scholarly journals Development of Single Nucleotide Polymorphism (SNP) Markers in Tropical Crops

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Yheni Dwiningsih ◽  
Miranti Rahmaningsih ◽  
Jawaher Alkahtani
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Breeding ◽  
Association Studies ◽  
Snp Markers ◽  
Snp Marker ◽  
Marker Genes ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Tropical Crops

Understanding genetic diversity, association studies, evolution analysis, quantitative trait loci, marker-assisted selection and genome-wide association in tropical crops are important for improving plant characteristics in order to increase food sustainability in tropical countries. Single nucleotide polymorphism (SNP) marker is becoming the most popular molecular marker for those studies. By using SNP marker, genes associated with important traits can be identified efficiently compared to the other molecular markers. This review describes about how SNP can be discovered in the plant genomes and the application of SNP in plant breeding, especially in tropical crops such as rice, maize, peas, potato, tomato, cassava, taro, etc.   Keywords: food sustainability, plant breeding, SNP marker, tropical crops

scholarly journals Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Wang ◽  
Xiaohua Wu ◽  
Yanwei Li ◽  
Zishan Feng ◽  
Zihan Mu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Snp Markers ◽  
Bottle Gourd ◽  
Snp Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Core ◽  
Germplasm Collections ◽  
Diversity Assessment

Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.

scholarly journals Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content by Genotyping-By-Sequencing (GBS) in teleost Larimichthys crocea

2016 ◽  
Author(s):  
Shijun Xiao ◽  
Panpan Wang ◽  
Linsong Dong ◽  
Yaguang Zhang ◽  
Zhaofang Han ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Association Studies ◽  
Snp Markers ◽  
Large Yellow Croaker ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Commercial Fish ◽  
Structure Conservation ◽  
Snp Development

Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. GBS provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by SequenomMassARRAYassay. The association studies with the muscle EPA and DHA content discovered 39 significant SNP markers, contributing as high up to ~63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA/DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.

scholarly journals Replication of Top Loci From COL4A1/2 Associated With White Matter Hyperintensity Burden in Patients With Ischemic Stroke

Stroke ◽  
2020 ◽  
Vol 51 (12) ◽  
pp. 3751-3755
Author(s):  
Jiang Li ◽  
Vida Abedi ◽  
Ramin Zand ◽  
Christoph J. Griessenauer ◽  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Ischemic Stroke ◽  
Odds Ratio ◽  
Association Studies ◽  
Genome Wide Association ◽  
White Matter Hyperintensity ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide

Background and Purpose: The purpose of this study was to replicate the top loci associated with white matter hyperintensity (WMH) phenotypes identified by large genome-wide association studies and the loci identified from the previous candidate gene studies. Methods: A total of 946 Geisinger MyCode patients with acute ischemic stroke with validated European ancestry and magnetic resonance imaging data were included in this study. Log-transformed WMH volume, as a quantitative trait, was calculated by a fully automated quantification process. The genome-wide association studies was carried out by a linear mixed regression model (GEMMA). A candidate-single nucleotide polymorphism analysis by including known single nucleotide polymorphisms, reported from a meta-analysis and several large GWAS for WMH, was conducted in all cases and binary converted extreme cases. Results: No genome-wide significantly associated variants were identified. In a candidate-single nucleotide polymorphism study, rs9515201 ( COL4A2 ) and rs3744028 ( TRIM65 ), 2 known genetic loci, showed nominal or trend of association with the WMH volume (β=0.13 and P =0.001 for rs9515201; β=0.094 and P =0.094 for rs3744028), and replicated in a subset of extreme cases versus controls (odds ratio=1.78, P =7.74×10 − 4 for rs9515201; odds ratio=1.53, P =0.047 for rs3744028, respectively). MTHFR677 cytosine/thymine (rs1801133) also showed an association with the binary WMH with odds ratio=1.47 for T allele ( P =0.019). Conclusions: Replication of COL4A1/2 associated with WMH reassures that the genetic risk factors for monogenic and polygenic ischemic stroke are shared at gene level.

scholarly journals An Analysis Pipeline for Genome-wide Association Studies

2008 ◽  
Vol 6 ◽  
pp. CIN.S966 ◽  
Author(s):  
Stefan Stefanov ◽  
James Lautenberger ◽  
Bert Gold
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Missing Values ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Population Difference ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
And Control

We developed an efficient pipeline to analyze genome-wide association study single nucleotide polymorphism scan results. Perl scripts were used to convert genotypes called using the BRLMM algorithm into a modified PB format. We computed summary statistics characteristic of our case and control populations including allele counts, missing values, heterozygosity, measures of compliance with Hardy-Weinberg equilibrium, and several population difference statistics. In addition, we computed association tests, including exact tests of association for genotypes, alleles, the Cochran-Armitage linear trend test, and dominant, recessive, and overdominant models at every single nucleotide polymorphism (SNP). In addition, pairwise linkage disequilbrium statistics were elaborated, using the command line version of HaploView, which was possible by writing a reformatting script. Additional Perl scripts permit loading the results into a MySQL database conjoined with a Generic Genome Browser (gbrowse) for comprehensive visualization. This browser incorporates a download feature that provides actual case and control genotypes to users in associated genomic regions. Thus, re-analysis “on the fly” is possible for casual browser users from anywhere on the Internet.

scholarly journals Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content by Genotyping-By-Sequencing (GBS) in teleost Larimichthys crocea

2016 ◽  
Author(s):  
Shijun Xiao ◽  
Panpan Wang ◽  
Linsong Dong ◽  
Yaguang Zhang ◽  
Zhaofang Han ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Association Studies ◽  
Snp Markers ◽  
Large Yellow Croaker ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Commercial Fish ◽  
Structure Conservation ◽  
Snp Development

Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. GBS provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by SequenomMassARRAYassay. The association studies with the muscle EPA and DHA content discovered 39 significant SNP markers, contributing as high up to ~63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA/DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.

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