradiance responses (HIR), and the low fluence responses (LFR) characteristic of phyB. This functional diversity is likely to be connected with its heterogeneity: there are two native pools, possibly differing by serine phosphorylation at the N-terminus - phyA' mediating the VLFR and phyA″ responsible for the HIR and LFR. In this work, we investigated their nature by in vivo spectrofluorimetry, turning to the chlorophyll-less albino barley mutant. It was characterized both by the higher total phyA content and the proportion of phyA' in etiolated coleoptile tips. The lack of protochlorophyllide (PChlide) allowed characterization of phyA pools in primary leaves (of the mutant) - the phyA'/phyA″ proportion was the same as in the coleoptiles, whereas their content was substantially lower. phyA' in the mutant coleoptiles revealed less lability under light as compared with the wild type, suggesting that the mutation may affect the phyA's proteolytic system. A specific effect of FR light on phyA in coleoptiles was observed - a relatively fast (tens of minutes) conversion of phyA' into phyA″ that may be part of the complex process of plant light adaptation.</p>","PeriodicalId":12483,"journal":{"name":"Functional Plant Biology","volume":"52 ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143965001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}