Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout

Background: Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm. The pathogenesis of CML is based on the oncoprotein termed BCR‐ABL1. TET2 initiates DNA demethylation and is frequently mutated in hematological malignancies including CML.(1) The relation between TET2 acquisition and CML transformation and/or imitinab resistance is needed to be investigated. (2) Aim: To evaluate Ten Eleven Translocation 2 gene (TET2) single nucleotide polymorphism (SNP) (rs2454206, rs34402524, rs61744960) in chronic myeloid leukemia (CML) in relation to the disease prognostic criteria. Materials & Method: The study included 84 subjects; 54 CML in chronic phase and 30 healthy subjects as control group matched for age and sex. Routine investigations including CBC, bone marrow aspiration, biochemical investigations and molecular study were performed in CML patients to identify the disease stage. DNA extraction and SNP assay for TET2 gene polymorphism was done using (Thermo-Fisher predesigned SNP, USA) PCR prism 7500. Results: The mean age was 45.98±15.7 yrs in CML patients and 39.3±6.587 yrs in control group (p>0.05). TET2 SNP rs 34402524 was either heterozygous and homozygous in CML (48%,and 46.2%) but was mainly homozygous among control (80%) group (p=0.012). TET2 SNP rs 2454206 cases within CML (65.4%) and control (63.3%) group had wild patterns (p=0.046). TET2 SNP rs 61744960 showed a homozygous pattern among all groups (CML and control) showing no statistical significance (p=0.528). TET2 SNP in CML cases did not alter the prognostic criteria as no statistical significance was noted (p>0.05) yet, it was significantly related to spleen size in rs 34402524 where homozygous group had huger sizes and higher BCR-ABL1 levels 6 months after starting TKIs (p<0.05). Conclusions/Recommendation: TET2 SNP is a common in Egyptian chronic myeloid leukemia. TET2 SNP rs 3442524 was associated with huger spleen size and higher BCR-ABL1 levels after 6 months of starting TKIs suggesting disease progression.

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Single nucleotide polymorphism associated with disease resistance in Penaeus vannamei

Journal of Invertebrate Pathology ◽

10.1016/j.jip.2020.107498 ◽

2020 ◽

Vol 177 ◽

pp. 107498

Author(s):

Iasmim Santos Mangabeira-Silva ◽

Paulo Eduardo Toscano Soares ◽

Daniel Carlos Ferreira Lanza

Keyword(s):

Single Nucleotide Polymorphism ◽

Disease Resistance ◽

Penaeus Vannamei ◽

Nucleotide Polymorphism ◽

Single Nucleotide

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Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

BMC Genomics ◽

10.1186/1471-2164-10-559 ◽

2009 ◽

Vol 10 (1) ◽

Cited By ~ 97

Author(s):

Cecilia Castaño Sánchez ◽

Timothy PL Smith ◽

Ralph T Wiedmann ◽

Roger L Vallejo ◽

Mohamed Salem ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Rainbow Trout ◽

Deep Sequencing ◽

Single Nucleotide Polymorphism Discovery ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Reduced Representation ◽

Polymorphism Discovery ◽

Reduced Representation Library

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Fishing for SNPs: A Targeted Locus Approach for Single Nucleotide Polymorphism Discovery in Rainbow Trout

Transactions of the American Fisheries Society ◽

10.1577/t05-291.1 ◽

2006 ◽

Vol 135 (6) ◽

pp. 1698-1721 ◽

Cited By ~ 16

Author(s):

A. E. Sprowles ◽

M. R. Stephens ◽

N. W. Clipperton ◽

B. P. May

Keyword(s):

Single Nucleotide Polymorphism ◽

Rainbow Trout ◽

Single Nucleotide Polymorphism Discovery ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Polymorphism Discovery

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Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing

PLoS ONE ◽

10.1371/journal.pone.0138435 ◽

2015 ◽

Vol 10 (9) ◽

pp. e0138435 ◽

Cited By ~ 54

Author(s):

Yniv Palti ◽

Roger L. Vallejo ◽

Guangtu Gao ◽

Sixin Liu ◽

Alvaro G. Hernandez ◽

...

Keyword(s):

Disease Resistance ◽

Rainbow Trout ◽

Dna Sequencing ◽

Restriction Site ◽

Cold Water ◽

Bacterial Cold Water Disease

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Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

BMC Plant Biology ◽

10.1186/s12870-021-03366-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xin Gu ◽

Shanshan Huang ◽

Zhiguo Zhu ◽

Yansong Ma ◽

Xiaohe Yang ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Disease Resistance ◽

Candidate Genes ◽

Genome Wide Association ◽

Effective Strategy ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Cercospora Sojina ◽

Haplotype Blocks ◽

Genome Wide

Abstract Background Frogeye leaf spot (FLS) is a destructive fungal disease that affects soybean production. The most economical and effective strategy to control FLS is the use of resistant cultivars. However, the use of a limited number of resistant loci in FLS management will be countered by the emergence of new high-virulence Cercospora sojina races. Therefore, we identified quantitative trait loci (QTL) that control resistance to FLS and identified novel resistant genes using a genome-wide association study (GWAS) on 234 Chinese soybean cultivars. Results A total of 30,890 single nucleotide polymorphism (SNP) markers were used to estimate linkage disequilibrium (LD) and population structure. The GWAS results showed four loci (p < 0.0001) distributed over chromosomes (Chr.) 5 and 20, that are significantly associated with FLS resistance. No previous studies have reported resistance loci in these regions. Subsequently, 45 genes in the two resistance-related haplotype blocks were annotated. Among them, Glyma20g31630 encoding pyruvate dehydrogenase (PDH), Glyma05g28980, which encodes mitogen-activated protein kinase 7 (MPK7), and Glyma20g31510, Glyma20g31520 encoding calcium-dependent protein kinase 4 (CDPK4) in the haplotype blocks deserves special attention. Conclusions This study showed that GWAS can be employed as an effective strategy for identifying disease resistance traits in soybean and narrowing SNPs and candidate genes. The prediction of candidate genes in the haplotype blocks identified by disease resistance loci can provide a useful reference to study systemic disease resistance.

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Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

BioMed Research International ◽

10.1155/2018/5646213 ◽

2018 ◽

Vol 2018 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Abinaya Manivannan ◽

Jin-Hee Kim ◽

Eun-Young Yang ◽

Yul-Kyun Ahn ◽

Eun-Su Lee ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Disease Resistance ◽

Next Generation Sequencing ◽

Molecular Mechanisms ◽

Next Generation ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genome Wide ◽

The Impact ◽

Generation Sequencing

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

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