Plant Gene最新文献

{"title":"Expression of anthocyanin biosynthesis-related genes during flower development in Lilium spp.","authors":"Hasan N.N. Fatihah ,&nbsp;Katarzyna Wolinska ,&nbsp;Jan G. Schaart ,&nbsp;Marian Oortwijn ,&nbsp;Richard G.F. Visser ,&nbsp;Frans A. Krens","doi":"10.1016/j.plgene.2022.100372","DOIUrl":"10.1016/j.plgene.2022.100372","url":null,"abstract":"<div><p><span>Sterility of hybrids produced from interspecific hybridization in lilies (</span><span><em>Lilium</em></span>, Liliaceae) is a great limitation in the breeding program, especially for <span><em>Lilium longiflorum</em><em>,</em></span> which only has white-flowered cultivars. Because modification of flower colour in L. <em>longiflorum</em><span> by conventional breeding is limited by pre- and post-fertilization barriers, we think genetic modification could be used as an alternative in the future. For this, we need to understand what determines white colouration in L. </span><em>longiflorum</em><span> and other species and identify the molecular mechanisms regulating flower colour. In this study, we determined the accumulation of anthocyanins and related compounds in flower tissues during flower developmental stages in L. </span><em>longiflorum</em> cultivar ‘Lincoln’ and in the Oriental hybrid lily cultivars ‘Rialto’, ‘Perth’ and ‘Gran Tourismo’, respectively with white, pink and red flowers. Furthermore, the presence/absence and the expression of eight structural genes (<em>CHSa, CHSb, CHIa, CHIb, F3H, F3’H, DFR, ANS</em>) and three transcription factor genes (<em>MYB12, MYB15, bHLH2</em>) in flower tissues were investigated. Two structural genes (<em>LlLinF3’H</em> and <em>LlLinDFR</em>) and one transcription factor gene (<em>LlLinbHLH2</em><span>) were not detected in ‘Lincoln’ flowers. In ‘Rialto’, an amino acid substitution in the R2 repeat of </span><em>LhRiaMYB12</em> which was previously reported to be responsible for the white flower colour is also found in the <em>LhPerMYB12</em> of the pink ‘Perth’ flowers. Moreover, <em>LhRiaDFR</em><span> is present but not expressed in ‘Rialto’ flowers. Accumulation of cyanidin was observed in the flowers of ‘Perth’ and ‘Gran Tourismo’. High amounts of dihydrokaempferol accumulated in flowers of all four lily cultivars confirming the expression and functionality of early structural genes in the pathway. The elevated expression of the structural genes is strongly correlated with the expression of </span><em>LhMYB12</em> and <em>LhMYB15</em>. This information can be used in the future to generate new L. <em>longiflorum</em> or Oriental lily hybrid cultivars with novel flower colours.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42677876","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":"Comparative RNA sequencing for deciphering nodes of multiple abiotic stress tolerance in lentil (Lens culinaris Medikus)","authors":"Dharmendra Singh ,&nbsp;Jyoti Taunk ,&nbsp;Chandan Kumar Singh ,&nbsp;Priya Chaudhary ,&nbsp;Kishor Gaikwad ,&nbsp;Rajendra Kumar Yadav ,&nbsp;Deepti Singh ,&nbsp;Madan Pal","doi":"10.1016/j.plgene.2022.100373","DOIUrl":"10.1016/j.plgene.2022.100373","url":null,"abstract":"<div><p><span><span><span><span>Lentil is a highly proteinaceous crop whose productivity is severely hampered by various abiotic stresses. </span>Transcriptome analysis unveils important metabolic pathways, </span>regulatory genes<span><span> and can help in identification of genomic resources which can be utilized for ameliorating abiotic stress tolerance. Therefore, the present study was undertaken to dissect transcriptomes of contrasting lentil genotypes under different stresses; drought, heat, salinity and alkalinity. Differential gene expression analysis and annotation were conducted by de novo </span>transcriptomics<span> and their functional correlation under diverse stresses was established using gene ontology analyses. Major differentially expressed genes (DEGs) which were found to be up-regulated under drought and heat stresses were involved in organic acid synthesis and </span></span></span>translational regulation. Similarly, DEGs which were co-upregulated under salinity and alkalinity stresses belonged to </span>abscisic acid<span><span><span><span> (ABA) signaling, epigenetic regulation, </span>sucrose transport, vesicular trafficking and regulation of </span>cation transport at the root symplast-xylem interface. Data generated in this study can be used to elucidate converging tolerance pathways under multiple abiotic stresses. The information can be utilized in </span>molecular breeding<span> and gene pyramiding programmes of lentil and related species.</span></span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46956873","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 analysis of cowpea NAC transcription factor family elucidating the genetic & molecular relationships that interface stress and growth regulatory signals","authors":"Richa Srivastava,&nbsp;Lingaraj Sahoo","doi":"10.1016/j.plgene.2022.100363","DOIUrl":"10.1016/j.plgene.2022.100363","url":null,"abstract":"<div><p><span>Being a key transcriptional mediator of stress and growth responses, NAC transcription factors hold the paramount potential to develop climate-smart pulse crops. Despite their seminal role, they are yet unexplored in many important orphan legumes like cowpea. The recent availability of a comprehensive reference genome motivated us to investigate and assess the functional importance of the remarkable NAC family in cowpea for sustainable crop research. This study identified 130 NAC proteins in cowpea, namely VuNAC01-130, classified into 8 phylogenetic groups. 27 cowpea-specific members were clustered as a distinct clade with no close orthologs from other species, implicating novel functions. VuNAC proteins carried </span>multipartite<span><span><span> nuclear signals and unique transactivation<span> regions with conserved patterns. 18 proteins were associated with non-NAC chimeric domains. The genes owned a unique promoter architecture encompassing pyrimidine-rich elements. The family manifested prominent segmental and tandem chromosomal duplication resulting in numerous stress-responsive members and large paralogous groups. The promoter and interactome analysis revealed multi-tier regulation through light, hormone, and transcription factors (NAC/MYB/WRKY/ERF and Dof/TCP), suggesting a cross-talk between stress and growth-regulating signals. Besides, the TFs were associated with metabolic processes such as </span></span>trehalose<span><span> and folate synthesis, carbohydrate transport, lipid signaling, and </span>electron transfer. Comparatively, ATAF-like members (Group Ia) would be the most promising candidates to develop climate-smart crops with improved stress adaptation and </span></span>agronomic traits by translational approach, due to their predicted functional versatility.</span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44400466","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":"Ozone stress responsive gene database (OSRGD ver. 1.1): A literature curated database for insight into plants' response to ozone stress","authors":"Prachi Yadav,&nbsp;Usha Mina","doi":"10.1016/j.plgene.2022.100368","DOIUrl":"10.1016/j.plgene.2022.100368","url":null,"abstract":"<div><p>Ozone (O₃<span>) is a major abiotic stress<span> which severely affects the growth and development<span> of plants. In order to cope up with ozone stress, plants exhibit a plethora of morphological, physiological and molecular changes. Various molecular studies have been performed and a variety of genes exhibiting expression in response to ozone stress have been identified. However, no existing database has been designed yet to present information on ozone stress responsive genes differentially expressed across different plant species. The lack of a curated database limits the research potential in the area and therefore a cohesive database should be designed as a data repository of the ozone responsive genes. OSRGD ver. 1.1 is a user-friendly web interface to explore ozone stress specific transcriptomic<span> and microarray dataset of different plant species. It allows users to retrieve the ozone stress responsive gene data by keyword-based search. Each entry upon keyword query contains detailed information about the specific species, its foliar injury symptoms, pattern of gene expression, and platform used for gene expression analysis with reference literature. This comprehensive bio-curation will offer researchers a better biological insight into plants' response to ozone stress which will focus on development of climate smart crops through crop breeding. The web interface is freely accessible at </span></span></span></span><span>http://www.osrgd.com</span><svg><path></path></svg>.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46106758","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":"miRNAs in agriculture: controlling plant growth, development and stress responses","authors":"Chittabrata Mal ,&nbsp;Surajit Bhattacharya","doi":"10.1016/j.plgene.2022.100367","DOIUrl":"10.1016/j.plgene.2022.100367","url":null,"abstract":"","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48939992","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":"Screening of Cicer arietinum L. genotypes under combined presence of NaCl and anthracene using membership function value of stress tolerance","authors":"Harleen Kaur ,&nbsp;Ravneet Kaur ,&nbsp;Geetanjali Manchanda ,&nbsp;Shayla Bindra ,&nbsp;Ashish Sharma","doi":"10.1016/j.plgene.2022.100371","DOIUrl":"10.1016/j.plgene.2022.100371","url":null,"abstract":"<div><p><span>Polycyclic Aromatic Hydrocarbons (PAHs) are mutagenic, carcinogenic compounds that are persistent in environment and limits overall growth of plants. Anthracene is a starting member and one of the simplest compound of all 16 known PAHs. It is an integral part of many carcinogenic PAHs. Being ubiquitous, PAHs can be present in saline soils also. Salinity is the one of major catastrophic stress affecting plant development. Thus, the present study aimed at studying the combined effect of salt and PAHs on the </span><span><em>Cicer</em><em> arietinum</em></span> L. (Chickpea). 10 Chickpea genotypes were screened on the basis of their response to the combined presence of NaCl and Anthracene. Optimum NaCl, Anthracene and Combined NaCl and Anthracene concentration calculated using Stress Injury Index was 40 mM, 5 mg and 60 + 5 mg A respectively. Various morphological and Physiological traits were studied and the data collected was evaluated by calculating the Stress Tolerance Index and Membership Function Value of stress tolerance as well as regression analysis was done for further validation. Results revealed that combined stress of NaCl and Anthracene have a synergistic effect on plant growth. On the basis of results obtained, GPF2 and PDG4 were selected as most tolerant and most sensitive chickpea genotypes. Of all the traits studied, dry weight of shoot was found to be the most reliable trait for studying the effect of NaCl and Anthracene alone whereas root length was found to be the most reliable trait for studying the combined effect of NaCl and Anthracene.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43156842","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":"Phylogenetic analysis and expression profiling of Nuclear Factor-Y gene family in Dendrobium catenatum Lindl. (Orchidaceae)","authors":"Devina Ghai ,&nbsp;Jaspreet K. Sembi","doi":"10.1016/j.plgene.2022.100365","DOIUrl":"10.1016/j.plgene.2022.100365","url":null,"abstract":"<div><p><span>Nuclear factor-Y (NF-Y) are transcription factors that play vital role in various developmental processes such as flowering<span>, embryogenesis<span>, root formation, nodulation and stress tolerance. In the present study, 27 </span></span></span><em>NF-Y</em> genes were identified in <span><em>Dendrobium</em><em> catenatum</em></span><span><span> which were grouped into three sub-families: DcNF-YA (5), DcNF-YB (10) and DcNF-YC (12), on the basis of presence of specific conserved domains. The phylogenetic relationship between DcNF-Y </span>protein sequences with their orthologs in </span><span><em>Vanilla planifolia</em></span> and <span><em>Arabidopsis thaliana</em></span> confirmed the classification of these proteins into the specified three groups. Physico-chemical characterization reported a wide range in the protein length (111 to 433 amino acids), with DcNF-YAs being longer than the others. Strong interaction between most of the DcNF-Y proteins suggests towards the formation of complexes which might be playing a role in different developmental processes. Gene architectural studies predicted the presence of multiple (3–6) introns in <em>DcNF-YA</em> in contrast with the intron-less status of majority of <em>DcNF-YB</em> and <em>DcNF-YC</em><span> genes. The abundance of stress related cis-regulatory elements in the promoter regions of </span><em>DcNF-Y</em><span> genes indicate the potential of these genes in stress tolerance. Additionally, variable expression of these genes in diverse tissues point towards their widespread role in growth and development. This work can act as a harbinger for functional characterization of </span><em>NF-Y</em> genes with a view for genetic improvement in <em>Dendrobium catenatum</em> Lindl.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44965509","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 splicing plays a vital role in regulating pollen allergen (Ole e 1) P19963 protein in Gossypium arboreum","authors":"Syeda Maryam Zahid ,&nbsp;Muhammad Farooq ,&nbsp;Memona Yasmin ,&nbsp;Muhammad Qasim Aslam ,&nbsp;Shahid Mansoor ,&nbsp;Imran Amin","doi":"10.1016/j.plgene.2022.100362","DOIUrl":"10.1016/j.plgene.2022.100362","url":null,"abstract":"<div><p><span>Alternative splicing regulation (AS) is an important post-transcriptional gene regulatory mechanism for increasing the complexity and diversity of transcriptomes<span><span> and subsequently proteomes. In this study, we performed </span>transcriptomic analysis of </span></span><span><em>Gossypium</em><em> arboreum</em></span> to explore the process of alternative splicing regulation in pollen allergen (<em>Ole e 1</em><span>) P19963 protein. The P19963 causes skin allergies because of its acidic properties. The P19963 protein was observed to undergo intron retention at seedling stage (IR); a type of alternative splicing regulation events when intron is not spliced out after the action of splicing machinery. Experimental validation using RT-PCR and sanger sequencing also proved retention of intronic region in the mature mRNA transcript of P19963 protein. We observed that even if this gene was expressing at later stages of plant development i.e., pollen producing stage, but due to alternative splicing it became disrupted at the seedling stage. The non-functionality of protein can be beneficial or harmful but in our case as the gene is having IR and becomes non-functional, it is beneficial as the pollen allergies and skin allergies can be minimized at this stage or not required at all.</span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43437438","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":"CRISPR-Cas9 mediated genome tailoring to improve nutritional quality and shelf life in crops: A review","authors":"Manami Chakravorty ,&nbsp;Manisha Nanda ,&nbsp;Neha Arora ,&nbsp;Shalini Singh ,&nbsp;Vinod Kumar ,&nbsp;Sandhya Deshwal","doi":"10.1016/j.plgene.2022.100369","DOIUrl":"10.1016/j.plgene.2022.100369","url":null,"abstract":"<div><p><span><span><span>The ever-increasing population, combined with the agriculture sector's ongoing challenges, necessitates the use of </span>plant genome<span><span> modifying technologies to improve nutritional quality as well as crop yields. In this regard, the CRISPR/Cas system has evolved into a game-changing genetic modification technique for increasing crop yield and </span>pest resistance in a variety of agricultural crops. In </span></span>prokaryotes<span><span>, the CRISPR/Cas system serves as a line of defense against pathogens. In the genetic engineering system, the protein Cas9 </span>endonuclease and a </span></span>guide RNA reaches the target site and modifies the target gene. This review focuses on the CRISPR/Cas9 system's action pathway, recent advancements, applications, and future prospects in redesigning the plant genome for crop improvement.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46663349","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":"Novel NF-Y genes expressed during somatic embryogenesis in Medicago truncatula","authors":"Elina Potsenkovskaia ,&nbsp;Varvara Tvorogova ,&nbsp;Daria Yakovleva ,&nbsp;Natalia Zlydneva ,&nbsp;Ludmila Lutova","doi":"10.1016/j.plgene.2022.100364","DOIUrl":"10.1016/j.plgene.2022.100364","url":null,"abstract":"<div><p><span>Somatic embryogenesis is widely used in biotechnology as a regeneration process conditioning many protocols for plant transformation and </span><em>in vitro</em> propagation. The main objective of this study was to search for new potential somatic embryogenesis regulators among the genes belonging to the <em>NF-Y</em> family and to analyse the mechanism of their action in <span><em>Medicago</em><em> truncatula</em></span>. We found that two LEC1-type <em>NF-YB</em> genes, <em>MtNF-YB3</em> and <em>10</em>, are highly expressed in the calli of the embryogenic 2HA line during somatic embryogenesis in <em>M. truncatula</em>. Overexpression of these genes did not have a significant effect on the somatic embryogenesis capacity. Several genes from <em>NF-YA</em> and <em>C</em> groups with high expression levels during somatic embryogenesis were found. We demonstrated that transcription factors, encoded by some of them, were able to interact with MtNF-YB3 and 10, and overexpression of one of these genes, <em>MtNF-YA3</em>, increased callus weight. The results obtained provide new information about <em>NF-Y</em><span> genes functioning during plant regeneration and can be used for the search of new somatic embryogenesis stimulants.</span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48806901","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}