Plant Gene最新文献

{"title":"Transcriptome profiling in peanut (Arachis hypogaea) in response to biotic stress produce by Bacillus amyloliquefaciens TA-1","authors":"Wang Chen ,&nbsp;Taswar Ahsan ,&nbsp;Di Han ,&nbsp;Wen-Rui Wang ,&nbsp;Si-Tong Du ,&nbsp;Chao-Qun Zang ,&nbsp;Yu-Qian Huang ,&nbsp;Ejaz Hussain Siddiqi","doi":"10.1016/j.plgene.2024.100479","DOIUrl":"10.1016/j.plgene.2024.100479","url":null,"abstract":"<div><div>This study aimed to investigate the transcriptional response of peanut plants against the biocontrol agent <em>Bacillus amyloliquefaciens</em> TA-1. Gene expression analysis showed the highest number of Differentially expressed genes (DEGs) in downregulation in samples Bam_Am_1_vs_Bam_CK_1 compared to other samples (Bam_Am_2_vs_Bam_CK_2, and Bam_Am_3_vs_Bam_CK_3) After de novo annotation of the transcriptome, we analyzed the GO (Gene Ontology) enrichment of the DEGs to elucidate the main functional pathways impacted by TA-1. TA-1 induced qualitatively transcriptional modifications in all replicates, with a substantial impact on following GO terms, i.e., response to external stimulus, membrane parts, cell periphery, and catalytic activity. Further, (we analyzed the KEGG enrichment of DEGs to elucidate the main functional pathways that TA-1 impacts). The most enriched pathways were plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathways, and phenylpropanoid biosynthesis. We also analyzed the KOG enrichment of DEGs. Most of the annotation was associated with functional groups in all treatments, which primarily pertained to signal transduction mechanisms, secondary metabolite biosynthesis, post-translational modification, protein turnover, and chaperones. These results highlight the qualitative transcriptional changes in peanut plants due to the application of the biocontrol agent, underscoring its potential impact on crop protection and enhancement.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"41 ","pages":"Article 100479"},"PeriodicalIF":2.2,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142720351","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}

{"title":"Identified and validation of EST-SSR in the transcriptome sequences by RNA-Seq in cumin (Cuminum Cyminum L.)","authors":"Seyed Mohammad Mahdi Mortazavian ,&nbsp;Mahdieh Arshadi-Bidgoli ,&nbsp;Dariush Sadeghi ,&nbsp;Mohammad Reza Bakhtiarizadeh","doi":"10.1016/j.plgene.2024.100477","DOIUrl":"10.1016/j.plgene.2024.100477","url":null,"abstract":"<div><div>Cumin (<em>Cuminum cyminum</em> L.), a member of the Apiaceae family, exhibits a wide range of native ecotypes from the Eastern Mediterranean to India. Despite its significant culinary and medicinal applications, the availability of transcriptomic and genomic data for cumin remains limited, hindering advances in molecular genetics and breeding research. This study presents the first sequencing of the cumin transcriptome using RNA sequencing technology, generating 34,711,979, 48,649,265, 127,370,622, and 52,990,923 reads from the flowers of cumin plants. In total, 51,777 transcripts were de novo assembled, with an average length of 717.09 bp and an N50 value of 1110 bp. Approximately 70 % (36,166) of these transcripts were annotated in at least one public database (UniprotKB, Nr, Pfam, GO, and KEGG). Furthermore, 1556 simple sequence repeats (SSRs) were identified, distributed across 1465 transcripts. The most prevalent SSR motifs were di-nucleotide (70.05 %) and tri-nucleotide (26.16 %) repeats, followed by tetra-nucleotide (2.18 %), penta-nucleotide (0.90 %), and hexanucleotide repeats (0.71 %). The most frequent di-nucleotide and tri-nucleotide repeats were GA/TC (33.58 %) and CAG/CTG (10.32 %), respectively. Functional enrichment analysis indicated that transcripts containing SSRs play significant roles in metabolic processes, DNA/nucleotide binding, protein modification processes, and biosynthetic/developmental processes. For marker validation, 10 EST-SSR primer pairs were tested across 31 cumin genotypes, identifying 34 alleles with polymorphism information content (PIC) values ranging from 0.32 to 0.46. The mean genetic diversity index (MI) and effective multiplex ratio (EMR) were 1.22 and 2.98, respectively. Additionally, two clusters were identified through UPGMA analysis. The SSR markers identified in this study hold potential for applications in genetic mapping, population genetic analysis, genetic diversity studies, and marker-assisted breeding in cumin and related species.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100477"},"PeriodicalIF":2.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704970","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}

{"title":"Gene editing for allergen amelioration in plants – A review","authors":"Anindita Chakraborty ,&nbsp;Stephen J. Wylie","doi":"10.1016/j.plgene.2024.100476","DOIUrl":"10.1016/j.plgene.2024.100476","url":null,"abstract":"<div><div>The aim of this review is to summarize current advancements in the application of CRISPR to ameliorate allergenicity in plant-based foods. The literature on food allergens highlights the negative impacts on quality of life for many sufferers. Efforts to select low-allergenicity crop varieties through conventional means have had limited success. Here we review the literature describing gene editing to eliminate allergenicity genes and measure subsequent allergen expression. Gene editing is a means of inserting or deleting nucleotides at precise locations/genes in the genome, and the most widely used technology is CRISPR (clustered regularly interspaced short palindromic repeats) along with an endonuclease such as Cas9 (CRISPR/Cas9). An example are the α-amylase/trypsin inhibitors (ATIs) in wheat that are responsible for bakers' asthma. CRISPR was utilized to simultaneously knock down two ATI subunits, resulting in reduced expression of both subunits. Between 1.4 % and 4.5 % of children suffer from peanut allergy. Progress toward knock down of expression of genes encoding known allergens in peanuts is reviewed. Other allergenic plant species of interest in this review are soy and mustard. Gene editing has the potential to manipulate expression of allergen genes to reduce allergenicity, but as some allergens play important roles in physiological processes such as biotic and abiotic stress amelioration, simply targeting their genes with CRISPR to abolish expression is not always feasible.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100476"},"PeriodicalIF":2.2,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704349","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}

{"title":"Alternative oxidase of plants mitochondria is related with increased resistance of tomato mtDNA to the difenoconazole exposure","authors":"Alina A. Alimova ,&nbsp;Maria V. Gureeva ,&nbsp;Mariya I. Gladkikh ,&nbsp;Ekaterina Yu Nesterova ,&nbsp;Mikhail Yu Syromyatnikov ,&nbsp;Artem P. Gureev","doi":"10.1016/j.plgene.2024.100475","DOIUrl":"10.1016/j.plgene.2024.100475","url":null,"abstract":"<div><div>It is known that plant mitochondria and mitochondrial DNA (mtDNA) are more resistant to damage than animal mitochondria. We hypothesized that this phenomenon may be related to alternative respiratory pathways in plants mitochondria, in particular alternative oxidase (AOX). The results of a pot experiment demonstrated that the application of the fungicide difenoconazole at concentrations that were 3-, 5-, and 10-times higher than the recommended dosage resulted in a 106 %, 76 %, and 90 % increase in mitochondrial DNA damage in tomato shoots, respectively, in comparison to the shoots treated with difenoconazole at the dosage recommended by the manufacturer. Inhibition of shoot growth was observed in response to treatment with difenoconazole at a dose 10times higher than recommended. It is noteworthy that when tomatoes were treated with difenoconazole at this concentration, there was a tendency for the expression of inducible <em>aox1a</em>. In a field experiment, difenoconazole at a concentration of 5 times higher than recommended resulted in a 10 % increase in mtDNA damage in the fruits compared to the control. Similar results were obtained in an in vitro experiment. The addition of low doses of difenoconazole to intact tomato mitochondria did not cause mtDNA damage. The observed damages occured only when 200 μM difenoconazole was added. In contrast, incubation of 20 μM difenoconazole with SHAM, which inhibits AOX, resulted in a 115 % increase in mtDNA damage compared to the use of the same concentration without difenoconazole. This finding is consistent with the damaging effect induced by 200 μM difenoconazole. The increase in difenoconazole toxicity induced by SHAM and the elevation in aox1a gene expression resulting from the treatment with a 10 times higher than the recommended dose of difenoconazole may signify a pivotal function of AOX in the increased resistance of plant mtDNA to the pesticide exposure.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100475"},"PeriodicalIF":2.2,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663665","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}

{"title":"Genome-wide identification and characterization of FORMIN genes in cotton: Implications for abiotic stress tolerance","authors":"Rasmieh Hamid ,&nbsp;Feba Jacob ,&nbsp;Zahra Ghorbanzadeh ,&nbsp;Mohsen Mardi ,&nbsp;Shohreh Ariaeenejad ,&nbsp;Mehrshad Zeinalabedini ,&nbsp;Mohammad Reza Ghaffari","doi":"10.1016/j.plgene.2024.100474","DOIUrl":"10.1016/j.plgene.2024.100474","url":null,"abstract":"<div><h3>Background</h3><div>Formins are highly conserved proteins with multiple domains that play an important role in the interaction with microfilaments and microtubules and thus regulate actin organisation and cytoskeletal dynamics. Despite their importance in plant development and response to stress, the study of FORMIN (FH) genes in cotton, an important fibre crop, remains limited. The genetic diversity of these genes is critical for improving the adaptability of cotton to environmental stress, which is a major challenge for cotton breeding programmes aimed at improving abiotic stress tolerance.</div></div><div><h3>Results</h3><div>Through comprehensive bioinformatics approaches, we identified 46, 50 and 27 putative <em>FH</em> genes in <em>Gossypium hirsutum</em>, <em>G. barbadense</em> and their diploid ancestors <em>G. arboreum</em> and G. <em>raimondii</em>, respectively. A phylogenetic analysis classified these genes into five subfamilies and revealed evolutionary relationships to <em>Arabidopsis thaliana</em>. Syntenic and collinear analyses showed that genomic duplications in cotton have driven the expansion of the FH gene family. Structural analysis showed significant variations in sequence length and conserved motifs. Promoter analysis revealed several cis-acting elements associated with growth, stress response and hormonal signalling. Protein-protein interaction predictions suggest involvement in hormone signalling, cytoskeletal regulation and cell wall dynamics. Differential expression of <em>G. hirsutum</em> FH (GhFH) genes in different cotton tissues under drought and osmotic stress was confirmed by qRT-PCR.</div></div><div><h3>Conclusion</h3><div>This study provides new insights into the functional diversity and evolutionary dynamics of FH genes in cotton and emphasises their potential role in improving abiotic stress tolerance. By identifying key regulatory genes involved in stress adaptation, this research contributes to the development of more resilient cotton varieties through targeted breeding strategies. The results underline the importance of genetic diversity in enabling cotton breeding programmes to overcome the challenges posed by abiotic stress.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100474"},"PeriodicalIF":2.2,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554879","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}

{"title":"Analysis of marker gene transfer from chloroplasts to mitochondria in heat-shocked and selection-pressured tobacco","authors":"Masaki Odahara ,&nbsp;Maai Mori ,&nbsp;Keiji Numata","doi":"10.1016/j.plgene.2024.100473","DOIUrl":"10.1016/j.plgene.2024.100473","url":null,"abstract":"<div><div>Angiosperm mitochondrial genomes have highly complex and diverse structures that are partly due to frequent insertions of nuclear and chloroplast DNA (cpDNA) into mitochondrial DNA (mtDNA). This suggests the existence of mechanisms for gene transfer from chloroplasts to mitochondria, but these have yet to be discovered. In this study, we aimed to capture chloroplast-to-mitochondrion gene transfer by analyzing the translocation of a marker gene, <em>sul</em>, encoding a bacterial dihydropteroate synthase that confers sulfonamide resistance in tobacco (<em>Nicotiana tabacum</em>), to mtDNA. First, we created tobacco chloroplast transformants in which <em>sul</em>, surrounded on both sides by ∼1 kb of mitochondrial homologous sequences that enable targeted integration into mtDNA, was introduced into the chloroplast genome. Heat shock enhanced <em>sul</em> expression in the transformants, suggesting that chloroplast degradation can stimulate gene transfer from chloroplasts to mitochondria. Shoot regeneration using the heat-shocked chloroplast transformants under sulfadiazine selection resulted in several transformants with moderate resistance to sulfadiazine. Deep sequencing analysis of the target mitochondrial locus detected <em>sul</em> in the sulfadiazine-resistant (SR) plants, but an integration efficiency was 0.0011–0.0051 %. We validated the results by ruling out <em>sul</em> integration into nuclear mitochondrial DNA (NuMT). From these results, we propose the established system is capable of capturing gene transfer from chloroplasts to mitochondria in tobacco, but the transfer efficiency is substantially lower than those from organelles to nucleus.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100473"},"PeriodicalIF":2.2,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142572965","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}

{"title":"Transgressive segregation and generation mean analysis reveal the gene action underlying the inheritance of drought tolerance in rice","authors":"Kossi Lorimpo Adjah ,&nbsp;Maxwell Darko Asante ,&nbsp;Aboubacar Toure ,&nbsp;Mawuli Aziadekey ,&nbsp;Shailesh Yadav ,&nbsp;Felix Frimpong ,&nbsp;Francis Osei Amoako-Andoh ,&nbsp;Daniel Dzorkpe Gamenyah","doi":"10.1016/j.plgene.2024.100472","DOIUrl":"10.1016/j.plgene.2024.100472","url":null,"abstract":"<div><div>Climate change, an effective driver of unprecedented seasonal droughts, is greatly affecting rice production in Africa by threatening food security and safety. Rice, one of the major staple crops on the continent, can save the situation through the development of drought-tolerant cultivars, presenting a major challenge for future rice improvement programs as drought is regarded as a critical limitation in rain-fed ecosystems. This study sought to understand the genetic basis and inheritance behind the expression of tolerance of rice breeding lines to drought-stress through generation mean analysis. To achieve these objectives, two drought-sensitive genotypes (Jasmine 85 and CRI-Agrarice) were crossed with a drought-tolerant genotype (APO) to develop six populations (F₁, F₂, BC₁, BC₂, P₁ and P₂) under screenhouse drought-stress and non-stress evaluation. Data were collected on grain yield and yield-related traits among which the generation mean analysis was conducted. At least one transgressive phenotype was produced in the F₂ population for each trait whether there is a significant difference or not among the parental lines under drought-stress. Under non-stress conditions, there was a significance for all six types of gene action for days to flowering in both crosses. Among both crosses and water-regimes, additive x additive gene interaction was significant for most of the traits even though the scaling tests were not significant indicating the effectiveness of selection in early generations. Therefore, either forward breeding or backcross breeding can be adopted as breeding strategies for rapid improvement for these lines to drought tolerance.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100472"},"PeriodicalIF":2.2,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142530805","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}

{"title":"Targeted editing of susceptibility genes for plant disease resistance: Current state and future hopes","authors":"Lingareddy Usha Rani ,&nbsp;Manisha Shelke ,&nbsp;Maddi Sandhya ,&nbsp;Govindasamy Senthilraja","doi":"10.1016/j.plgene.2024.100471","DOIUrl":"10.1016/j.plgene.2024.100471","url":null,"abstract":"<div><div>Plants are constantly exposed to a plethora of pathogens including bacteria, fungi, and viruses posing significant challenges to global food security. The susceptibility of plants to these pathogens is often determined by specific genes within their genome. Understanding the role of susceptibility genes in plant-pathogen interactions is crucial for devising effective strategies to combat crop diseases. This review elucidates the importance of susceptibility genes in plants concerning their interactions with fungal, bacterial and viral pathogens. Susceptibility genes often encode proteins involved in crucial cellular processes such as signal transduction, defense response and pathogen recognition. Pathogens exploit vulnerabilities in these genes to establish infection and multiply within the host plant. In addition, advances in genome editing technologies offer promising avenues to enhance plant resistance against pathogens by targeting susceptibility genes. Techniques such as genome editing tools and epigenomic modification allow precise changes to be made in plant genomes, including the elimination or modification of susceptibility genes to confer resistance. However, ethical considerations and regulatory frameworks need to be addressed to ensure the potential use of gene editing in agriculture.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100471"},"PeriodicalIF":2.2,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142530806","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}

{"title":"Genome-wide identification and expression analysis of genes encoding late embryogenesis proteins in Cicer arietinum","authors":"Reetu Singh ,&nbsp;Varnika Rana ,&nbsp;Sudesh Kumar Yadav ,&nbsp;Vinay Kumar","doi":"10.1016/j.plgene.2024.100469","DOIUrl":"10.1016/j.plgene.2024.100469","url":null,"abstract":"<div><div>Late embryogenesis abundant (LEA) proteins play defensive roles during seed maturation and seed germination processes. However, there is no such investigation was carried out in chickpea. In present study, genome wide identification and characterization of LEA encoding genes has been investigated, and identified 65 and 74 LEA encoding genes in desi and kabuli cultivar of chickpea, respectively. All these genes have been classified into eight subfamilies on the bases of their phylogenetic analysis and conserved domain. Maximum members of LEA encoding genes were found to be a part of the LEA_2 gene family. The analysis of physicochemical properties of LEAs was also conducted. LEA encoding genes have been found to be located in all chromosomes (8 chr) of chickpea and identified as involved in response to stimulus, biological processes, molecular functions and cellular components based upon gene ontology analysis. Gene expression analysis of randomly selected 8 LEA encoding genes has been carried out during different seed developmental stages which revealed the higher expression of LEA encoding genes during later stage of seed development in chickpea and proved their potential role in desiccation process during seed maturation. During seed germination, expression analysis of LEA encoding genes was found to be higher during the initial stages of seed germination. In conclusion, this work highlights the genome wide identification and characterization of LEA encoding genes in chickpea and proposed potential roles during seed developmental processes. This information could also be useful as a reference investigation for molecular breeding of chickpea for recalcitrant behaviour of seed.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100469"},"PeriodicalIF":2.2,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142423509","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}

{"title":"Genome-wide identification of clock-associated genes and circadian rhythms in Fragaria × ananassa seedlings","authors":"Misaki Ishibashi ,&nbsp;Norihito Nakamichi ,&nbsp;Yuki Hayashida ,&nbsp;Haruka Kazumori ,&nbsp;Shungo Otagaki ,&nbsp;Shogo Matsumoto ,&nbsp;Akira Oikawa ,&nbsp;Katsuhiro Shiratake","doi":"10.1016/j.plgene.2024.100470","DOIUrl":"10.1016/j.plgene.2024.100470","url":null,"abstract":"<div><div>Flowering time in plants is regulated by a photoperiod-responsive mechanism. Some plant species use a circadian clock-based control mechanism to adapt to variable environments. Strawberry is a horticultural crop that responds to certain photoperiods and temperatures to induce flowering. However, clock-associated genes in octoploid cultivated strawberry (<em>Fragaria × ananassa</em>) have not been defined, and their regulatory mechanism for responding to photoperiods is unclear. We herein targeted 12 clock-associated genes reported in other plant species and performed a genome-wide analysis and expression comparison in <em>F. × ananassa</em> seedlings. Seventy-eight sequences were selected from the <em>F. × ananassa</em> genome. The major domains and <em>cis</em>-acting elements were conserved in each sequence. Transcripts were clearly expressed under continuous light conditions in <em>F. × ananassa</em> seedlings (‘Yotsuboshi’) acclimated to long days. Among them, 9 genes maintained their unique autonomous circadian rhythms and may function as clock genes. LHY (LATE ELONGATED HYPOCOTYL) had the Myb domain and <em>LHY</em> expression peaked in the dawn. PRR (PSEUDO-RESPONSE REGULATOR) family members (<em>PRR9</em>, <em>PRR7</em>, <em>PRR5</em>, and <em>TOC1</em> (<em>TIMING OF CAB EXPRESSION 1</em>)) had a pseudo-receiver domain and CCT domain, and peak expression times began sequentially from the afternoon for <em>PRR9</em> to the evening for <em>TOC1</em>. LUX (LUXARRHYTHMO) had a Myb domain, and <em>LUX</em> expression peaked in evening with <em>ELF3</em> (<em>EARLY FLOWERING 3</em>). FKF1 (<em>FLAVIN-BINDING KELCH REPEAT F BOX 1</em>) had PAS and F-box domains, and <em>FKF1</em> expression peaked in the afternoon. <em>GI</em> (<em>GIGANTEA</em>) expression also peaked in the afternoon. <em>F.</em> × <em>ananassa</em> (‘Yotsuboshi’) appears to have multiple feedback loops comprising clock-associated genes. Although the rhythmic expression of <em>CHE</em> (<em>CCA1 HIKING EXPEDITION</em>) and <em>ZTL</em> (<em>ZEITLUPE</em>) was not observed, they had conserved domains, CHE with the TCP domain and ZTL with the PAS and F-box domains. The present results provide basic information on the circadian clock for the control of <em>F.</em> × <em>ananassa</em> flowering.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"40 ","pages":"Article 100470"},"PeriodicalIF":2.2,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142423998","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}