scholarly journals Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Rajni Parmar ◽  
Romit Seth ◽  
Ram Kumar Sharma
Keyword(s):  
Transcription Factor ◽  
Stress Tolerance ◽  
Ssr Markers ◽  
Single Amino Acid ◽  
Large Set ◽  
Genome Wide ◽  
Transcription Factor Genes ◽  
Ssr Loci ◽  
Transcriptome Resource

AbstractTea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.

scholarly journals Genome-wide identification and characterization of functionally relevant microsatellites from putative transcription factor genes of tea for efficient genotyping.

2020 ◽  
Author(s):  
Rajni Parmar ◽  
Romit Seth ◽  
RAM Kumar SHARMA
Keyword(s):  
Ssr Markers ◽  
Genome Mapping ◽  
Normal Activity ◽  
Single Amino Acid ◽  
Functional Markers ◽  
Coding Region ◽  
Putative Transcription Factor ◽  
Ssr Loci ◽  
And Function

Abstract Background: SSR markers derived from coding region and non-coding un-translated regions (UTRs) act as potential “functional genetic markers”. Tea, one among the most popular herbal drink with multiple medicinal properties is greatly suffered due to several bottlenecks of self-incompatibility, genome heterozygosity and long gestation period. Despite the huge genomic resources, experimentally validated functionally relevant SSR markers are still scarce in tea. Transcription factors (TFs) accounts for larger proportion of plant genomes regulating expression of various desirable traits have not been explored for development of functional marker resource in tea.Results: In current study, putative 2776 transcripts encoding TFs were identified harbouring 3687 SSR loci. High abundance of repeats in ORF (44.37%), UTRs (5'UTR: 32.57%; 3'UTR: 23.0%) suggests significant functional and regulatory relevance of novel SSR loci in trait dissection. 589 polymorphic novel experimentally validated SSR markers (ORF: 297; 5’UTR: 211; 3'UTR: 81) amplified 2864 alleles with allele numbers (Na) of 2 to 17 per locus. Interestingly, repetitive pattern of tri/hexa-repeats in coding region revealed single amino acid repeats reiteration of serine, glycine and proline, leucine in TFs of tea. Moreover, high representation of TF derived polymorphic SSR markers in bHLH (53), WRKY (37), C3H (32), and Myb-related (31) can be utilised for candidate-gene based mapping in tea. Successful utilization of polymorphic SSR makers for genetic diversity characterization of 115 tea cultivars suggests their wider utility in arge-scale fingerprinting studies. Furthermore, 185 SSR markers representing hk x hk, lm x ll, nn x np, ab x cd and ef x eg segregating patterns in selective genotyping of bi-parental mapping population can be potentially employed in genome mapping studies in tea. Conclusion: SSR repeats in regulatory genes influencing normal activity and function of the gene due to the repeat length (expansion and contraction) causing phenotypic variation in plants. Therefore, identification of first set of 1843 novel putative TFs derived microsatellite markers resource with experimentally validated potential polymorphic markers stipulates their importance in various genotyping studies in tea. Interestingly, SSRs retrieved in important TFs may have direct implications for molecular dissection desirable in tea. Genic functional markers developed in the study are powerful tools and can be potentially utilized to accelerate molecular breeding and trait dissection efforts for implantation of marker-asserted selection in tea.

scholarly journals Genome-wide strategies reveal target genes of Npas4l associated with cardiovascular development in zebrafish

2018 ◽  
Author(s):  
Michele Marass ◽  
Arica Beisaw ◽  
Claudia Gerri ◽  
Francesca Luzzani ◽  
Nana Fukuda ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Chromatin Immunoprecipitation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Building Blocks ◽  
Phenotypic Characterization ◽  
Cardiovascular Development ◽  
Genome Wide ◽  
Transcription Factor Genes

ABSTRACTThe development of a vascular network is essential to nourish tissues and sustain organ function throughout life. Endothelial cells (ECs) are the building blocks of blood vessels, yet our understanding of EC specification remains incomplete. zebrafish cloche/npas4l mutants have been used broadly as an avascular model, but little is known about the molecular mechanisms of action of the Npas4l transcription factor. Here, to identify its direct and indirect target genes, we combined complementary genome-wide approaches including transcriptome analyses and chromatin immunoprecipitation (ChIP). The cross-analysis of these datasets indicates that Npas4l functions as a master regulator by directly inducing a group of transcription factor genes crucial for hematoendothelial specification such as etv2, tal1 and lmo2. We also identified new targets of Npas4l and investigated the function of a subset of them using the CRISPR/Cas9 technology. Phenotypic characterization of tspan18b mutants reveals a novel player in developmental angiogenesis, confirming the reliability of the datasets generated. Collectively, these data represent a useful resource for future studies aimed to better understand EC fate determination and vascular development.

Characterization of a transcription factor SlNAC7 gene from Suaeda liaotungensis and its role in stress tolerance

2021 ◽  
Author(s):  
Hong-Fei Wang ◽  
Hong-Yan Shan ◽  
He Shi ◽  
Dan-Dan Wu ◽  
Tong-Tong Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Stress Tolerance

Identification and Functional Characterization of R3 MYB Transcription Factor Genes in Soybean

2018 ◽  
Vol 61 (2) ◽  
pp. 85-96 ◽  
Author(s):  
Hongwei Xun ◽  
Zhibing Zhang ◽  
Yunxiao Zhou ◽  
Xueyan Qian ◽  
Yingshan Dong ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Functional Characterization ◽  
Myb Transcription Factor ◽  
Transcription Factor Genes

scholarly journals Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations

2019 ◽  
Author(s):  
Olivera Grujic ◽  
Tanya N. Phung ◽  
Soo Bin Kwon ◽  
Adriana Arneson ◽  
Yuju Lee ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Regulatory Sequence ◽  
Human Genetic Variation ◽  
Sequence Motifs ◽  
Variant Prioritization ◽  
Factor Binding ◽  
Genome Wide ◽  
Identification And Characterization

AbstractAnnotations of evolutionarily constraint provide important information for variant prioritization. Genome-wide maps of epigenomic marks and transcription factor binding provide complementary information for interpreting a subset of such prioritized variants. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the human genome being in a constrained non-exonic element from over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting constrained non-exonic bases from such data. However, a subset of such bases are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) using conservation state and constrained element annotations that is predictive of those bases. Using human genetic variation, regulatory sequence motifs, mouse epigenomic data, and retrospectively considered additional human data we further characterize the nature of constrained non-exonic bases with low CNEP scores.

scholarly journals New Insights into the Pleiotropic Drug Resistance Network from Genome-Wide Characterization of the YRR1 Transcription Factor Regulation System

2002 ◽  
Vol 22 (8) ◽  
pp. 2642-2649 ◽  
Author(s):  
Stéphane Le Crom ◽  
Frédéric Devaux ◽  
Philippe Marc ◽  
Xiaoting Zhang ◽  
W. Scott Moye-Rowley ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Transcription Factor ◽  
Binding Site ◽  
Time Course ◽  
Target Genes ◽  
Regulation System ◽  
Dependent Manner ◽  
Pleiotropic Drug Resistance ◽  
Genome Wide

ABSTRACT Yrr1p is a recently described Zn2Cys6 transcription factor involved in the pleiotropic drug resistance (PDR) phenomenon. It is controlled in a Pdr1p-dependent manner and is autoregulated. We describe here a new genome-wide approach to characterization of the set of genes directly regulated by Yrr1p. We found that the time-course production of an artificial chimera protein containing the DNA-binding domain of Yrr1p activated the 15 genes that are also up-regulated by a gain-of-function mutant of Yrr1p. Gel mobility shift assays showed that the promoters of the genes AZR1, FLR1, SNG1, YLL056C, YLR346C, and YPL088W interacted with Yrr1p. The putative consensus Yrr1p binding site deduced from these experiments, (T/A)CCG(C/T)(G/T)(G/T)(A/T)(A/T), is strikingly similar to the PDR element binding site sequence recognized by Pdr1p and Pdr3p. The minor differences between these sequences are consistent with Yrr1p and Pdr1p and Pdr3p having different sets of target genes. According to these data, some target genes are directly regulated by Pdr1p and Pdr3p or by Yrr1p, whereas some genes are indirectly regulated by the activation of Yrr1p. Some genes, such as YOR1, SNQ2, and FLR1, are clearly directly controlled by both classes of transcription factor, suggesting an important role for the corresponding membrane proteins.

Cloning and characterization of BES1/BZR1 transcription factor genes in maize

2018 ◽  
Vol 86 (2) ◽  
pp. 235-249 ◽  
Author(s):  
Haoqiang Yu ◽  
Wenqi Feng ◽  
Fuai Sun ◽  
YuanYuan Zhang ◽  
JingTao Qu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Genes
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