scholarly journals Coevolutionary Dynamics of Rice Blast Resistance Gene Pi-ta and Magnaporthe oryzae Avirulence Gene AVR-Pita 1

2016 ◽  
Vol 106 (7) ◽  
pp. 676-683 ◽  
Author(s):  
Yulin Jia ◽  
Erxun Zhou ◽  
Seonghee Lee ◽  
Tracy Bianco
Keyword(s):  
Magnaporthe Oryzae ◽  
Marker Assisted Selection ◽  
Defense Mechanism ◽  
Allelic Variation ◽  
Blast Resistance ◽  
Quantitative Resistance ◽  
Association Studies ◽  
The United States ◽  
Avirulence Gene ◽  
Genome Wide Association Studies

The Pi-ta gene in rice is effective in preventing infections by Magnaporthe oryzae strains that contain the corresponding avirulence gene, AVR-Pita1. Diverse haplotypes of AVR-Pita1 have been identified from isolates of M. oryzae from rice production areas in the United States and worldwide. DNA sequencing and mapping studies have revealed that AVR-Pita1 is highly unstable, while expression analysis and quantitative resistance loci mapping of the Pi-ta locus revealed complex evolutionary mechanisms of Pi-ta-mediated resistance. Among these studies, several Pi-ta transcripts were identified, most of which are probably derived from alternative splicing and exon skipping, which could produce functional resistance proteins that support a new concept of coevolution of Pi-ta and AVR-Pita1. User-friendly DNA markers for Pi-ta have been developed to support marker-assisted selection, and development of new rice varieties with the Pi-ta markers. Genome-wide association studies revealed a link between Pi-ta-mediated resistance and yield components suggesting that rice has evolved a complicated defense mechanism against the blast fungus. In this review, we detail the current understanding of Pi-ta allelic variation, its linkage with rice productivity, AVR-Pita allelic variation, and the coevolution of Pi-ta and AVR-Pita in Oryza species and M. oryzae populations, respectively. We also review the genetic and molecular basis of Pi-ta and AVR-Pita interaction, and its value in marker-assisted selection and engineering resistance.

scholarly journals Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel

2021 ◽  
Author(s):  
Guangchao Sun ◽  
Ravi V. Mural ◽  
Jonathan D. Turkus ◽  
James C. Schnable
Keyword(s):  
Disease Severity ◽  
Quantitative Resistance ◽  
Association Studies ◽  
Disease Incidence ◽  
Genome Wide Association Studies ◽  
Maize Germplasm ◽  
Photosynthetic Productivity ◽  
Maize Diversity ◽  
Puccinia Polysora ◽  
Candidate Loci

Southern rust is a severe foliar disease of maize (Zea mays) resulting from infection with the obligate biotrophic fungus Puccinia polysora. This disease reduces photosynthetic productivity, which in turn reduces yields, with the greatest yield losses (up to 50%) associated with earlier onset infections. P. polysora urediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the US corn belt. In summer 2020, a severe outbreak of southern rust was observed in eastern Nebraska (NE), USA. We scored a replicated maize association panel planted in Lincoln, NE for disease severity and found that disease incidence and severity showed significant variation among maize genotypes. Genome-wide association studies identified four loci associated with significant quantitative variation in disease severity. These loci were associated with candidate genes with plausible links to quantitative disease resistance. A transcriptome-wide association study identified additional genes associated with disease severity. Together, these results indicate that substantial diversity in resistance to southern rust exists among current temperate-adapted maize germplasm, including several candidate loci that may explain the observed variation in resistance to southern rust.

scholarly journals Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251745
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Caio Cesar Ferrari Barbosa ◽  
Gabriel de Moraes Cunha Gonçalves ◽  
Roberto Fritsche-Neto ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Association Studies ◽  
Colletotrichum Lindemuthianum ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide Association Studies ◽  
Anthracnose Resistance ◽  
Resistant Cultivars ◽  
Genome Wide ◽  
Selection Of

Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.

Abstract 439: Trajectory Analysis of Left Ventricular Dimensions From Biobank Data Uncovers Novel Genetic Associations

2020 ◽  
Vol 127 (Suppl_1) ◽  
Author(s):  
Tess Pottinger ◽  
Megan J Puckelwartz ◽  
Lorenzo L Pesce ◽  
Anthony Gacita ◽  
Isabella Salamone ◽  
...  
Keyword(s):  
Heart Failure ◽  
Longitudinal Data ◽  
Association Studies ◽  
The United States ◽  
Left Ventricular ◽  
Genome Wide Association Studies ◽  
Qtc Interval ◽  
Regulatory Regions ◽  
Genome Wide ◽  
Over Time

Background: Approximately 6 million adults in the United States have heart failure. The progression of heart failure is variable arising from differences in sex, age, genetic background including ancestry, and medication response. Many population-based genetic studies of heart failure have been cross-sectional in nature, failing to gain additional power from longitudinal analyses. As heart failure is known to change over time, using longitudinal data trajectories as a quantitative trait will increase power in genome wide association studies (GWAS). Methods: We used the electronic health record in a racially and ethnically diverse medical biobank from a single, metropolitan US center. We used whole genome data from 896 unrelated participants analyzed, including 494 who had at least 1 electrocardiogram and 324 who had more than 1 echocardiogram (average of 3 observations per person). A mixture model based semiparametric latent growth curve model was used to cluster outcome measures used for genome-wide analyses. Results: GWAS on the trajectory probability of QTc interval identified significant associations with variants in regulatory regions proximal to the WLS gene, which encodes Wntless, a Wnt ligand secretion mediator. WLS was previously associated with QTc and myocardial infarction, thus confirming the power of the method. GWAS on the trajectory probability of left ventricular diameter (LVIDd) identified significant associations with variants in regulatory regions near MYO10 , which encodes unconventional Myosin-10. MYO10 was previously associated with obesity and metabolic syndrome. Conclusions: This is the first study to show an association with variants in or near MYO10 and left ventricular dimension changes over time. Further, we found that using trajectory probabilities can provide increased power to find novel associations with longitudinal data. This reduces the need for larger cohorts, and increases yield from smaller, well-phenotyped cohorts, such as those found in biobanks. This approach should be useful in the study of rare diseases and underrepresented populations.

Results of the BRD CAP project: progress toward identifying genetic markers associated with BRD susceptibility

2014 ◽  
Vol 15 (2) ◽  
pp. 157-160 ◽  
Author(s):  
Alison Van Eenennaam ◽  
Holly Neibergs ◽  
Christopher Seabury ◽  
Jeremy Taylor ◽  
Zeping Wang ◽  
...  
Keyword(s):  
Association Studies ◽  
Clinical Signs ◽  
The United States ◽  
Feedlot Cattle ◽  
United States Department ◽  
Genome Wide Association Studies ◽  
Dairy Calf ◽  
Definition Of ◽  
Genetic Evaluations ◽  
Quantitative Definition

AbstractThe Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP) is a 5-year project funded by the United States Department of Agriculture (USDA), with an overriding objective to use the tools of modern genomics to identify cattle that are less susceptible to BRD. To do this, two large genome wide association studies (GWAS) were conducted using a case:control design on preweaned Holstein dairy heifers and beef feedlot cattle. A health scoring system was used to identify BRD cases and controls. Heritability estimates for BRD susceptibility ranged from 19 to 21% in dairy calves to 29.2% in beef cattle when using numerical scores as a semi-quantitative definition of BRD. A GWAS analysis conducted on the dairy calf data showed that single nucleotide polymorphism (SNP) effects explained 20% of the variation in BRD incidence and 17–20% of the variation in clinical signs. These results represent a preliminary analysis of ongoing work to identify loci associated with BRD. Future work includes validation of the chromosomal regions and SNPs that have been identified as important for BRD susceptibility, fine mapping of chromosomes to identify causal SNPs, and integration of predictive markers for BRD susceptibility into genetic tests and national cattle genetic evaluations.

scholarly journals Fusarium Head Blight in Durum Wheat: Recent Status, Breeding Directions, and Future Research Prospects

2019 ◽  
Vol 109 (10) ◽  
pp. 1664-1675 ◽  
Author(s):  
Jemanesh K. Haile ◽  
Amidou N’Diaye ◽  
Sean Walkowiak ◽  
Kirby T. Nilsen ◽  
John M. Clarke ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Fusarium Head Blight ◽  
Seed Quality ◽  
Association Studies ◽  
Tetraploid Wheat ◽  
The United States ◽  
Genome Wide Association Studies ◽  
Head Blight ◽  
Food And Feed ◽  
Fhb Resistance

Fusarium head blight (FHB) is a major fungal disease affecting wheat production worldwide. Since the early 1990s, FHB, caused primarily by Fusarium graminearum, has become one of the most significant diseases faced by wheat producers in Canada and the United States. The increasing FHB problem is likely due to the increased adoption of conservation tillage practices, expansion of maize production, use of susceptible wheat varieties in rotation, and climate variability. Durum wheat (Triticum turgidum sp. durum) is notorious for its extreme susceptibility to FHB and breeding for resistance is complicated because sources of FHB resistance are rare in the primary gene pool of tetraploid wheat. Losses due to this disease include yield, test weight, seed quality, food and feed quality, and when severe, market access. More importantly, it is the contamination with mycotoxins, such as deoxynivalenol, in Fusarium-infected durum kernels that causes the most serious economic as well as food and feed safety concerns. Several studies and thorough reviews have been published on germplasm development and breeding for FHB resistance and the genetics and genomics of FHB resistance in bread or common wheat (T. aestivum); however, similar reviews have not been conducted in durum wheat. Thus, the aim of this review is to summarize and discuss the recent research efforts to mitigate FHB in durum wheat, including quantitative trait locus mapping, genome-wide association studies, genomic prediction, mutagenesis and characterization of genes and pathways involved in FHB resistance. It also highlights future directions, FHB-resistant germplasm, and the potential role of morphological traits to enhance FHB resistance in durum wheat.

Neuroblastoma: A Tough Nut to Crack

2016 ◽  
pp. e548-e557 ◽  
Author(s):  
Frank Speleman ◽  
Julie R. Park ◽  
Tara O. Henderson
Keyword(s):  
Clinical Trials ◽  
Late Effects ◽  
Association Studies ◽  
Genomic Analysis ◽  
The United States ◽  
Malignant Neoplasms ◽  
Genome Wide Association Studies ◽  
Second Malignant Neoplasms ◽  
Tumor In Childhood

Neuroblastoma, an embryonal tumor arising from neural crest–derived progenitor cells, is the most common solid tumor in childhood, with more than 700 cases diagnosed per year in the United States. In the past several decades, significant advances have been made in the treatment of neuroblastoma. Treatment advances reflect improved understanding of the biology of neuroblastoma. Although amplification of MYCN was discovered in the early 1980s, our understanding of neuroblastoma oncogenesis has advanced in the last decade as a result of high-throughput genomic analysis, exome and whole-genome sequencing, genome-wide association studies, and synthetic lethal drug screens. Our refined understanding of neuroblastoma biology and genetics is reflected in improved prognostic stratification and appropriate tailoring of therapy in recent clinical trials. Moreover, for high-risk neuroblastoma, a disease that was uniformly fatal 3 decades ago, recent clinical trials incorporating autologous hematopoietic transplant and immunotherapy utilizing anti-GD2 antibody plus cytokines have shown improved event-free and overall survival. These advances have resulted in a growing population of long-term survivors of neuroblastoma. Examination of the late effects and second malignant neoplasms (SMNs) in both older generations of survivors and more recently treated survivors will inform both design of future trials and surveillance guidelines for long-term follow-up. As a consequence of advances in understanding of the biology of neuroblastoma, successful clinical trials, and refined understanding of the late effects and SMNs of survivors, the promise of precision medicine is becoming a reality for patients with neuroblastoma.

scholarly journals Smad3 Regulates Smooth Muscle Cell Fate and Governs Adverse Remodeling and Calcification of Atherosclerotic Plaque

2021 ◽  
Author(s):  
Paul Cheng ◽  
Robert Wirka ◽  
Juyong Kim ◽  
Trieu Nguyen ◽  
Ramendra Kundu ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Cell Fate ◽  
Vascular Calcification ◽  
Allelic Variation ◽  
Association Studies ◽  
Direct Interaction ◽  
Inflammatory Cells ◽  
Plaque Burden ◽  
Genome Wide Association Studies ◽  
Cad Risk

Abstract Atherosclerotic plaques consist mostly of smooth muscle cells (SMC), and genes that influence SMC biology can modulate coronary artery disease (CAD) risk. Allelic variation at 15q22.33 has been identified by genome-wide association studies to modify the risk of CAD, and is associated with expression of SMAD3 in SMC, but the mechanism by which this gene modifies CAD risk remains poorly understood. SMC-specific deletion of Smad3 in a murine atherosclerosis model resulted in greater plaque burden, more positive remodeling, and increased vascular calcification. Single-cell transcriptomic analyses revealed that loss of Smad3 altered SMC transition cell state toward two fates: a novel SMC phenotype that governs both vascular remodeling and recruitment of inflammatory cells, as well as a chondromyocyte fate. The remodeling population was marked by uniquely high Mmp3 and Cxcl12 expression, and its appearance correlated with higher risk plaque features such as increased positive remodeling and macrophage content. Further, investigation of transcriptional mechanisms by which Smad3 alters SMC cell fate revealed novel roles for Hox and Sox transcription factors whose direct interaction with Smad3 regulate an extensive transcriptional program balancing remodeling and vascular extracellular matrix with significant implications for atherosclerotic and Mendelian aortic aneurysmal diseases. Together, these data suggest that Smad3 expression in SMC inhibits the emergence of specific SMC phenotypic transition cells that mediate adverse plaque features, including positive remodeling, monocyte recruitment, and vascular calcification.

scholarly journals Genome Wide Association Studies for Four Physiological Traits in Groundnut (Arachis hypogaea L.) Minicore Collection

2019 ◽  
Author(s):  
Abdulwahab Saliu Shaibu ◽  
Clay Sneller ◽  
Babu N. Motagi ◽  
Jackline Chepkoech ◽  
Mercy Chepngetich ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Association Studies ◽  
Canopy Temperature ◽  
Snp Markers ◽  
Physiological Traits ◽  
Rapid Decline ◽  
Genome Wide Association Studies ◽  
Area Index ◽  
Trait Association ◽  
Genome Wide

Abstract Background In order to integrate genomics in breeding and development of drought tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used SNP markers for a genetic analysis of the ICRISAT groundnut minicore collection for genome wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD) present in the genetic resources. Results The LD analysis showed that about 36% of loci pairs were in significant LD (P < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. There was rapid decline in LD with distance and the LD was <0.2 at a distance of 41635 bp. The marker trait association (MTAs) studies revealed 20 significant MTAs (p <0.001) with 11 markers for leaf area index (4), canopy temperature (13), chlorophyll content (1) and NDVI (2). The markers explained 2 to 21% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. The duplications of effect observed could be due to common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes seen in the current study. Conclusions The present study identified a total of 20 highly significant marker trait associations with 11 markers for four physiological traits of importance in groundnut; LAI, CT, SCMR and NDVI. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance. The identified markers in this study may be useful for marker assisted selection after further validation.

scholarly journals Diverse Functions Associate With Non-Coding Trans-species Polymorphisms in Humans

2021 ◽  
Author(s):  
Keila Velazquez-Arcelay ◽  
Mary Lauren Benton ◽  
John A. Capra
Keyword(s):  
Immune System ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Association Studies ◽  
Regulatory Function ◽  
Genome Wide Association Studies ◽  
Functional Annotations ◽  
Coding Regions ◽  
Genome Wide ◽  
Mhc Locus

Abstract Background: Long-term balancing selection (LTBS) can maintain allelic variation at a locus over millions of years and through speciation events. Variants shared between species, hereafter “trans-species polymorphisms” (TSPs), often result from LTBS due to host-pathogen interactions. For instance, the major histocompatibility complex (MHC) locus contains TSPs present across primates. Several hundred candidate TSPs have been identified in humans and chimpanzees; however, because many are in non-coding regions of the genome, the functions and adaptive roles for most TSPs remain unknown. Results: We integrated diverse genomic annotations, with a focus on non-coding regions, to explore the functions of 125 previously identified regions containing multiple TSPs in humans and chimpanzees. We analyzed genome-wide functional assays, expression quantitative trait loci (eQTL), genome-wide association studies (GWAS), and phenome-wide association studies (PheWAS). We identify functional annotations for 119 TSP regions, including 71 with evidence of gene regulatory function from GTEx or genome-wide functional genomics data and 21 with evidence of trait association from GWAS and PheWAS. TSPs in humans associate with many immune system phenotypes, including response to pathogens, but we also find associations with a range of other phenotypes, including body mass, alcohol intake, urate levels, chronotype, and risk-taking behavior. Conclusions: The diversity of traits associated with non-coding human TSPs further support previous hypotheses that functions beyond the immune system are subject to LTBS. Furthermore, several of these trait associations provide support and candidate genetic loci for previous hypothesis about behavioral diversity in great ape populations, such as the importance of variation in sleep cycles and risk sensitivity.

scholarly journals Genome-wide genetic data on ~500,000 UK Biobank participants

2017 ◽  
Author(s):  
Clare Bycroft ◽  
Colin Freeman ◽  
Desislava Petkova ◽  
Gavin Band ◽  
Lloyd T. Elliott ◽  
...  
Keyword(s):  
Quality Control ◽  
Allelic Variation ◽  
Association Studies ◽  
Genetic Data ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genotype Data ◽  
Uk Biobank ◽  
Genome Wide ◽  
Wide Range

AbstractThe UK Biobank project is a large prospective cohort study of ~500,000 individuals from across the United Kingdom, aged between 40-69 at recruitment. A rich variety of phenotypic and health-related information is available on each participant, making the resource unprecedented in its size and scope. Here we describe the genome-wide genotype data (~805,000 markers) collected on all individuals in the cohort and its quality control procedures. Genotype data on this scale offers novel opportunities for assessing quality issues, although the wide range of ancestries of the individuals in the cohort also creates particular challenges. We also conducted a set of analyses that reveal properties of the genetic data – such as population structure and relatedness – that can be important for downstream analyses. In addition, we phased and imputed genotypes into the dataset, using computationally efficient methods combined with the Haplotype Reference Consortium (HRC) and UK10K haplotype resource. This increases the number of testable variants by over 100-fold to ~96 million variants. We also imputed classical allelic variation at 11 human leukocyte antigen (HLA) genes, and as a quality control check of this imputation, we replicate signals of known associations between HLA alleles and many common diseases. We describe tools that allow efficient genome-wide association studies (GWAS) of multiple traits and fast phenome-wide association studies (PheWAS), which work together with a new compressed file format that has been used to distribute the dataset. As a further check of the genotyped and imputed datasets, we performed a test-case genome-wide association scan on a well-studied human trait, standing height.

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