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Comprehensive meta-analysis and machine learning approaches identified the role of novel drought specific genes in Oryza sativa 综合荟萃分析和机器学习方法确定了水稻中新的干旱特异性基因的作用
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100382
Raja Rajeswary Thanmalagan, Abhijeet Roy, Aiswarya Jayaprakash, P.T.V. Lakshmi
{"title":"Comprehensive meta-analysis and machine learning approaches identified the role of novel drought specific genes in Oryza sativa","authors":"Raja Rajeswary Thanmalagan,&nbsp;Abhijeet Roy,&nbsp;Aiswarya Jayaprakash,&nbsp;P.T.V. Lakshmi","doi":"10.1016/j.plgene.2022.100382","DOIUrl":"10.1016/j.plgene.2022.100382","url":null,"abstract":"<div><p><span>Rice is a major food crop and provides nutrition for half of the world's population. Rice production is majorly affected by drought at different developmental stages and accounted for annual yield loss depending on the intensity of drought. Hence, the need to study the molecular mechanism in a holistic manner behind drought tolerance is a prerequisite to mitigating this problem. Therefore, in the current study, the drought tolerance mechanism of rice plants was elucidated through a meta-analysis on the publically available </span>transcriptomic<span> datasets by integrating these datasets using a R package to remove the batch effects and applying machine learning approaches for prediction robustness and accuracy. Thus, the classifier model identified 128 essential genes through feature selection algorithms and classification methods on training datasets. The comprehensive study revealed that Naïve Bayes<span> classification and correlation-based feature selection was robust in the prediction of essential genes. The accuracy and performance of the classification model was validated with the independent test dataset and the prediction accuracy of the classifier was 93% with ROC (0.972) and F-measures (0.927). Further, the biological significance of the identified genes in drought tolerance was assessed. The current analysis highlighted the regulatory roles of novel genes such as Os01g0844300, Os06g0246500, Os05g03733900, Os05g0550600 Os08g0442900, Os08g0104400, Os01g0256500, Os02g0259900 and Os05g0572700 in the enhancement of drought tolerance mechanisms. Thus the identified genes might be the potential targets for molecular breeding of drought-tolerant rice cultivars.</span></span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100382"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41709584","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}
引用次数: 1
Inactivating a herbicide-resistance transgene in Nicotiana tabacum plants using CRISPR/Cas9 利用CRISPR/Cas9灭活烟草植株抗除草剂转基因
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100387
Anindita Chakraborty , Hua Li , John Fosu-Nyarko , Sadia Iqbal , Michael G.K. Jones , Stephen J. Wylie
{"title":"Inactivating a herbicide-resistance transgene in Nicotiana tabacum plants using CRISPR/Cas9","authors":"Anindita Chakraborty ,&nbsp;Hua Li ,&nbsp;John Fosu-Nyarko ,&nbsp;Sadia Iqbal ,&nbsp;Michael G.K. Jones ,&nbsp;Stephen J. Wylie","doi":"10.1016/j.plgene.2022.100387","DOIUrl":"10.1016/j.plgene.2022.100387","url":null,"abstract":"<div><p><span>Herbicide and antibiotic tolerance genes serve as useful selectable markers<span><span> for the development of transgenic plants expressing other transgenes. It may be desirable for regulatory or safety reasons to silence the </span>herbicide tolerance trait after transformants have been selected. However, because the genes of interest and the marker gene are usually tightly linked, traditional segregation-based strategies for elimination of undesirable transgenes are usually unsuccessful. Here, we created </span></span><span><em>Nicotiana tabacum</em></span> plants that carry a single copy of a <span><em>Cas9</em></span><span> gene, a nuclease<span> in the clustered regularly interspaced short palindromic repeats (CRISPR) system, physically linked to the selectable marker gene </span></span><span><em>bar</em></span><span> for tolerance to the herbicide glufosinate (Basta, Liberty). Here, </span><em>bar</em> was targeted within the genome by introducing <em>bar</em><span>-specific single guide RNAs (sgRNAs) to the </span><em>N. tabacum</em> line <em>in vitro</em><span>, resulting in abolishment of the glufosinate-tolerance trait in mature plants. Sequence analysis of the </span><em>bar</em> gene revealed a frame-shift mutation at a sgRNA target site, confirming efficacy of the strategy.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100387"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48528201","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}
引用次数: 0
Biotechnology and crop improvement under changing environment: Current interventions 环境变化下的生物技术和作物改良:当前的干预措施
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100376
Sarvajeet Singh Gill , Anca Macovei , Juan Francisco Jimenez-Bremont , Nafees A. Khan , Narendra Tuteja
{"title":"Biotechnology and crop improvement under changing environment: Current interventions","authors":"Sarvajeet Singh Gill ,&nbsp;Anca Macovei ,&nbsp;Juan Francisco Jimenez-Bremont ,&nbsp;Nafees A. Khan ,&nbsp;Narendra Tuteja","doi":"10.1016/j.plgene.2022.100376","DOIUrl":"10.1016/j.plgene.2022.100376","url":null,"abstract":"<div><p>In the era of frequently changing global climatic conditions (like temperature extremes, drought or flooding, soil and air quality or light levels) along with rapidly increasing global population, reducing agriculturally viable land area and soil microflora and soil quality degradation pose a serious threat on crop performance thus on global food security. The climatic variables significantly affect the species reproduction and performance in terms of crop produce. Plant biotechnology has progressed a lot starting from conventional breeding approaches to genetic engineering, genome editing and speed breeding, but so far little has been achieved to develop climate resilient/abiotic stress tolerant and high yielding crop varieties. The reasons may be the complex nature of stress factors, as well as the complexity of genetic regulatory networks. Therefore, the ‘plant gene regulatory network’ is crucial to understand the plant development and survival under various environmental insults.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100376"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48532414","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}
引用次数: 1
Analyses of gene copy number variation in diverse epigenetic regulatory gene families across plants: Increased copy numbers of BRUSHY1/TONSOKU/MGOUN3 (BRU1/TSK/MGO3) and SILENCING DEFECTIVE 3 (SDE3) in long-lived trees 不同表观遗传调控基因家族在植物间的拷贝数变异分析:BRUSHY1/TONSOKU/MGOUN3 (BRU1/TSK/MGO3)和SILENCING DEFECTIVE 3 (SDE3)在长寿树中拷贝数增加
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100384
Yuta Aoyagi Blue , Akiko Satake
{"title":"Analyses of gene copy number variation in diverse epigenetic regulatory gene families across plants: Increased copy numbers of BRUSHY1/TONSOKU/MGOUN3 (BRU1/TSK/MGO3) and SILENCING DEFECTIVE 3 (SDE3) in long-lived trees","authors":"Yuta Aoyagi Blue ,&nbsp;Akiko Satake","doi":"10.1016/j.plgene.2022.100384","DOIUrl":"10.1016/j.plgene.2022.100384","url":null,"abstract":"<div><p><span><span><span>Long-lived trees experience high risk of damage due to the various types of stresses over their lifespans. Epigenetic regulation is involved in gene regulation, genome integrity, and inhibition of exogenous </span>genetic<span> elements, which are functions important for long-term survival. To narrow down the candidate genes related to tree longevity among diverse epigenetic regulatory genes<span>, it is necessary to identify epigenetic regulatory genes with increased copy number in long-lived tree species as compared to in short-lived annual and perennial herb species. In the present study, to find out the epigenetic regulatory genes with increased copy number in tree species as compared to in annual and perennial herb species, we conducted the systematic comparison of </span></span></span>copy number variation<span> in 121 gene families involved in various epigenetic regulatory pathways across 85 plant species with different lifespans using a genome database. Among these 121 gene families, the gene family encoding </span></span><em>BRUSHY1/TONSOKU/MGOUN3</em> (<em>BRU1/TSK/MGO3</em>) and that encoding <em>SILENCING DEFECTIVE 3</em> (<em>SDE3</em><span>) were found to exhibit significantly higher copy number of genes in tree species than in both perennial and annual herb species. BRU1/TSK/MGO3 is involved in chromatin modifications and plays an important role in the maintenance of meristems<span>, genome integrity, and the inheritance of chromatin states. SDE3 is involved in RNA silencing and has an important role in antiviral defense through posttranscriptional gene silencing. The systematic comparison of copy number variation in diverse epigenetic regulatory gene families among plant species can find out epigenetic regulatory genes with increased copy number in long-lived tree species and enhance subsequent studies for understanding the relationship between epigenetic regulation and tree longevity.</span></span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100384"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43608670","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}
引用次数: 3
Aluminum induced malate transporter (ALMT1) is regulating the Aluminum stress tolerance responses of mungbean seedlings 铝诱导苹果酸转运蛋白(ALMT1)调控绿豆幼苗对铝胁迫的抗性反应
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100388
Subharthi Das, Markkandan Ganesan
{"title":"Aluminum induced malate transporter (ALMT1) is regulating the Aluminum stress tolerance responses of mungbean seedlings","authors":"Subharthi Das,&nbsp;Markkandan Ganesan","doi":"10.1016/j.plgene.2022.100388","DOIUrl":"10.1016/j.plgene.2022.100388","url":null,"abstract":"<div><p><span><span>Under acidic soil and Aluminum (Al) stress conditions, the crop plants are facing several growth defects. Particularly significant decrease in root growth, nutrient uptake and low yield are the very common problems. Besides, several organic acid transporters are involved in Al sensing, transport and detoxification mechanisms. In this study, Al stress tolerance of mungbean plants was studied under different Al stress conditions. The results showed that the mungbean plants are severely affected by Al stress and released significant amount of malate in </span>hydroponics media when compared with control plants. Based on this study and expression analysis of Al stress responsive genes, further, we developed </span><em>ALMT1</em> overexpressors and <em>ALMT1-RNAi</em><span> transgenic plants of mungbean to analyse the acid soil tolerance. Later, these transgenic mungbean plants were challenged with different Al concentrations to check their stress responses. The </span><em>ALMT1-RNAi</em> lines showed almost no root growth variations in hydroponics media when compared to wild-type (WT) plants under normal growth conditions but displayed significant decrease in root length on exposure to Al. Further, when <em>AtALMT1</em> was overexpressed, even in absence of Al ions, there was approximately 12% increase in length of primary roots when compared with WT. Malate efflux was almost doubled in the <em>AtALMT1</em> overexpressed plant lines whereas KD lines showed around 36% drop in malate efflux under Al stress conditions. Therefore, based on these observations, we concluded that <em>VrALMT1</em> has a significant role on Al stress tolerance responses in mungbean plants.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100388"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49307676","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}
引用次数: 1
Identification of suitable internal control genes for gene expression analysis of banana in response to BBTV infection 香蕉抗BBTV感染基因表达分析的内控基因鉴定
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100383
Jen Daine L. Nocum , Anand Noel C. Manohar , Jay-Vee S. Mendoza , Fe M. Dela Cueva , Roanne R. Gardoce , Grace C. Lachica , Darlon V. Lantican
{"title":"Identification of suitable internal control genes for gene expression analysis of banana in response to BBTV infection","authors":"Jen Daine L. Nocum ,&nbsp;Anand Noel C. Manohar ,&nbsp;Jay-Vee S. Mendoza ,&nbsp;Fe M. Dela Cueva ,&nbsp;Roanne R. Gardoce ,&nbsp;Grace C. Lachica ,&nbsp;Darlon V. Lantican","doi":"10.1016/j.plgene.2022.100383","DOIUrl":"10.1016/j.plgene.2022.100383","url":null,"abstract":"<div><p><span>Banana is one of the most abundant crops produced annually in the Philippines. The presence of banana bunchy top virus<span> (BBTV) leading to banana bunchy top disease is one of the factors hindering the continuous production of the fruit crop<span>. The use of an appropriate and stable internal control gene as reference in validation of differentially-expressed genes in an organism is important. This study aims to identify appropriate internal control genes for differential gene expression analysis in </span></span></span><span><em>Musa</em><em> balbisiana</em></span> and <em>Musa acuminata</em><span> specific for BBTV infection. RNA extraction, complementary DNA (cDNA) synthesis and RT-qPCR (quantitative real time polymerase chain reaction) of BBTV-resistant and BBTV-susceptible </span><em>Musa</em> genotypes were performed. The RT-qPCR quantification data were then subjected to analysis on RefFinder software and geomean ranking values were calculated along with the four statistical algorithms (delta C<sub>q</sub>, Genorm, BestKeeper and NormFinder). Based on the comprehensive ranking values in the software, <em>L2</em> gene was the most suitable internal control gene for the differential expression analysis of both BBTV-resistant and BBTV-susceptible banana accessions. The internal control gene is recommended for the validation of selected candidate resistance and host factor genes in response to BBTV infection<strong><em>.</em></strong></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100383"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46285965","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}
引用次数: 2
Unraveling the miRnome of Nicotiana rustica (Aztec tobacco) - A Genomewide computational assessment 解开Nicotiana rustica(阿兹特克烟草)的基因组-全基因组计算评估
Plant Gene Pub Date : 2022-12-01 DOI: 10.1016/j.plgene.2022.100378
Mansi Bhavsar , Naman Mangukia , Saumya Patel , Rakesh Rawal , Archana Mankad
{"title":"Unraveling the miRnome of Nicotiana rustica (Aztec tobacco) - A Genomewide computational assessment","authors":"Mansi Bhavsar ,&nbsp;Naman Mangukia ,&nbsp;Saumya Patel ,&nbsp;Rakesh Rawal ,&nbsp;Archana Mankad","doi":"10.1016/j.plgene.2022.100378","DOIUrl":"10.1016/j.plgene.2022.100378","url":null,"abstract":"<div><p><span>MicroRNAs<span> (miRNAs) are endogenous small non-coding RNAs, known as chief regulators for cellular growth and development in plants. </span></span><span><em>Nicotiana rustica</em></span> (<em>N. rustica</em>), also known as Aztec tobacco is the second most widely used lucrative crop for tobacco production across the globe. Since the miRNAs of <em>Nicotiana rustica</em><span> have never been reported, we employed a genome-wide computational approach which resulted in 101 potential candidates of miRNAs, belonging to 73 families, followed by stringent filtration criteria. Statistical analysis confirmed the occurrence of uracil as the dominant initial biased nucleotide base at 5 prime ends of mature miRNAs that may lead to a significant role in miRNA biogenesis and or miRNA mediated gene regulation. Due to unavailability of target sequences, the RNAseq data of </span><em>N. rustica</em><span><span> leaf, flower, stem, and root were retrieved, assembled de novo and concatenated into a clustered customized transcript dataset. The study validates miR160, miR393, miR397, miR403 &amp; miR529 miRNAs and confirmed their targets through experimentally proven literature evidence. These miRNAs can modulate the biological role in transcription regulation, defense response, transporter activity, hormonal signaling and different </span>protein kinase activities. Collectively, this study reports putative miRNAs and their role in Aztec tobacco development and stress response.</span></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"32 ","pages":"Article 100378"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46628072","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}
引用次数: 1
Small heat shock protein (Hsp20) gene family in Phaseolus vulgaris L.: Genome-wide identification, evolutionary and expression analysis 菜豆中Hsp20基因家族的全基因组鉴定、进化和表达分析
Plant Gene Pub Date : 2022-09-01 DOI: 10.1016/j.plgene.2022.100370
Jean Silva de Souza Resende , Tiago Benedito dos Santos , Silvia Graciele Hülse de Souza
{"title":"Small heat shock protein (Hsp20) gene family in Phaseolus vulgaris L.: Genome-wide identification, evolutionary and expression analysis","authors":"Jean Silva de Souza Resende ,&nbsp;Tiago Benedito dos Santos ,&nbsp;Silvia Graciele Hülse de Souza","doi":"10.1016/j.plgene.2022.100370","DOIUrl":"10.1016/j.plgene.2022.100370","url":null,"abstract":"<div><p><span>Understanding the mechanisms responsible for plant tolerance under various abiotic stresses<span> is linked to understanding heat shock proteins (Hsps). The Hsp20 subfamily is the main family of heat shock proteins, but little is known about this family in common bean (</span></span><span><em>Phaseolus</em><em> vulgaris</em></span> L.), an important agricultural crop sensitive to temperature and salt stress. We identified 41 candidate common bean <em>Hsp20</em> genes (<em>PvHsp20</em>). We mapped the <em>PvHsp20</em><span> genes according to their chromosomal locations and found 49 duplications, 35 segmental and 14 tandem. Subsequent gene structure analysis identified regions of exons, introns, and conserved motifs. In the phylogenetic analysis, all </span><em>PvHsp20</em><span> genes were grouped into 11 subfamilies, except for two genes that could not be classified. Synteny analysis revealed that </span><em>Hsp20</em> genes from the common bean are highly related to soybean. Promoter analysis of <em>PvHsp20</em> genes showed the presence of hormone-related, light-responsive and stress-responsive cis-regulatory elements. 8 <em>PvHsp20</em> genes were under the regulation of 8 PvmiRNA genes. The <em>in silico</em> expression profile showed that <em>PvHsp20</em> was differentially expressed. The gene expression of the <em>PvHsp20-31</em>, <em>PvHsp20-27</em>, <em>PvHsp-2</em>, and <em>PvHsp20-39</em><span> genes in the roots of the Ispir genotype suggested that these genes might play a vital role in the salt tolerance mechanism. Our results provide new information, contribute to understanding </span><em>PvHsp20</em> genes, and validate their role in mitigating the adverse effects triggered by abiotic stresses.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"31 ","pages":"Article 100370"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48022734","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}
引用次数: 2
Expression of anthocyanin biosynthesis-related genes during flower development in Lilium spp. 百合花发育过程中花青素生物合成相关基因的表达。
Plant Gene Pub Date : 2022-09-01 DOI: 10.1016/j.plgene.2022.100372
Hasan N.N. Fatihah , Katarzyna Wolinska , Jan G. Schaart , Marian Oortwijn , Richard G.F. Visser , Frans A. Krens
{"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":"31 ","pages":"Article 100372"},"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}
引用次数: 1
Genome-wide analysis of cowpea NAC transcription factor family elucidating the genetic & molecular relationships that interface stress and growth regulatory signals 豇豆NAC转录因子家族的全基因组分析揭示了胁迫与生长调控信号之间的遗传和分子关系
Plant Gene Pub Date : 2022-09-01 DOI: 10.1016/j.plgene.2022.100363
Richa Srivastava, Lingaraj Sahoo
{"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":"31 ","pages":"Article 100363"},"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}
引用次数: 1
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