scholarly journals Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice (Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing

2018 ◽  
Vol 9 ◽  
Author(s):  
Jiayu Song ◽  
Jinqun Li ◽  
Jian Sun ◽  
Tao Hu ◽  
Aiting Wu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Oryza Sativa ◽  
Association Mapping ◽  
Core Collection ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Specific Locus

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 Study Meta-Analysis of Stroke in 22 000 Individuals of African Descent Identifies Novel Associations With Stroke

Stroke ◽  
2020 ◽  
Vol 51 (8) ◽  
pp. 2454-2463
Author(s):  
Keith L. Keene ◽  
Hyacinth I. Hyacinth ◽  
Joshua C. Bis ◽  
Steven J. Kittner ◽  
Braxton D. Mitchell ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Meta Analysis ◽  
African Descent ◽  
Genome Wide Association ◽  
Minority Population ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome

Background and Purpose: Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. Methods: The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. Results: In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance ( P =4.62×10 −8 ) and an additional 29 variants with suggestive evidence of association ( P <1×10 −6 ), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10 −3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN ( P =8.18×10 −4 ) and METASTROKE ( P =1.72×10 −3 ) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. Conclusions: These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.

scholarly journals Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach

Heredity ◽  
2020 ◽  
Author(s):  
Panthita Ruang-areerate ◽  
Anthony J. Travis ◽  
Shannon R. M. Pinson ◽  
Lee Tarpley ◽  
Georgia C. Eizenga ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Mapping ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Genome Wide
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