Plant Gene最新文献

{"title":"MicroRNAs for understanding and improving agronomic traits in oilseed Brassicas","authors":"Astuti Rani ,&nbsp;Shubhangi Singh ,&nbsp;Pinky Yadav ,&nbsp;Heena Arora ,&nbsp;Inderjeet Kaur ,&nbsp;Namrata Dhaka","doi":"10.1016/j.plgene.2023.100422","DOIUrl":"10.1016/j.plgene.2023.100422","url":null,"abstract":"<div><p>Oilseed Brassicas are economically important crops, with <em>Brassica napus, B. juncea</em>, and <em>B. rapa</em> constituting prominent oilseed resources in the Indian subcontinent and across the world. Improving of oil yield, quality, and resistance to abiotic and biotic stresses in oilseed Brassicas warrants concerted efforts. Owing to quantitative nature, the genetic basis of these traits is complex, and can be significantly improved by incorporating the knowledge of precise genetic regulation of these traits. MicroRNAs (miRNAs) can act as attractive targets for crop improvement as they fine-tune gene expression by targeting genes negatively. Here we highlight the emerging evidences of miRNA-mediated regulation of genes controlling several development traits and stress-related traits in oilseed Brassicas. At least 13 miRNAs have so far been well elucidated in oilseed Brassicas using miRNA overexpression, mutation and target mimic approaches, in regulation of different agronomic traits. Further, at least 29 high-throughput small RNA profiling studies have proffered crucial miRNA-target pair candidates for further investigation. This knowledge so far remains unutilized in designing crop improvement programs in oilseed Brassicas. However, there are sufficient evidences to suggest that miRNAs as well as their target genes can be successfully employed in breeding as well as genome editing-mediated engineering of oilseed crops for improving their agricultural traits.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100422"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41321373","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":"Complete genome of the kikuyu grass chloroplast (Cenchrus clandestinus) and comparative analysis within the subfamily Panicoideae","authors":"Juliana Arango ,&nbsp;Juan F. Alzate ,&nbsp;Albeiro López ,&nbsp;Edna J. Márquez ,&nbsp;José J. Echeverri","doi":"10.1016/j.plgene.2023.100414","DOIUrl":"10.1016/j.plgene.2023.100414","url":null,"abstract":"<div><p>Within the subfamily Panicoideae<em>,</em> the <em>Cenchrus</em> genus which is distributed in both tropical and subtropical regions worldwide—is economically important in terms of their production levels. For milkshed areas, one of the most important pastures is kikuyu (<em>Cenchrus clandestinus</em>), which represents the basic forage used for feeding in a number of countries. In this study, the kikuyu grass (<em>Cenchrus clandestinus</em>) plastome was sequenced, assembled, and annotated to broaden the information and the set of available genomic data. One whole-genome shotgun (WGS) library was constructed using Nextera preparation kits and was sequenced in an Illumina MiSeq platform. In addition, the genomic organization and arrangement of genes as well as their phylogenetic relationship with other species of the family Poaceae were compared using 81 protein-coding genes. The present study characterized and annotated the complete plastome of kikuyu grass, <em>Cenchrus clandestinus</em>, as an informative contribution for future studies potentially investigating the evolution of plant genomes and, specifically, aiming to elucidate the phylogenetic relationships within the family Poaceae,Overall, the results indicate that the structure and organization are conserved compared with other references within the family Poaceae. Phylogenetic relationships confirmed the position of kikuyu within the <em>Cenchrus</em> genus, and they are consistent with previous results obtained for other species of the subfamily Panicoideae<em>.</em></p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100414"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49545036","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 comparative analysis of Glycolate oxidase (GOX) gene family in plants","authors":"Érica Monik Silva Roque,&nbsp;Felipe de Castro Teixeira,&nbsp;Alex Martins de Aguiar,&nbsp;Victor Breno Faustino Bezerra,&nbsp;Ana Carolina Moreira da Costa,&nbsp;Sâmia Alves Silva,&nbsp;Ana Luiza Sobral Paiva,&nbsp;Humberto Henrique de Carvalho,&nbsp;Murilo Siqueira Alves","doi":"10.1016/j.plgene.2023.100407","DOIUrl":"10.1016/j.plgene.2023.100407","url":null,"abstract":"<div><p>Glycolate Oxidase (GOX) is a key enzyme in photorespiration, a complex metabolic pathway in plants that affects photosynthesis efficiency and one of its most prominent products is hydrogen peroxide (H₂O₂). Photosynthetic pathways and H₂O₂ production can drastically differ between C3 and C4 plants which have distinctions in the photorespiration machinery. Such contrasts critically impact physiological processes in plants, such as development and stress responses. However, few studies bring light to evolutionary and structural aspects of the photorespiration components, and comparative analyses of gene families related to photorespiration in C3 and C4 plants are lacking. In the present study, we present the first genome-wide comparative analysis of the <em>GOX</em> gene family in plants, comparing relevant evolutionary and structural aspects of distinct <em>GOX</em> orthologs in plant families. The evolutionary relationships, gene structure, conserved motifs, promoter <em>cis</em>-element prediction, chromosome location, and interspecific collinearity were analyzed in order to gain a better understanding of the <em>GOX</em> gene family in plants. Family-dependent evolutionary and structural divergence were observed among distinct <em>GOX</em> genes, with higher gene conservation among <em>Fabaceae</em> family members. High sequence divergence found among <em>Fabaceae</em> and <em>Poaceae GOX</em> orthologs may impact functional divergence among these gene families. This comparative study provides a comprehensive picture of evolutionary and structural aspects of the <em>GOX</em> gene family in plants, as well as emphasizes the involvement of <em>GOX</em> orthologs in plant stress responses.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100407"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47168283","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":"In silico characterization of Ajmaline biosynthesis pathway genes in plants","authors":"Rittika Ray ,&nbsp;Smita Ray,&nbsp;Sritama Mukherjee","doi":"10.1016/j.plgene.2023.100420","DOIUrl":"10.1016/j.plgene.2023.100420","url":null,"abstract":"<div><p>Alkaloids sourced from medicinally important plants have wide impact on human health and well-being. Ajmaline, a monoterpenoid indole alkaloid have divergent pharmacological applications and require large scale production. <em>Rauvolfia serpentina</em> (Apocynaceae) is an important source of ajmaline. Our present work encompasses computational phylogenetic approach towards understanding the ancestry and divergence of six of the most important enzymes of ajmaline biosynthetic pathway- Strictosidine synthase (STR1, EC 4.3.3.2), Strictosidine glucosidase (SGR1, EC 3.2.1.105), Polyneuridine aldehyde esterase (PNAE, EC 3.1.1.78), Vinorine synthase (ACT/VS, EC 2.3.1.160), Vinorine hydroxylase (CYP5437/VH, EC 1.14.13.75) and Acetylajmalan esterase (AAE, EC 3.1.1.80). The highly restricted distribution of the genes represents their conservative nature and other than the members of Apocynaceae the genes of Ajmaline biosynthesis were found to be distributed in Rubiaceae, Malvaceae, Solanaceae, Oleaceae, Gelsemiaceae, Fabaceae, Fragaceae etc. Identification of conserved domains of the enzymes were analysed based on the sequence homology of related plants. Amino acid sequences of STR1 showed highly variable N-terminal region in contrast to SGR1 and VH where the N-terminal sequence showed more conservation than C-terminal half. PNAE and VS showed high conservation throughout the sequence. Homology modeling and in silico structural analysis of the enzymes provide valuable insight for further structural and functional experimentation. The results reflected conservation of the core catalytic domain in all the six enzymes studied which is useful for structure-based evolution studies or for rational design and modulation of the enzyme's substrate specificity. Extensive literature survey resulted in identification of homologous genes of the aforementioned enzymes in <em>Arabidopsis thaliana</em> whose expressions at different stress conditions and developmental stages were investigated in publicly available microarray-based platform. The genes were found to be upregulated under different biotic and abiotic stresses. Also differential expression was detected at developmental stages.The data presented here will positively contribute towards deciphering the intricacies of reaction mechanism and steer bioengineering of alkaloid production to benefit mankind.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100420"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41713277","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":"Potential role of a maize metallothionein gene in pest resistance","authors":"Patrick F. Dowd ,&nbsp;Todd A. Naumann ,&nbsp;Eric T. Johnson","doi":"10.1016/j.plgene.2023.100409","DOIUrl":"10.1016/j.plgene.2023.100409","url":null,"abstract":"<div><p>Maize is grown worldwide and much of the world depends on its production, which is lessened by insect and fungal pests. Many maize genes with the potential to improve pest resistance exist in non-functional forms in several inbreds but are functional in those that show resistance. One such gene, encoding a metallothionein protein, was located from a resistance locus of maize inbred GE440, which shows resistance to some <em>Fusarium</em> spp. pathogens. The identified gene, encoding ZmMT10, is disrupted in many maize inbreds, including the commonly used inbred B73. When introduced into maize callus, transformants often significantly increased resistance to <em>F. proliferatum,</em> but were often less effective against <em>F. graminearum</em>. Some transformed callus with the ZmMT10 gene also retarded growth of two classes of insect pests, fall armyworms and corn earworms. Recombinant ZmMT10 was purified from <em>Escherichia coli</em>. The purified protein was found to bind zinc, copper, and nickel and scavenged reactive oxygen species in vitro, which are possible mechanisms for its antiinsect and antifungal activities. In bioassays, the purified protein retarded growth of fall armyworms and corn earworms, but did not show activity against fungi, suggesting that the antifungal activity observed in callus tissue is dependent on the interaction with other plant factors. The inclusion of the identified gene in new plant varieties should increase resistance to both insects and fungi.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100409"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41837406","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":"Mechanisms of hormonal-mediated stress regulation in plants","authors":"Anket Sharma ,&nbsp;Marco Landi ,&nbsp;Claudio Pugliesi ,&nbsp;Bingsong Zheng","doi":"10.1016/j.plgene.2023.100417","DOIUrl":"10.1016/j.plgene.2023.100417","url":null,"abstract":"","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100417"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43997070","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 and expression analyses of MADS-box genes in the tetraploid Coffea arabica L. and its diploid parental subgenomes","authors":"Gabriel de Campos Rume,&nbsp;Raphael Ricon de Oliveira,&nbsp;Thales Henrique Cherubino Ribeiro,&nbsp;Antonio Chalfun-Júnior","doi":"10.1016/j.plgene.2023.100413","DOIUrl":"10.1016/j.plgene.2023.100413","url":null,"abstract":"<div><p>MADS-box is a family of transcription factors widely found in different kingdoms and essential for plant development. Understanding the evolution and functioning of such genes in developmental processes is essential to develop more adapted crops and guarantee food production. However, genome-wide analyses of MADS-box genes are poorly explored in tropical perennial species with complex phenological cycles and floral synapomorphic characters, such as <em>Coffea</em> sp. Moreover, <em>Coffea arabica</em> L. is unique in its genre being the only autogamous and tetraploid species, formed from the hybridization of the parental diploid genomes <em>C. canephora</em> and <em>C. eugenioides</em>, offering an opportunity to study recent ploidization and functionalization events. Here, we identified a total of 102 MADS-box unigenes in <em>Coffea</em> sp., being 81 unpublished. They were classified into Type I and II proteins (MIKC* and MIKC^C), 42 and 60 respectively, and categorized in the currently described subgroups. A chromosomal map revealed an irregular distribution and low positional variation of genes between homologous parental chromosomes. Gene structure analysis showed higher similarity for genes closely related, but a variable number of introns and its lengths between distant ones. Next, in order to provide functional insights, we determined the expression profiles of these genes in RNA-Seq libraries of different coffee tissues. Transcripts relative to Type II proteins presented a broader expression pattern than Type I, with low expression values and restricted to specific libraries. Thus, our work contributed to elucidating the evolutionary history of MADS-box genes in Rubiaceae, providing perspectives to functional studies and useful to direct breeding programs.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100413"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43223310","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":"Diverse morphological and molecular patterns of tomato (Solanum lycopersicum Linn.) accessions","authors":"O.J. Olawuyi ,&nbsp;V.I. Ajie","doi":"10.1016/j.plgene.2023.100423","DOIUrl":"10.1016/j.plgene.2023.100423","url":null,"abstract":"<div><p>Field and molecular experiments were conducted between May and August 2021 at the research farm of the Department of Botany, University of Ibadan and International Institute of Tropical Agriculture, Ibadan respectively. Morphological and molecular variability in 40 tomato accessions were investigated in this study. Five accessions from local markets in Ibadan, two varieties from seed companies, three varieties from Benue State and Oyo State, and thirty accessions from the National Center for Genetic Resources and Biotechnology (NACGRAB) were evaluated. The experiment was arranged in a randomised complete block design (RCBD) with three replicates. Significant (<em>p</em> &lt; 0.05) variation was observed for days to germination, hypocotyl colour, primary leaf length, primary leaf width, number of leaves, plant height, number of leaves under first inflorescence, number of inflorescence, days to first fruiting, foliage density and internode length (cm). The cumulative values for the first three components (74.80%) accounted for variation among the 40 accessions in the principal component analysis. All yield related characters correlated positively with both the number of leaves and plant height. The study revealed that NGB/05081, NGB/00714, NGB/05075, NGB/00696, NGB/00735b and Hausa (Dugbe) accessions performed the best in growth and yield characters, while NGB/00735b and NGB/00759 were early maturing accessions. The Tp 124 and Tp 121 primers were highly polymorphic and had high gene diversities. Sixteen tomato accessions were amplified for marker genes <em>nodZ-A</em> and <em>nodZ-B</em>. Five of these accessions showed high growth, while seven produced high yield, implying positive influence on the improvement of these accessions. However, the <em>nifh</em> marker gave no amplification.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100423"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44162668","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":"Molecular and ionomic responses of Solanum lycopersicum L. (cv. Micro-Tom) plants treated with a novel calcium-based plant biostimulant","authors":"Giovanni Bertoldo ,&nbsp;Maria Cristina Della Lucia ,&nbsp;Ali Baghdadi ,&nbsp;Francesca Mangione ,&nbsp;Massimo Cagnin ,&nbsp;Claudia Chiodi ,&nbsp;Giuseppe Concheri ,&nbsp;Piergiorgio Stevanato ,&nbsp;Serenella Nardi","doi":"10.1016/j.plgene.2023.100408","DOIUrl":"10.1016/j.plgene.2023.100408","url":null,"abstract":"<div><p>In this study, we investigated the leaf treatment effects of a novel trace elements calcium-based fluid mixture with a supposed biostimulant action on <em>Solanum lycopersicum</em> L. cv. Micro-Tom. Seedlings were grown on standard peat substrate and treated with two different products: a calcium-based fluid mixture and a common calcium fertilizer, CaCl₂. Both treatments were compared to an untreated control. We first investigated the effects of treatments on fruit yield and dry matter production in greenhouse-grown tomato. These effects were then assessed in leaves by gene expression profiling of 60 genes involved in different biological pathways and functional categories, and by ionomic analysis. Leaf treatment on tomato with the calcium-based fluid mixture allowed the highest fruit yield per plant (6.17 fruits plant⁻¹) and above-ground dry matter (13.99 g plant⁻¹) to be obtained. Also, 4 genes related to the nutrient transporter category, <em>NCX</em>, <em>NRAMP3</em>, <em>SI BOR2</em>, and <em>CHLM</em>, were upregulated in plants treated with the novel product. <em>CRK</em>, a gene related to the calcium-dependent protein kinases (<em>CDPK</em>), was upregulated in plants treated with the novel product whereas <em>SODCC.1</em>, a gene related to the superoxide dismutase family, was downregulated in the same plants. A substantial reduction of elemental contents was observed for CaCl₂-treated plants, while the novel Ca-based mixture increased the leaf mineral content of Zn (+61%) and Mn (+65%). These results highlighted the biostimulant activity of the novel product resulting in changes in fruit yield and dry matter production, gene expression, and ionome profiles of tomato leaves.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100408"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48009998","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":"Start codon targeted (SCoT) variability analysis and its association with hydroxy citric acid (HCA) in Garcinia gummi-gutta (L.) Roxb.","authors":"Babu Vishnu,&nbsp;Remya Ramachandran,&nbsp;A. Gangaprasad,&nbsp;E.A. Siril","doi":"10.1016/j.plgene.2023.100415","DOIUrl":"10.1016/j.plgene.2023.100415","url":null,"abstract":"<div><p>Hydroxycitric acid (HCA) is one of the proven natural antiobesity agents enriched in the fruits of <em>Garcinia gummi-gutta</em> (L.) Roxb. (Family: Clusiaceae). The present research work was carried out to evaluate the genetic variability among 35 candidate plus trees (CPTs) using HCA estimated through HPLC and start codon targeted (SCoT) molecular markers. The association analysis between phenotypic and genotypic traits was also conducted. The selected CPTs showed an average HCA content of 29.11 mg/g and Gar 17 had the highest (48.32 mg/g) followed by Gar 6 (45.48 mg/g). SCoT marker analysis revealed that 19 primers, out of 30 yielded a total of 151 bands with 66.89% polymorphic bands. Principal coordinate analysis (PCoA) organized the CPTs into the four quadrants of a scatterplot irrespective of HCA content. Dendrogram based on neighbour joining method proved its reproducibility by its bootstrapping values, and it has three clusters. STRUCTURE analysis opened the probability of two assumed subpopulations within the selected individuals. Association analysis based on a general linear model (GLM) agreed with the strong association of SCoT 5d allele with HCA content, which also supports the promising nature of Gar 6 as per previous findings. Analysis based on HCA and SCoT markers was effective in tracing out the genetic variabilities among the CPTs and the marker-trait association. The findings are the first in <em>G. gummi-gutta</em>, best of our knowledge.</p></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"34 ","pages":"Article 100415"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47011341","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}