scholarly journals Grapevine Phenological Quantitative Trait SSR Genotyping Using High-Throughput HRM-PCR Analysis

Phyton ◽  
2020 ◽  
Vol 89 (4) ◽  
pp. 905-923
Author(s):  
Murad Awad ◽  
Photini V. Mylona ◽  
Alexios N. Polidoros
Keyword(s):  
High Throughput ◽  
Quantitative Trait ◽  
Pcr Analysis ◽  
Ssr Genotyping

scholarly journals Quantitative trait loci identification and genetic diversity analysis of panicle structure and grain shape in rice

2019 ◽  
Vol 90 (1) ◽  
pp. 89-100 ◽  
Author(s):  
Xin Xu ◽  
Mengchen Zhang ◽  
Qun Xu ◽  
Yue Feng ◽  
Xiaoping Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Grain Shape ◽  
Rice Yield ◽  
Pcr Analysis ◽  
Diversity Analysis ◽  
Dh Population ◽  
Genetic Diversity Analysis ◽  
Trait Loci

Abstract Panicle structure and grain shape are important components of rice architecture that directly contribute to rice yield and are regulated by quantitative trait loci (QTLs). In this study, a doubled haploid (DH) population derived from a cross between japonica “Maybelle” and indica “Baiyeqiu” was used to determine genetic effects on panicle structure and grain shape. All detected traits exhibited a continuous, transgressive distribution in the DH population. QTL analysis showed that a total of 24 QTLs related to panicle structure and grain shape were detected on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, and 12, and three epistatic interaction QTLs were detected. Some genes related to panicle structure and grain shape were predicted in the major QTLs, and variations existed between the parents in all genes. Only OsIDS1, GS5, and SRS3 had nonsynonymous mutations that led to protein changes. Quantitative real-time PCR analysis showed that the expression levels of GS5 and OsFOR1 significantly differed between the two parents. In addition, genetic diversity analysis showed that the H3-35–H3-37, H6-18–H6-19, and H7-12–H7-14 intervals might be selected in the breeding program.

scholarly journals High-Throughput RT-PCR Analysis of Multiple Transcripts Using a Microplate RNA Isolation Procedure

BioTechniques ◽  
1997 ◽  
Vol 22 (6) ◽  
pp. 1107-1113 ◽  
Author(s):  
S. Su ◽  
R.G. Vivier ◽  
M.C. Dickson ◽  
N. Thomas ◽  
M.K. Kendrick ◽  
...  
Keyword(s):  
High Throughput ◽  
Rna Isolation ◽  
Isolation Procedure ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Multiple Transcripts

scholarly journals Identification of Differentially Expressed MicroRNAs in Osteosarcoma

Sarcoma ◽  
2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Rishi R. Lulla ◽  
Fabricio F. Costa ◽  
Jared M. Bischof ◽  
Pauline M. Chou ◽  
Maria de F. Bonaldo ◽  
...  
Keyword(s):  
High Throughput ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Osteosarcoma Cell ◽  
Human Osteoblasts ◽  
Normal Human ◽  
Mirna Expression Profiling

A limited number of reports have investigated the role of microRNAs in osteosarcoma. In this study, we performed miRNA expression profiling of osteosarcoma cell lines, tumor samples, and normal human osteoblasts. Twenty-two differentially expressed microRNAs were identified using high throughput real-time PCR analysis, and 4 (miR-135b, miR-150, miR-542-5p, and miR-652) were confirmed and validated in a different group of tumors. Both miR-135b and miR-150 have been previously shown to be important in cancer. We hypothesize that dysregulation of differentially expressed microRNAs may contribute to tumorigenesis. They might also represent molecular biomarkers or targets for drug development in osteosarcoma.

scholarly journals Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e68433 ◽  
Author(s):  
Zemao Yang ◽  
Daiqing Huang ◽  
Weiqi Tang ◽  
Yan Zheng ◽  
Kangjing Liang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Cold Tolerance ◽  
High Throughput ◽  
Quantitative Trait ◽  
High Throughput Sequencing ◽  
Rice Seedlings ◽  
Trait Loci

scholarly journals Unraveling microRNA Mediated Gene Regulation in Centella asiatica (L.) Urb. by High-throughput Sequencing based Small-RNA Profiling.

2022 ◽  
Author(s):  
Gouri Priya Ranjith ◽  
Jisha Satheesan ◽  
K K Sabu
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
Centella Asiatica ◽  
Plant Secondary Metabolite ◽  
Pcr Analysis ◽  
Shoot Cultures ◽  
Regulatory Pathways ◽  
Mrna Targets ◽  
Computational Screening ◽  
Wide Range

Abstract Centella asiatica is a widely spread herb mostly found in the tropics having extensive medicinal values. Here, we report for the first time, transcriptome-wide characterization of miRNA profile from the leaves of C. asiatica using high-throughput Illumina sequencing. We identified 227 conserved and 109 putative novel miRNAs. Computational screening revealed potential mRNA targets for both the conserved and novel miRNAs encoding diverse transcription factors and enzymes involved in plant development, disease resistance, metabolic and signaling pathways. Gene ontology annotation and KEGG analysis revealed the miRNA targets to be involved in a wide range of metabolomic and regulatory pathways. The differential expression of the miRNA encoding genes in diverse tissues was determined by real-time PCR analysis. We also found that gene expression levels of miR156, 159 and 1171 was reduced in salicylic acid treated axenic shoot cultures of C. asiatica compared to its control. Furthermore, RLM-RACE experiments mapped miRNA-mediated cleavage at two of the mRNA targets. The present study represents the large-scale identification of microRNAs from C. asiatica and contributes to the base for the up-coming studies on miRNA-mediated gene regulation of plant secondary metabolite pathways in particular.

scholarly journals Unraveling MicroRNA Mediated Gene Regulation in Centella Asiatica (L.) Urb. by High-Throughput Sequencing based Small-RNA Profiling.

2021 ◽  
Author(s):  
Gouri Priya Ranjith ◽  
Jisha Satheesan ◽  
K K Sabu
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
Centella Asiatica ◽  
Plant Secondary Metabolite ◽  
Pcr Analysis ◽  
Shoot Cultures ◽  
Regulatory Pathways ◽  
Mrna Targets ◽  
Computational Screening ◽  
Wide Range

Abstract Centella asiatica is a widely spread herb mostly found in the tropics having extensive medicinal values. Here, we report for the first time, transcriptome-wide characterization of miRNA profile from the leaves of C. asiatica using high-throughput Illumina sequencing. We identified 227 conserved and 109 putative novel miRNAs. Computational screening revealed potential mRNA targets for both the conserved and novel miRNAs encoding diverse transcription factors and enzymes involved in plant development, disease resistance, metabolic and signaling pathways. Gene ontology annotation and KEGG analysis revealed the miRNA targets to be involved in a wide range of metabolomic and regulatory pathways. The differential expression of the miRNA encoding genes in diverse tissues was determined by real-time PCR analysis. We also found that gene expression levels of miR156, 159 and 1171 was reduced in salicylic acid treated axenic shoot cultures of C. asiatica compared to its control. Furthermore, RLM-RACE experiments mapped miRNA-mediated cleavage at two of the mRNA targets. The present study represents the large-scale identification of microRNAs from C. asiatica and contributes to the base for the up-coming studies on miRNA-mediated gene regulation of plant secondary metabolite pathways in particular.

scholarly journals KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping

2019 ◽  
Vol 35 (17) ◽  
pp. 3187-3190 ◽  
Author(s):  
Alsamman M Alsamman ◽  
Shafik D Ibrahim ◽  
Aladdin Hamwieh
Keyword(s):  
High Throughput ◽  
In Silico ◽  
Genetic Maps ◽  
Supplementary Information ◽  
Pcr Analysis ◽  
Analysis Tool ◽  
Data Types ◽  
Kasp Assay ◽  
In Silico Pcr

Abstract Motivation Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool. Results To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes/SNPs/simple sequence repeats and those that are shared between in vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results. Availability and implementation Code available under GNU GPL at (http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon). Supplementary information Supplementary data are available at Bioinformatics online.

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