Genome-wide identification and expression analysis revealed cinnamyl alcohol dehydrogenase genes correlated with fruit-firmness in strawberry

2021 ◽  
pp. 1-18
Author(s):  
Ping Wang ◽  
Jing Yang ◽  
Zi-Yi Li ◽  
Jia-Jun Zhu ◽  
Qing-Hua Gao ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Alcohol Dehydrogenase ◽  
Lignin Content ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Class Ii ◽  
Class I ◽  
Fruit Firmness ◽  
Cinnamyl Alcohol ◽  
Genome Wide ◽  
A Genome

BACKGROUND: Strawberry fruits are perishable with a short post-harvest life. Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis strengthening plant cell wall. A systematic characterization of strawberry CAD family is absent and their involvement in fruit firmness is largely elusive. OBJECTIVE: Current work aims for a genome-wide identificationof CAD family and its expression correlation with fruit firmness in strawberry varieties. METHODS: A genome-scale identification and molecular characterization for CADs were performed in the commercial strawberry (Fragaria×ananassa) and woodland strawberry (F. vesca). qPCR analysis of CAD homoeologs in three cultivars varying with fruit firmness revealed candidate CAD members positively correlated with lignin content and fruit firmness. RESULTS: A total of 14 and 24 CAD loci were identified in the genomes of F.vesca var. Hawaii4 and F. ×ananassa cv. Camarosa, respectively.Phylogenetic analysis supported a division of this family into three classes. Class I FvCAD each has four homoeologs in commercial strawberry, while those of Class II and Class III have only one or two homoeologs. Except for FvCAD2 and -6, there exits at least one pair of CADs sharing ∼97% or above amino acid identity between F. vesca and F. ×ananassa.The flesh firmness and lignin content varied greatly among strawberry germplasm. Distinct dynamic changes in fruit lignin content were observed before the large green stage, but fruit firmness displayed a similar decrease profile during fruit development in three varieties. Of the eight genes detected in F.×ananassa, FvCAD3 and -12 did not display a F. vesca-biased expression pattern during fruit development.FvCAD4 of Class I was expressed at levels positively correlated with variation in fruit lignin content at white stage.Transcript abundance of five Class IIgenes including FvCAD3, -8, -10, -11, and -12 was positively correlated with lignin content and fruit firmness, with FvCAD10 and -11 (FaCAD in previous publication) reaching an extremely significant correlation with the genetic variation in fruit firmness across three varieties. CONCLUSION: Strawberry Class II CADs were significantly correlated with the genetic variation in fruit firmness,whichmight expand the potential choices for improving strawberry shelf life.

scholarly journals Isolation and Characterization of Full-Length Phenylalanine Ammonium Lyase and Cinnamyl Alcohol Dehydrogenase Genes Involved in Lignin Biosynthesis of Erianthus Arundinaceus

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 174
Author(s):  
Lakshmi Kasirajan ◽  
Prathima Perumal Thirugnanasambandam ◽  
Agnelo Furtado ◽  
Frikkie C. Botha ◽  
Robert J. Henry
Keyword(s):  
Alcohol Dehydrogenase ◽  
Untranslated Region ◽  
Plant Cell Wall ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Raw Material ◽  
Sequence Information ◽  
Cinnamyl Alcohol ◽  
Isolation And Characterization

Lignocellulosic biomasses available in abundance is the most promising raw material for alternate energy production considering the issues of dwindling oil prices, and global warming. Recently, Erianthus arundinaceous has been identified as a potential target for second generation biofuel crop due to its high biomass production, and adaptability to extreme growth environments. Lignin is a major plant cell wall polymer indispensable for plant growth and development, however it hinders the saccharification of lignocellulosic biomass. Based on the previous transcriptome studies in a set of sugarcane genotypes differing for lignin content, genes encoding cinnamyl alcohol dehydrogenase (CAD), and Phenylalanine ammonia lyase (PAL) genes playing major roles in genetic regulation of lignin production have been cloned and characterized from an Erianthus clone IK 76-81. The genomic region of EriCAD was 3524 bp sequence containing four exons and three introns, among which the exon 1&2 of 88 and 80 bp were conserved with sorghum and Miscanthus CADs. The coding region of CAD was identified with 1086 bp open reading frame (ORF), a 68 bp 5′ untranslated region (UTR), and a 86 bp 3′ untranslated region (UTR). In the PROSITE analysis, a zinc-containing alcohol dehydrogenase signature (GHEVVGEVVEVGPEV) and an NADP-binding domain motif (GLGGLG) was identified. Similarly sequence analysis of PAL showed an ORF of 2106 bp encoding for 702 amino acid residues. It was flanked by 172 bp of 5′ UTR and 121 bp of 3′ UTR. This sequence information on PAL and CAD from Erianthus might be useful for subsequent research on lignin modification for improved biomass conversion.

scholarly journals Improved chemical pulping and saccharification of a natural mulberry mutant deficient in cinnamyl alcohol dehydrogenase

Holzforschung ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Tsutomu Ikeda ◽  
Naoki Takata ◽  
Shingo Sakamoto ◽  
Shi Hu ◽  
Nuoendagula ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Lignin Content ◽  
Compositional Analysis ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Raw Material ◽  
Pulp Yield ◽  
Cinnamyl Alcohol ◽  
Traditional Use ◽  
Width Measurements

Abstract Lignin content and its molecular structure influence various wood characteristics. In this study, the anatomical and physicochemical properties of wood derived from a naturally occurring mulberry mutant deficient in cinnamyl alcohol dehydrogenase (CAD), a key enzyme in lignin biosynthesis, were analyzed using conventional staining assays on stem sections, length and width measurements of xylem fiber cells, wood pulping and saccharification assays, and sugar compositional analysis of extractive-free wood powder. The present data indicate that the mutation in the CAD gene leads to improved wood delignification efficiency, increased pulp yield under alkaline pulping conditions, and enhanced saccharification efficiency following alkaline pretreatment. This study opens up new avenues for the multipurpose use of the mulberry CAD-deficient mutant as a raw material for biorefinery processes, in addition to its traditional use as a favored feed for silkworms.

scholarly journals Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl.

2021 ◽  
Vol 22 (19) ◽  
pp. 10269
Author(s):  
Li Zhang ◽  
Cheng Li ◽  
Danni Yang ◽  
Yuhua Wang ◽  
Yongping Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Class Ii ◽  
Class I ◽  
Genome Wide Analysis ◽  
Cell Proliferation And Differentiation ◽  
Genome Wide ◽  
A Genome ◽  
Transcription Factor Genes ◽  
Transient Activity

Teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family members are plant-specific transcription factors that regulate plant growth and development by controlling cell proliferation and differentiation. However, there are no reported studies on the TCP gene family in Dendrobium catenatum Lindl. Here, a genome-wide analysis of TCP genes was performed in D. catenatum, and 25 TCP genes were identified. A phylogenetic analysis classified the family into two clades: Class I and Class II. Genes in the same clade share similar conserved motifs. The GFP signals of the DcaTCP-GFPs were detected in the nuclei of tobacco leaf epidermal cells. The activity of DcaTCP4, which contains the miR319a-binding sequence, was reduced when combined with miR319a. A transient activity assay revealed antagonistic functions of Class I and Class II of the TCP proteins in controlling leaf development through the jasmonate-signaling pathway. After different phytohormone treatments, the DcaTCP genes showed varied expression patterns. In particular, DcaTCP4 and DcaTCP9 showed opposite trends after 3 h treatment with jasmonate. This comprehensive analysis provides a foundation for further studies on the roles of TCP genes in D. catenatum.

scholarly journals Genome-Wide Identification and Characterization of the TCP Gene Family in Cucumber (Cucumis sativus L.) and Their Transcriptional Responses to Different Treatments

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1379
Author(s):  
Haifan Wen ◽  
Yue Chen ◽  
Hui Du ◽  
Leyu Zhang ◽  
Keyan Zhang ◽  
...  
Keyword(s):  
Class Ii ◽  
Class I ◽  
Signal Pathways ◽  
Transcript Expression ◽  
Organ Development ◽  
Leaf Morphogenesis ◽  
Transcriptional Responses ◽  
Lateral Branching ◽  
Genome Wide ◽  
A Genome

TCP proteins are plant-specific transcription factors widely implicated in leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, the relationship between the transcription pattern of TCPs and organ development in cucumber has not been systematically studied. In this study, we performed a genome-wide identification of putative TCP genes and analyzed their chromosomal location, gene structure, conserved motif, and transcript expression. A total of 27 putative TCP genes were identified and characterized in cucumber. All 27 putative CsTCP genes were classified into class I and class II. Class I comprised 12 CsTCPs and Class II contained 15 CsTCPs. The 27 putative CsTCP genes were randomly distributed in five of seven chromosomes in cucumber. Four putative CsTCP genes were found to contain putative miR319 target sites. Quantitative RT-PCR revealed that 27 putative CsTCP genes exhibited different expression patterns in cucumber tissues and floral organ development. Transcript expression and phenotype analysis showed that the putative CsTCP genes responded to temperature and photoperiod and were induced by gibberellin (GA)and ethylene treatment, which suggested that CsTCP genes may regulate the lateral branching by involving in multiple signal pathways. These results lay the foundation for studying the function of cucumber TCP genes in the future.

scholarly journals Sugarcane expressed sequences tags (ESTs) encoding enzymes involved in lignin biosynthesis pathways

2001 ◽  
Vol 24 (1-4) ◽  
pp. 235-241 ◽  
Author(s):  
Rose Lucia Braz Ramos ◽  
Francisco Javier Tovar ◽  
Ricardo Magrani Junqueira ◽  
Fabiane Borges Lino ◽  
Gilberto Sachetto-Martins
Keyword(s):  
Cell Wall ◽  
Alcohol Dehydrogenase ◽  
Caffeic Acid ◽  
Lignin Content ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Cinnamyl Alcohol ◽  
Cinnamoyl Coa Reductase ◽  
Coa Reductase ◽  
Lignin Metabolism

Lignins are phenolic polymers found in the secondary wall of plant conductive systems where they play an important role by reducing the permeability of the cell wall to water. Lignins are also responsible for the rigidity of the cell wall and are involved in mechanisms of resistance to pathogens. The metabolic routes and enzymes involved in synthesis of lignins have been largely characterized and representative genes that encode enzymes involved in these processes have been cloned from several plant species. The synthesis of lignins is liked to the general metabolism of the phenylpropanoids in plants, having enzymes (e.g. phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H) and caffeic acid O-methyltransferase (COMT)) common to other processes as well as specific enzymes such as cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD). Some maize and sorghum mutants, shown to have defective in CAD and/or COMT activity, are easier to digest because they have a reduced lignin content, something which has motivated different research groups to alter the lignin content and composition of model plants by genetic engineering try to improve, for example, the efficiency of paper pulping and digestibility. In the work reported in this paper, we have made an inventory of the sugarcane expressed sequence tag (EST) coding for enzymes involved in lignin metabolism which are present in the sugarcane EST genome project (SUCEST) database. Our analysis focused on the key enzymes ferulate-5-hydroxylase (F5H), caffeic acid O-methyltransferase (COMT), caffeoyl CoA O-methyltransferase (CCoAOMT), hydroxycinnamate CoA ligase (4CL), cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD). The comparative analysis of these genes with those described in other species could be used as molecular markers for breeding as well as for the manipulation of lignin metabolism in sugarcane.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 283-294 ◽  
Author(s):  
Kristie Ashton ◽  
Ana Patricia Wagoner ◽  
Roland Carrillo ◽  
Greg Gibson
Keyword(s):  
Heart Rate ◽  
Genetic Variation ◽  
Recombinant Inbred Lines ◽  
Model Organism ◽  
Interval Mapping ◽  
Activity Levels ◽  
Environmental Variance ◽  
Genome Wide ◽  
A Genome ◽  
Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

Sign in / Sign up

Export Citation Format

Share Document