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 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 Sex Differences in the Genetics of Sarcoidosis Across European and African Ancestry Populations

2021 ◽  
Author(s):  
Ying Xiong ◽  
Susanna Kullberg ◽  
Lori Garman ◽  
Nathan Pezant ◽  
David Ellinghaus ◽  
...  
Keyword(s):  
Sex Differences ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
The United States ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
A Genome ◽  
Löfgren’S Syndrome

Abstract Background: Sex differences in the susceptibility of sarcoidosis are unknown. The study aims to identify sex-dependent genetic variations in two sarcoidosis clinical phenotypes: Löfgren's syndrome (LS) and non- Löfgren's syndrome (non-LS).Methods: A meta-analysis of genome-wide association studies was conducted in Europeans and African Americans, totaling 10,103 individuals from three population-based cohorts, Sweden (n = 3,843), Germany (n = 3,342), and the United States (n = 2,918), followed by replication look-up in the UK Biobank (n = 387,945). A genome-wide association study based on Immunochip data consisting of 141,000 single nucleotide polymorphisms (SNPs) was conducted in males and females in each cohort, respectively. The association test was based on logistic regression using the additive model in LS and non-LS independently. Additionally, gene-based analysis, expression quantitative trait loci (eQTL) assessments, and enrichment analysis were performed to discover functionally relevant mechanisms related to biological sex. Results: In LS sarcoidosis, we identified various sex-dependent genetic variations (798 SNPs in males and 703 SNPs in females). Genetic findings in sex groups were explicitly located in the extended major histocompatibility complex. In non-LS, we detected 16 SNPs in males and 38 in females, primarily localized to the MHC class II region. Additionally, the ANXA11 gene, a well-documented locus in sarcoidosis, was associated exclusively with non-LS males. Gene-based, eQTL assessment and enrichment analyses revealed distinct sex-dependent genomic loci and gene expression variation in the sex groups. Conclusions: Our findings provide new evidence of the existence of sex-dependent genetic variations underlying sarcoidosis genetic architecture. These findings suggest a sex bias in molecular mechanisms of sarcoidosis.

Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population

2021 ◽  
Vol 118 (47) ◽  
pp. e2107830118
Author(s):  
Andrey K. Shevchenko ◽  
Daria V. Zhernakova ◽  
Sergey V. Malov ◽  
Alexey Komissarov ◽  
Sofia M. Kolchanova ◽  
...  
Keyword(s):  
United States ◽  
Genetic Variants ◽  
Association Studies ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Gene Association ◽  
Genome Wide ◽  
Aids Progression ◽  
Hiv Aids

Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States–African American or United States–European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.

scholarly journals New QTLs for Spot Blotch Disease Resistance in Wheat (Triticum aestivum L.) Using Genome-Wide Association Mapping

2021 ◽  
Vol 11 ◽  
Author(s):  
Vipin Tomar ◽  
Daljit Singh ◽  
Guriqbal Singh Dhillon ◽  
Ravi Prakash Singh ◽  
Jesse Poland ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Studies ◽  
Bipolaris Sorokiniana ◽  
Spot Blotch ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Protein Families ◽  
Wheat Production ◽  
Genome Wide ◽  
Diverse Field

Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker–trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.

Genome-Wide Association Studies: Back to the Future

2013 ◽  
Author(s):  
Margaret Lock
Keyword(s):  
United States ◽  
High Speed ◽  
Association Studies ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Research Projects ◽  
Genome Wide ◽  
Increased Risk ◽  
Control Samples

This chapter examines findings from the newly developed technology of genome-wide association studies (GWAS) being applied to the investigation of Alzheimer disease (AD), primarily in the United States, United Kingdom, and France. These linked research projects make use of many thousands of DNA samples procured from individuals diagnosed with AD, which are then assessed using high-speed throughput technology and compared with control samples, in an attempt to find out what combinations of genes put individuals at increased risk. To date, these enormously expensive projects have provided few if any startling new insights, and many researchers are highly skeptical as to their value. However, others believe that GWAS is a first step toward a more sophisticated way of understanding the interrelated pathways of the numerous genes that appear to be implicated in AD.

scholarly journals Colorectal Cancer Risk by Genetic Variants in Populations With and Without Colonoscopy History

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Feng Guo ◽  
Xuechen Chen ◽  
Jenny Chang-Claude ◽  
Michael Hoffmeister ◽  
Hermann Brenner
Keyword(s):  
Colorectal Cancer ◽  
Prediction Models ◽  
Association Studies ◽  
Statistical Tests ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Large Genome ◽  
Genome Wide ◽  
History Of

Abstract Background Polygenic risk scores (PRS), which are derived from results of large genome-wide association studies, are increasingly propagated for colorectal cancer (CRC) risk stratification. The majority of studies included in the large genome-wide association studies consortia were conducted in the United States and Germany, where colonoscopy with detection and removal of polyps has been widely practiced over the last decades. We aimed to assess if and to what extent the history of colonoscopy with polypectomy may alter metrics of the predictive ability of PRS for CRC risk. Methods A PRS based on 140 single nucleotide polymorphisms was compared between 4939 CRC patients and 3797 control persons of the Darmkrebs: Chancen der Verhütung durch Screening (DACHS) study, a population-based case-control study conducted in Germany. Risk discrimination was quantified according to the history of colonoscopy and polypectomy by areas under the curves (AUCs) and their 95% confidence intervals (CIs). All statistical tests were 2-sided. Results AUCs and 95% CIs were higher among subjects without previous colonoscopy (AUC = 0.622, 95% CI = 0.606 to 0.639) than among those with previous colonoscopy and polypectomy (AUC = 0.568, 95% CI = 0.536 to 0.601; difference [Δ AUC] = 0.054, P = .004). Such differences were consistently seen in sex-specific groups (women: Δ AUC = 0.073, P = .02; men: Δ AUC = 0.046, P = .048) and age-specific groups (younger than 70 years: Δ AUC = 0.052, P = .07; 70 years or older: Δ AUC = 0.049, P = .045). Conclusions Predictive performance of PRS may be underestimated in populations with widespread use of colonoscopy. Future studies using PRS to develop CRC prediction models should carefully consider colonoscopy history to provide more accurate estimates.

scholarly journals Genome-wide Association Studies and Candidate Gene Identification for Leaf Scald and Net Blotch in Barley (Hordeum vulgare L.)

Plant Disease ◽  
2019 ◽  
Vol 103 (5) ◽  
pp. 880-889 ◽  
Author(s):  
Sintayehu D Daba ◽  
Richard Horsley ◽  
Robert Brueggeman ◽  
Shiaoman Chao ◽  
Mohsen Mohammadi
Keyword(s):  
Association Studies ◽  
Defense Responses ◽  
The United States ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Net Blotch ◽  
Hordeum Vulgare L ◽  
Seedling Resistance ◽  
Leaf Scald ◽  
Genome Wide

We report genomic regions that significantly control resistance to scald, net form (NFNB) and spot form net blotch (SFNB) in barley. Barley genotypes from Ethiopia, ICARDA, and the United States were evaluated in Ethiopia and North Dakota State University (NDSU). Genome-wide association studies (GWAS) were conducted using 23,549 single nucleotide polymorphism (SNP) markers for disease resistance in five environments in Ethiopia. For NFNB and SFNB, we assessed seedling resistance in a glasshouse at NDSU. A large proportion of the Ethiopian landraces and breeding genotypes were resistant to scald and NFNB. Most of genotypes resistant to SFNB were from NDSU. We identified 17, 26, 7, and 1 marker-trait associations (MTAs) for field-scored scald, field-scored net blotch, greenhouse-scored NFNB, and greenhouse-scored SFNB diseases, respectively. Using the genome sequence and the existing literature, we compared the MTAs with previously reported loci and genes for these diseases. For leaf scald, only a few of our MTAs overlap with previous reports. However, the MTAs found for field-scored net blotch as well as NFNB and SFNB mostly overlap with previous reports. We scanned the barley genome for identification of candidate genes within 250 kb of the MTAs, resulting in the identification of 307 barley genes for the 51 MTAs. Some of these genes are related to plant defense responses such as subtilisin-like protease, chalcone synthase, lipoxygenase, and defensin-like proteins.

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