Plant Gene最新文献_第9页

Genome wide identification and expression profiling of Early responsive to dehydration 6 (ERD6)-like gene family in chickpea (Cicer arietinum L.) 鹰嘴豆早期脱水反应6（ERD6）样基因家族的全基因组鉴定和表达谱

Plant Gene Pub Date : 2023-06-01 DOI: 10.1016/j.plgene.2023.100411

Surbhi Mali , Harsh Nayyar , Rajeev Rathour , Kamal Dev Sharma

{"title":"Genome wide identification and expression profiling of Early responsive to dehydration 6 (ERD6)-like gene family in chickpea (Cicer arietinum L.)","authors":"Surbhi Mali , Harsh Nayyar , Rajeev Rathour , Kamal Dev Sharma","doi":"10.1016/j.plgene.2023.100411","DOIUrl":"10.1016/j.plgene.2023.100411","url":null,"abstract":"<div>Early responsive to dehydration 6 (ERD6)-like is one of the least studied subfamily in plants. Initial evidences based on couple of genes suggest that members of this family are tonoplastic and export glucose to cytosol from tonoplast. However, no information is available on ERD6-like genes in agricultural crops except limited information on Brassica species. In this study, we identified 8, 12, 6 and 7 ERD6-like genes, respectively in Cicer arietinum, Arachis hypogea, Oryza sativa and Glycine max. These and A. thaliana genes were divided into five subgroups based on phylogenetic analysis of proteins. C. arietinum genes were characterized in detail and new nomenclature to these genes was proposed to overcome ambiguities in names of genes. Intron/exon numbers did not vary much among the genes, however, gene/mRNA/coding region/ untranslated regions and proteins showed considerable length variations. Though isoforms were reported for two genes, isoforms of only CaERD6-like 6.3 could be confirmed experimentally. While motifs and transmembrane domains varied among the ERD6-like proteins, all belonged to glucose transport subfamily suggesting those to be glucose transporters. Transcription of genes varied among four chickpea organs with higher expression in some organs and lower in others. Under cold-stress, three genes over-expressed in leaves and roots whereas four genes down-regulated in leaves and two in roots. This is the first report on genome wide identification of ERD6-like genes in four crops of agricultural importance and detailed characterization and expression analysis in chickpea organs under normal growth conditions and cold-stress.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100411"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46658064","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

Gene expression analysis of the ATP-binding cassette transporter ABCD1 in petunia (Petunia hybrida) and tobacco (Nicotiana spp.) ATP结合盒转运蛋白ABCD1在矮牵牛和烟草中的基因表达分析

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100391

Nobukazu Shitan , Shiori Nishitani , Akiko Inagaki , Yoko Nakahara , Yasuyuki Yamada , Takao Koeduka

{"title":"Gene expression analysis of the ATP-binding cassette transporter ABCD1 in petunia (Petunia hybrida) and tobacco (Nicotiana spp.)","authors":"Nobukazu Shitan , Shiori Nishitani , Akiko Inagaki , Yoko Nakahara , Yasuyuki Yamada , Takao Koeduka","doi":"10.1016/j.plgene.2022.100391","DOIUrl":"10.1016/j.plgene.2022.100391","url":null,"abstract":"<div>Most plant metabolites are biosynthesized via organelles, including peroxisome. From the mutant analyses, Arabidopsis ATP-binding cassette (ABC) transporter ABCD1 is reported to be implicated in the peroxisomal import of β-oxidation substrates, which are biosynthetic intermediates for central and specialized metabolites. However, little was explored about ABCD1 in plants except for AtABCD1 and two barley homologs, HvABCD1 and 2. The present study investigated the expression profiles of ABCD1 genes of petunia and tobacco that produce various metabolites, including volatile benzenoid/phenylpropanoids (VBPs) and ubiquinone. PhABCD1 expression was ubiquitous and at particularly high levels (2.2- to 2.8-fold compared to roots) in leaves, limbs, and tubes. NsABCD1 was expressed in roots, stems, leaves, sepals, and flowers; specifically, a relatively high expression level (3.2-fold compared to roots) was observed in sepals. Yeast extract and methyl jasmonate induced the expression of the NtABCD1 gene significantly (1.3- and 2.5-fold, respectively) in N. tabacum BY-2 cells. These results suggest that the expression of ABCD1 would be related to the biosynthesis of metabolites beneficial for plant environmental adaptation in petunia and tobacco. The current study provides new insights into the mechanism of metabolite biosynthesis and ABC transporter function in Solanaceae plants.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100391"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48067528","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

Further studies on nicotianamine aminotransferase (NAAT) genes involved in biofortification in bread wheat (Triticum aestivum L.) 参与面包小麦（Triticum aestivum L.）生物强化的烟酰胺氨基转移酶（NAAT）基因的进一步研究

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100389

Tinku Gautam , Irfat Jan , Ritu Batra , Kalpana Singh , Renu Pandey , Pradeep Kumar Sharma , Harindra Singh Balyan , Pushpendra Kumar Gupta

{"title":"Further studies on nicotianamine aminotransferase (NAAT) genes involved in biofortification in bread wheat (Triticum aestivum L.)","authors":"Tinku Gautam , Irfat Jan , Ritu Batra , Kalpana Singh , Renu Pandey , Pradeep Kumar Sharma , Harindra Singh Balyan , Pushpendra Kumar Gupta","doi":"10.1016/j.plgene.2022.100389","DOIUrl":"10.1016/j.plgene.2022.100389","url":null,"abstract":"<div>Graminaceous plants take up iron (Fe) from soil using specialized chelating agents known as phytosiderophores, which largely comprise mugineic acids (MAs). Biosynthesis of MAs involves three enzymes, of which nicotianamine aminotransferase (NAAT) catalyses the key step in the synthesis of 2′-deoxymugineic acids (DMA). In the present study, a total of 24 TaNAAT genes distributed on 15 of the 21 bread wheat chromosomes were identified using the whole genome sequence. We also identified NAAT genes in diploid and tetraploid relatives of bread wheat. Two gene duplication events involving NAAT genes were also identified, one in Triticum urartu (AA) and the other in Aegilops tauschii (DD). In the promoter regions, a number of cis-regulatory elements were also identified for responses to biotic and abiotic stresses and to different developmental stages. Phylogenetic analysis using NAAT proteins of wheat and seven other plant species led to the identification of six clusters. Both in silico and qRT-PCR expression analyses indicated relatively higher expression of TaNAAT genes in shoot and root of genotypes with low Fe content. The results provided insights into the structure and function of TaNAAT genes, which may further help in planning strategies to develop high yielding wheat varieties tolerant to Fe-deficiency.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100389"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42381915","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

Mapping and identification of QTL for agro-physiological traits in rice (Oryza sativa L.) under drought stress 干旱胁迫下水稻农业生理性状QTL定位与鉴定

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100397

Rizky Dwi Satrio , Miftahul Huda Fendiyanto , Ence Darmo Jaya Supena , S. Suharsono , M. Miftahudin

{"title":"Mapping and identification of QTL for agro-physiological traits in rice (Oryza sativa L.) under drought stress","authors":"Rizky Dwi Satrio , Miftahul Huda Fendiyanto , Ence Darmo Jaya Supena , S. Suharsono , M. Miftahudin","doi":"10.1016/j.plgene.2022.100397","DOIUrl":"10.1016/j.plgene.2022.100397","url":null,"abstract":"<div>Exploring novel QTLs for drought tolerance traits using a new rice genetic resource would be valuable to dissect the mechanisms underlying the complexity of the trait. Here, we used a recombinant inbred line population to detect the QTL associated with agro-physiological traits under drought stress, in particular incorporating the SNPs and 147 phenotype data, analyzed the transcript expression of genes within QTL using differential gene expression meta-analysis and qRT-PCR technique. Composite interval mapping analysis allowed the detection of 154 QTLs distributed into 66 regions, which included a large QTL cluster called ‘hotspot QTL’ that strongly associated with drought tolerance on rice chromosome 8. We found several genes within the QTL-containing regions that were highly expressed based on the meta-analysis approach. In the future, the QTL reported here may be utilized for marker-assisted breeding and the candidate drought-responsive genes could be characterized for dissecting a comprehensive molecular mechanism of drought tolerance in rice.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100397"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44128375","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

Molecular mapping of Chilli veinal mottle virus (ChiVMV) resistance in hot pepper (Capsicum annuum L.) 辣椒对辣椒脉斑病毒（ChiVMV）抗性的分子定位

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100396

Naresh Ponnam , Madhavi Reddy K , Krishna Reddy M , Lakshamana Reddy D.C , Anand C. Reddy , Hemachandra Reddy P

{"title":"Molecular mapping of Chilli veinal mottle virus (ChiVMV) resistance in hot pepper (Capsicum annuum L.)","authors":"Naresh Ponnam , Madhavi Reddy K , Krishna Reddy M , Lakshamana Reddy D.C , Anand C. Reddy , Hemachandra Reddy P","doi":"10.1016/j.plgene.2022.100396","DOIUrl":"10.1016/j.plgene.2022.100396","url":null,"abstract":"<div>Chilli veinal mottle virus (ChiVMV) is a serious potyvirus affecting chilli cultivation in India causing economic yield losses. Breeding resistant varieties/ hybrids is best advocated strategy for viral management. Molecular mapping and markers development greatly facilitates accelerated breeding. Genotyping-by-sequencing was employed for marker discovery and simultaneous genotyping of F2 population developed using contrast parents. Total 6628 single nucleotide polymorphisms (SNP) and 18,125 silicoDArT markers were determined. The SNPs and silicoDArT markers ranged from 280 on chromosome 8 to 625 on chromosome 3 and 857 on chromosome 8 to 1753 on chromosome 3, respectively. Genome wide association study (GWAS) detected 17 SNPs and 21 silicoDArT markers associated with ChiVMV resistance. A major genomic region on chromosome 9 was identified as major candidate loci for ChiVMV resistance. A cluster of defense related genes and elongation translation factors (eIFLE) responsible for disease resistance were predicted within the GWAS regions. A cleaved amplified polymorphic sequence ChiVMVR9_2 CAPS marker was developed for the major resistant locus which was physically mapped at 2,458,715 bp on chromosome 9. This marker can be used in marker-assisted breeding and genomic selection. Further fine mapping of the identified region will facilitate precise marker assisted selection for resistance.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100396"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46016815","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

Squalene synthase in plants – Functional intricacy and evolutionary divergence while retaining a core catalytic structure 植物中的角鲨烯合酶——功能复杂性和进化差异，同时保留核心催化结构

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2023.100403

Anjan Hazra, Madhurima Dutta, Rajashree Dutta, Ekta Bhattacharya, Rahul Bose, Suparna Mandal Biswas

{"title":"Squalene synthase in plants – Functional intricacy and evolutionary divergence while retaining a core catalytic structure","authors":"Anjan Hazra, Madhurima Dutta, Rajashree Dutta, Ekta Bhattacharya, Rahul Bose, Suparna Mandal Biswas","doi":"10.1016/j.plgene.2023.100403","DOIUrl":"10.1016/j.plgene.2023.100403","url":null,"abstract":"<div>Squalene is the crucial intermediate for the biosynthesis of many bioactive triterpenoids, such as phytosterol in plants or cholesterol in animals. Squalene synthase (SQS) is the essential gene of the squalene biosynthetic pathway, which catalyzes the head-to-head condensation of two farnesyl pyrophosphate or farnesyl diphosphate (FPP) molecules in a two-step reaction and formation of linear C30 squalene. SQS ubiquitously occurs in all eukaryotic organisms. However, the activity of this gene varies significantly, leading to diverse squalene content in plants. The present study focused on the variation in the expression landscape of SQS gene copies with varying evolutionary backgrounds. Afterward, a reflection of the sequence divergence on the catalytic structure of the protein was examined. The genome-scale mining of the SQS homologs revealed varying degrees of duplication events, sequence evolution of the gene sequence itself, and the adjoining regulatory architecture. Contrasting expressional patterns and the regulatory modules pinpoint the importance of transcriptional regulation of this essential gene. Three-dimensional organizations of SQS from diverse evolutionary taxa and their consensus structures enlightened the conservation of critical catalytic domains, nonetheless divergence in the majority of the protein. As a whole, the outputs of this study provide some valuable insights for understanding the functional regulation of SQS under different tissues and environments.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100403"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47649755","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

Erratum to “The complete chloroplast genome of Chinese medicine (Psoralea corylifolia): Molecular structures, barcoding and phylogenetic analysis” [Plant Gene 21C (2020) 100216] “中药补骨脂(Psoralea corylifolia)叶绿体全基因组:分子结构、条形码和系统发育分析”[植物基因21C (2020) 100216]

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100402

Wei Tan , Han Gao , Huanyu Zhang , Xiaolei Yu , Xiaoxuan Tian , Weiling Jiang , Kun Zhou

引用次数: 0

Genome-wide identification of the bHLH transcription factor family and analysis of bHLH genes related to puerarin biosynthesis in Pueraria lobata var. thomsonii (Benth.) 葛根bHLH转录因子家族的全基因组鉴定及葛根素生物合成相关基因分析

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100390

Liang Xiao , Ding Huang , Zhengdan Wu , Xiaohong Shang , Sheng Cao , Wendan Zeng , Liuying Lu , Pingli Shi , Huabing Yan

{"title":"Genome-wide identification of the bHLH transcription factor family and analysis of bHLH genes related to puerarin biosynthesis in Pueraria lobata var. thomsonii (Benth.)","authors":"Liang Xiao , Ding Huang , Zhengdan Wu , Xiaohong Shang , Sheng Cao , Wendan Zeng , Liuying Lu , Pingli Shi , Huabing Yan","doi":"10.1016/j.plgene.2022.100390","DOIUrl":"10.1016/j.plgene.2022.100390","url":null,"abstract":"<div>Plant basic helix-loop-helix (bHLH) transcription factors are involved in diverse biological process. So far, there has been no report to systematically carry out comprehensive identification of bHLH members in Pueraria lobata var. thomsonii (Benth.) (P. thomsonii), a traditional Chinese herb that is an excellent source of puerarin. Phylogenetic analysis showed that 219 bHLH genes were identified in the P. thomsonii and classified into 13 subfamilies. All the PlbHLH genes were distributed on the 11 chromosomes unevenly and the number of PlbHLH genes on each chromosome varied from 12 to 44. Both of tandem and segmental duplications were key factors driving bHLH gene family expansion in P. thomsonii. A total of 20 conserved motifs were found in PlbHLH gene family, 185 PlbHLH members contain more than two introns, and genes within the same subfamily appeared to share similar intron-exon gene structures. The Ka/Ks analysis indicated PlbHLH gene family undergo purifying selection during evolution. Combined the RNA-seq data with the qRT-PCR detection results, PlbHLH79/148/149 were found to be the most probably candidate genes which were involved in puerarin biosynthesis pathway. Together, our study provided a good foundation for further research into the regulatory mechanism of the candidate PlbHLH proteins for puerarin biosynthesis in P. thomsonii.</div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"33 ","pages":"Article 100390"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41909005","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

Gene expression differences related to pre-harvest sprouting uncovered in related wheat varieties by RNAseq analysis RNAseq分析发现相关小麦品种收获前发芽相关基因表达差异

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2023.100404

Bryan W. Penning

引用次数: 1

Erratum to “Identification of miRNAs and evaluation of candidate genes expression profile associated with drought stress in barley” [Plant Gene 20C (2019) 100205] “与大麦干旱胁迫相关的miRNA鉴定和候选基因表达谱评估”勘误表[Plant Gene 20C（2019）100205]

Plant Gene Pub Date : 2023-03-01 DOI: 10.1016/j.plgene.2022.100392

Sajjad Zare , Farhad Nazarian-Firouzabadi , Ahmad Ismaili , Hassan Pakniyat

引用次数: 0