scholarly journals Characterization of Insect Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies

2017 ◽  
Vol 8 ◽  
Author(s):  
Hao-Xun Chang ◽  
Glen L. Hartman
Keyword(s):  
Insect Resistance ◽  
Association Studies ◽  
Germplasm Collection ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Soybean Germplasm ◽  
Genome Wide

scholarly journals Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies

2016 ◽  
Vol 106 (10) ◽  
pp. 1139-1151 ◽  
Author(s):  
Hao-Xun Chang ◽  
Alexander E. Lipka ◽  
Leslie L. Domier ◽  
Glen L. Hartman
Keyword(s):  
Disease Resistance ◽  
Association Studies ◽  
Germplasm Collection ◽  
The United States ◽  
Genome Wide Association ◽  
Bacterial Disease ◽  
United States Department ◽  
Genome Wide Association Studies ◽  
Soybean Germplasm ◽  
Genome Wide

Genetic resistance is a key strategy for disease management in soybean. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many pathogens, resulting in the development of disease-resistant elite breeding lines and commercial cultivars. While biparental linkage mapping has been used to identify disease resistance loci, genome-wide association studies (GWAS) using high-density and high-quality markers such as single nucleotide polymorphisms (SNPs) has become a powerful tool to associate molecular markers and phenotypes. The objective of our study was to provide a comprehensive understanding of disease resistance in the United States Department of Agriculture Agricultural Research Service Soybean Germplasm Collection by using phenotypic data in the public Germplasm Resources Information Network and public SNP data (SoySNP50K). We identified SNPs significantly associated with disease ratings from one bacterial disease, five fungal diseases, two diseases caused by nematodes, and three viral diseases. We show that leucine-rich repeat (LRR) receptor-like kinases and nucleotide-binding site-LRR candidate resistance genes were enriched within the linkage disequilibrium regions of the significant SNPs. We review and present a global view of soybean resistance loci against multiple diseases and discuss the power and the challenges of using GWAS to discover disease resistance in soybean.

scholarly journals Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150070 ◽  
Author(s):  
Longjuan Qin ◽  
Yuyong Liu ◽  
Ya Wang ◽  
Guiju Wu ◽  
Jie Chen ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Post genome-wide association studies functional characterization of prostate cancer risk loci

BMC Genomics ◽  
2013 ◽  
Vol 14 (Suppl 8) ◽  
pp. S9 ◽  
Author(s):  
Junfeng Jiang ◽  
Weirong Cui ◽  
Wanwipa Vongsangnak ◽  
Guang Hu ◽  
Bairong Shen
Keyword(s):  
Prostate Cancer ◽  
Cancer Risk ◽  
Association Studies ◽  
Functional Characterization ◽  
Prostate Cancer Risk ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Discovery, Validation and Characterization of Erbb4 and Nrg1 Haplotypes Using Data from Three Genome-Wide Association Studies of Schizophrenia

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e53042 ◽  
Author(s):  
Zeynep Sena Agim ◽  
Melda Esendal ◽  
Laurent Briollais ◽  
Ozgun Uyan ◽  
Mehran Meschian ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Using Data

scholarly journals Genome-Wide Association Studies Identified Resistance Loci to Orange Rust and Yellow Leaf Virus Diseases in Sugarcane (Saccharum spp.)

2019 ◽  
Vol 109 (4) ◽  
pp. 623-631 ◽  
Author(s):  
Xiping Yang ◽  
Sushma Sood ◽  
Ziliang Luo ◽  
James Todd ◽  
Jianping Wang
Keyword(s):  
Disease Resistance ◽  
Association Studies ◽  
Germplasm Collection ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Yellow Leaf ◽  
Saccharum Spp ◽  
Genome Wide ◽  
A Genome ◽  
Leaf Virus

Sugarcane (Saccharum spp.) supplies globally ∼80% of table sugar and 60% of bioethanol. Sugarcane orange rust and Sugarcane yellow leaf virus (SCYLV) are major sugarcane diseases, causing up to 50 and 40% yield losses, respectively. Sugarcane cultivars resistant to these diseases are needed to sustain sugarcane production in several regions. Dissecting DNA sequence variants controlling disease resistance provides a valuable tool for fulfilling a breeding strategy to develop resistant cultivars. In this study, we evaluated disease reactions to orange rust and SCYLV of a sugarcane diversity panel in repeated trials. We conducted a genome-wide association study between high-density markers and disease resistance reactions. We identified 91 putative DNA markers and 82 candidate genes significantly associated with resistance to one of the two diseases. These provide an important genetic resource for finding genes and molecular markers for disease resistance. Our results emphasized the importance of utilizing a wide germplasm collection for breeding resistant sugarcane cultivars.

scholarly journals Multi-Ethnic Genome-Wide Association Study of Decomposed Cardioelectric Phenotypes Illustrates Strategies to Identify and Characterize Evidence of Shared Genetic Effects for Complex Traits

2020 ◽  
Vol 13 (4) ◽  
Author(s):  
Antoine R. Baldassari ◽  
Colleen M. Sitlani ◽  
Heather M. Highland ◽  
Dan E. Arking ◽  
Steve Buyske ◽  
...  
Keyword(s):  
Qt Interval ◽  
Association Studies ◽  
Genetic Effects ◽  
P Wave ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Shared Genetic

Background: We examined how expanding electrocardiographic trait genome-wide association studies to include ancestrally diverse populations, prioritize more precise phenotypic measures, and evaluate evidence for shared genetic effects enabled the detection and characterization of loci. Methods: We decomposed 10 seconds, 12-lead electrocardiograms from 34 668 multi-ethnic participants (15% Black; 30% Hispanic/Latino) into 6 contiguous, physiologically distinct (P wave, PR segment, QRS interval, ST segment, T wave, and TP segment) and 2 composite, conventional (PR interval and QT interval) interval scale traits and conducted multivariable-adjusted, trait-specific univariate genome-wide association studies using 1000-G imputed single-nucleotide polymorphisms. Evidence of shared genetic effects was evaluated by aggregating meta-analyzed univariate results across the 6 continuous electrocardiographic traits using the combined phenotype adaptive sum of powered scores test. Results: We identified 6 novels ( CD36, PITX2, EMB, ZNF592, YPEL2 , and BC043580 ) and 87 known loci (adaptive sum of powered score test P <5×10 −9 ). Lead single-nucleotide polymorphism rs3211938 at CD36 was common in Blacks (minor allele frequency=10%), near monomorphic in European Americans, and had effects on the QT interval and TP segment that ranked among the largest reported to date for common variants. The other 5 novel loci were observed when evaluating the contiguous but not the composite electrocardiographic traits. Combined phenotype testing did not identify novel electrocardiographic loci unapparent using traditional univariate approaches, although this approach did assist with the characterization of known loci. Conclusions: Despite including one-third as many participants as published electrocardiographic trait genome-wide association studies, our study identified 6 novel loci, emphasizing the importance of ancestral diversity and phenotype resolution in this era of ever-growing genome-wide association studies.

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