scholarly journals Using RNA Sequencing and In Silico Subtraction to Identify Resistance Gene Analog Markers for Lr16 in Wheat

2015 ◽  
Vol 8 (2) ◽  
Author(s):  
Nicole Rezac Harrison ◽  
Allan K. Fritz ◽  
Jarret I. Glasscock ◽  
Sara Ahmed ◽  
David N. Messina ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Rna Sequencing ◽  
In Silico ◽  
Resistance Gene Analog

Temporal Changes in Resistance Gene Analog Polymorphism of Major Rice Varieties in Guangdong Province

2013 ◽  
Vol 39 (7) ◽  
pp. 1206
Author(s):  
Zhi-Ming TANG ◽  
Jian-You CHEN ◽  
Yong-Fa LU ◽  
Hua-Cheng ZHOU ◽  
Xue-Jiao MO ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Guangdong Province ◽  
Temporal Changes ◽  
Resistance Gene Analog ◽  
Rice Varieties

scholarly journals Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Stevan D. Stojanović ◽  
Maximilian Fuchs ◽  
Chunguang Liang ◽  
Kevin Schmidt ◽  
Ke Xiao ◽  
...  
Keyword(s):  
Data Mining ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Rna Sequencing ◽  
In Silico ◽  
Rna Binding ◽  
Human Lung ◽  
Model Systems ◽  
Lung Fibroblasts ◽  
Sequencing Analysis

AbstractThe family of RNA-binding proteins (RBP) functions as a crucial regulator of multiple biological processes and diseases. However, RBP function in the clinical setting of idiopathic pulmonary fibrosis (IPF) is still unknown. We developed a practical in silico screening approach for the characterization of RBPs using multi-sources data information and comparative molecular network bioinformatics followed by wet-lab validation studies. Data mining of bulk RNA-Sequencing data of tissues of patients with IPF identified Quaking (QKI) as a significant downregulated RBP. Cell-type specific expression was confirmed by single-cell RNA-Sequencing analysis of IPF patient data. We systematically analyzed the molecular interaction network around QKI and its functional interplay with microRNAs (miRs) in human lung fibroblasts and discovered a novel regulatory miR-506-QKI axis contributing to the pathogenesis of IPF. The in silico results were validated by in-house experiments applying model systems of miR and lung biology. This study supports an understanding of the intrinsic molecular mechanisms of IPF regulated by the miR-506-QKI axis. Initially applied to human lung disease, the herein presented integrative in silico data mining approach can be adapted to other disease entities, underlining its practical relevance in RBP research.

In Silico Analysis of Micro-RNA Sequencing Data

2021 ◽  
pp. 231-251
Author(s):  
Ernesto Aparicio-Puerta ◽  
Bastian Fromm ◽  
Michael Hackenberg ◽  
Marc K. Halushka
Keyword(s):  
Rna Sequencing ◽  
In Silico ◽  
In Silico Analysis ◽  
Micro Rna ◽  
Sequencing Data ◽  
Silico Analysis

scholarly journals Fine mapping of Brassica napus blackleg resistance gene Rlm1 through bulked segregant RNA sequencing

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fuyou Fu ◽  
Xunjia Liu ◽  
Rui Wang ◽  
Chun Zhai ◽  
Gary Peng ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Resistance Gene ◽  
Rna Sequencing ◽  
Catalytic Domain ◽  
Leptosphaeria Maculans ◽  
Snp Markers ◽  
Specific Pcr ◽  
Dual Specificity ◽  
Kinase Catalytic Domain ◽  
Allele Specific

Abstract The fungal pathogen Leptosphaeria maculans causes blackleg disease on canola and rapeseed (Brassica napus) in many parts of the world. A B. napus cultivar, ‘Quinta’, has been widely used for the classification of L. maculans into pathogenicity groups. In this study, we confirmed the presence of Rlm1 in a DH line (DH24288) derived from B. napus cultivar ‘Quinta’. Rlm1 was located on chromosome A07, between 13.07 to 22.11 Mb, using a BC1 population made from crosses of F1 plants of DH16516 (a susceptible line) x DH24288 with bulked segregant RNA Sequencing (BSR-Seq). Rlm1 was further fine mapped in a 100 kb region from 19.92 to 20.03 Mb in the BC1 population consisting of 1247 plants and a F2 population consisting of 3000 plants using SNP markers identified from BSR-Seq through Kompetitive Allele-Specific PCR (KASP). A potential resistance gene, BnA07G27460D, was identified in this Rlm1 region. BnA07G27460D encodes a serine/threonine dual specificity protein kinase, catalytic domain and is homologous to STN7 in predicted genes of B. rapa and B. oleracea, and A. thaliana. Robust SNP markers associated with Rlm1 were developed, which can assist in introgression of Rlm1 and confirm the presence of Rlm1 gene in canola breeding programs.

Cloning of a Resistance Gene Analog from Wheat and Development of a Codominant PCR Marker for Pm21

2006 ◽  
Vol 48 (6) ◽  
pp. 715-721 ◽  
Author(s):  
Ya-Ping Chen ◽  
Hua-Zhong Wang ◽  
Ai-Zhong Cao ◽  
Chun-Mei Wang ◽  
Pei-Du Chen
Keyword(s):  
Resistance Gene ◽  
Resistance Gene Analog ◽  
Pcr Marker ◽  
Codominant Pcr Marker

scholarly journals In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data

Genomics Data ◽  
2016 ◽  
Vol 7 ◽  
pp. 46-53 ◽  
Author(s):  
Suyash Agarwal ◽  
Naresh Sahebrao Nagpure ◽  
Prachi Srivastava ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
...  
Keyword(s):  
Pineal Gland ◽  
Rna Sequencing ◽  
Danio Rerio ◽  
Small Rna ◽  
In Silico ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Genome Wide ◽  
The Brain

Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 509-516 ◽  
Author(s):  
Z X Shi ◽  
X M Chen ◽  
R F Line ◽  
H Leung ◽  
C R Wellings
Keyword(s):  
Molecular Markers ◽  
Resistance Gene ◽  
Stripe Rust ◽  
Puccinia Striiformis ◽  
Resistance Gene Analog ◽  
Stripe Rust Resistance ◽  
Isogenic Line ◽  
Wheat Cultivars ◽  
Development Of Resistance ◽  
Rye Translocations

The Yr9 gene, which confers resistance to stripe rust caused by Puccinia striiformis f.sp. tritici (P. s. tritici) and originated from rye, is present in many wheat cultivars. To develop molecular markers for Yr9, a Yr9 near-isogenic line, near-isogenic lines with nine other Yr genes, and the recurrent wheat parent 'Avocet Susceptible' were evaluated for resistance in the seedling stage to North American P. s. tritici races under controlled temperature in the greenhouse. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for Yr9. The BC7:F2 and BC7:F3 progeny, which were developed by backcrossing the Yr9 donor wheat cultivar Clement with 'Avocet Susceptible', were evaluated for resistance to stripe rust races. Genomic DNA was extracted from 203 BC7:F2 plants and used for cosegregation analysis. Of 16 RGAP markers confirmed by cosegregation analysis, 4 were coincident with Yr9 and 12 were closely linked to Yr9 with a genetic distance ranging from 1 to 18 cM. Analyses of nulli-tetrasomic 'Chinese Spring' lines with the codominant RGAP marker Xwgp13 confirmed that the markers and Yr9 were located on chromosome 1B. Six wheat cultivars reported to have 1B/1R wheat-rye translocations and, presumably, Yr9, and two rye cultivars were inoculated with four races of P. s. tritici and tested with 9 of the 16 RGAP markers. Results of these tests indicate that 'Clement', 'Aurora', 'Lovrin 10', 'Lovrin 13', and 'Riebesel 47/51' have Yr9 and that 'Weique' does not have Yr9. The genetic information and molecular markers obtained from this study should be useful in cloning Yr9, in identifying germplasm that may have Yr9, and in using marker-assisted selection for combining Yr9 with other stripe rust resistance genes.Key words: molecular markers, Puccinia striiformis f.sp. tritici, resistance gene analog polymorphism, Triticum aestivum.

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