scholarly journals Large-Scale Single-Nucleotide Polymorphism (SNP) and Haplotype Analyses, Using Dense SNP Maps, of 199 Drug-Related Genes in 752 Subjects: the Analysis of the Association between Uncommon SNPs within Haplotype Blocks and the Haplotypes Constructed with Haplotype-Tagging SNPs

2004 ◽  
Vol 75 (2) ◽  
pp. 190-203 ◽  
Author(s):  
Naoyuki Kamatani ◽  
Akihiro Sekine ◽  
Takuya Kitamoto ◽  
Aritoshi Iida ◽  
Susumu Saito ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Large Scale ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Haplotype Blocks

scholarly journals Genome-wide Association of Single Nucleotide Polymorphism Loci and Candidate Genes for Frogeye Leaf Spot (Cercospora Sojina) Resistance in Soybean

2021 ◽  
Author(s):  
Xin Gu ◽  
Shanshan Huang ◽  
Yansong Ma ◽  
Xiaohe Yang ◽  
Liangliang Yao ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Protein Kinase ◽  
Candidate Genes ◽  
Leaf Spot ◽  
Genome Wide Association ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cercospora Sojina ◽  
Haplotype Blocks ◽  
Genome Wide

Abstract Background: Frogeye leaf spot (FLS) is a destructive fungal disease in soybean production. The most economical and effective strategy to control FLS is to use resistant cultivars. However, the use of a limited number of resistant loci in FLS management will be countered by the emergence of new, and more virulent, Cercospora sojina races. Thus, 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 identified six loci (p<0.001) distributed over chromosomes (Chr.) 2, 5, 20 comprising 69 SNPs significantly associated with FLS resistance. No previous studies have reported resistance loci in these regions. Subsequently, 55 genes in three resistance-related haplotype blocks were annotated. Glyma20g31630 encoding pyruvate dehydrogenase (PDH), Glyma05g28980 encoding mitogen-activated protein kinase 7 (MPK7), and Glyma20g31510, Glyma20g31520 encoding the calcium-dependent protein kinase 4(CDPK4) in the haplotype blocks were found to be associated with FLS resistance.Conclusions: The proteins encoded by these four genes directly, or indirectly participate in the biological pathway of salicylic acid (SA) and jasmonic acid (JA). These two plant hormones can induce the expression of disease resistance related genes and are essential for plant systemic acquired resistance (SAR). Therefore, the novel loci and candidate genes provide genomic location information for further advances in FLS resistance gene cloning and molecular breeding.

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

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.

scholarly journals Saliva-Derived DNA Performs Well in Large-Scale, High-Density Single-Nucleotide Polymorphism Microarray Studies: Figure 1.

2010 ◽  
Vol 19 (3) ◽  
pp. 794-798 ◽  
Author(s):  
Melanie Bahlo ◽  
Jim Stankovich ◽  
Patrick Danoy ◽  
Peter F. Hickey ◽  
Bruce V. Taylor ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Large Scale ◽  
High Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Microarray Studies

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

2006 ◽  
Vol 112 (6) ◽  
pp. 1104-1114 ◽  
Author(s):  
Karl J. Schmid ◽  
Ottó Törjék ◽  
Rhonda Meyer ◽  
Heike Schmuths ◽  
Matthias H. Hoffmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Large Scale ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Scale Population
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