scholarly journals Genome-wide association study for deoxynivalenol production and aggressiveness in wheat and rye head blight by resequencing 92 isolates of Fusarium culmorum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Thomas Miedaner ◽  
Andrea Vasquez ◽  
Valheria Castiblanco ◽  
Hilda Elena Castillo ◽  
Nora Foroud ◽  
...  
Keyword(s):  
Association Study ◽  
Field Experiments ◽  
Genome Wide Association Study ◽  
Fusarium Culmorum ◽  
Genome Wide Association ◽  
Phytopathogenic Fungus ◽  
Phenotypic Traits ◽  
Head Blight ◽  
Trichothecene Mycotoxin ◽  
Genome Wide

Abstract Background Fusarium culmorum is an important pathogen causing head blight of cereals in Europe. This disease is of worldwide importance leading to reduced yield, grain quality, and contamination by mycotoxins. These mycotoxins are harmful for livestock and humans; therefore, many countries have strict regulatory limits for raw materials and processed food. Extensive genetic diversity is described among field populations of F. culmorum isolates for aggressiveness and production of the trichothecene mycotoxin deoxynivalenol (DON). However, the causes for this quantitative variation are not clear, yet. We analyzed 92 isolates sampled from different field populations in Germany, Russia, and Syria together with an international collection for aggressiveness and DON production in replicated field experiments at two locations in two years with two hosts, wheat and rye. The 30x coverage whole-genome resequencing of all isolates resulted in the identification of 130,389 high quality single nucleotide polymorphisms (SNPs) that were used for the first genome-wide association study in this phytopathogenic fungus. Results In wheat, 20 and 27 SNPs were detected for aggressiveness and DON content, respectively, of which 10 overlapped. Additionally, two different SNPs were significantly associated with aggressiveness in rye that were among those SNPs being associated with DON production in wheat. Most of the SNPs explained only a small proportion of genotypic variance (pG), however, four SNPs were associated with major quantitative trait loci (QTLs) with pG ranging from 12 to 48%. The QTL with the highest pG was involved in DON production and associated with a SNP most probably located within the Tri4 gene. Conclusions The diversity of 92 isolates of F. culmorum were captured using a heuristic approach. Key phenotypic traits, SNPs, and candidate genes underlying aggressiveness and DON production were identified. Clearly, many QTLs are responsible for aggressiveness and DON content in wheat, both traits following a quantitative inheritance. Several SNPs involved in DON metabolism, among them the Tri4 gene of the trichothecene pathway, were inferred as important source of variation in fungal aggressiveness. Using this information underlying the phenotypic variation will be of paramount importance in evaluating strategies for successful resistance breeding.

scholarly journals Genome-wide association study of Alzheimer’s disease CSF biomarkers in the EMIF-AD Multimodal Biomarker Discovery dataset

2019 ◽  
Author(s):  
Shengjun Hong ◽  
Dmitry Prokopenko ◽  
Valerija Dobricic ◽  
Fabian Kilpert ◽  
Isabelle Bos ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Biomarker Discovery ◽  
Case Control ◽  
Genome Wide Association ◽  
Great Promise ◽  
Phenotypic Traits ◽  
Genome Wide

AbstractAlzheimer’s disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Susceptibility to AD is considerably determined by genetic factors which hitherto were primarily identified using case-control designs. Elucidating the genetic architecture of additional AD-related phenotypic traits, ideally those linked to the underlying disease process, holds great promise in gaining deeper insights into the genetic basis of AD and in developing better clinical prediction models. To this end, we generated genome-wide single-nucleotide polymorphism (SNP) genotyping data in 931 participants of the European Medical Information Framework Alzheimer’s Disease Multimodal Biomarker Discovery (EMIF-AD MBD) sample to search for novel genetic determinants of AD biomarker variability. Specifically, we performed genome-wide association study (GWAS) analyses on 16 traits, including 14 measures of amyloid-beta (Aβ) and tau-protein species in the cerebrospinal fluid (CSF). In addition to confirming the well-established effects of apolipoprotein E (APOE) on diagnostic outcome and phenotypes related to Aβ42, we detected novel potential signals in the zinc finger homeobox 3 (ZFHX3) for CSF-Aβ38 and CSF-Aβ40 levels, and confirmed the previously described sex-specific association between SNPs in geminin coiled-coil domain containing (GMNC) and CSF-tau. Utilizing the results from independent case-control AD GWAS to construct polygenic risk scores (PRS) revealed that AD risk variants only explain a small fraction of CSF biomarker variability. In conclusion, our study represents a detailed first account of GWAS analyses on CSF-Aβ and -tau related traits in the EMIF-AD MBD dataset. In subsequent work, we will utilize the genomics data generated here in GWAS of other AD-relevant clinical outcomes ascertained in this unique dataset.

scholarly journals Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Y. Tilahun ◽  
T. A. Gipson ◽  
T. Alexander ◽  
M. L. McCallum ◽  
P. R. Hoyt
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Predictive Power ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Dairy Traits

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

scholarly journals Genome-wide association study on metabolite accumulation in a wild barley NAM population reveals natural variation in sugar metabolism

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246510
Author(s):  
Mathias Ruben Gemmer ◽  
Chris Richter ◽  
Thomas Schmutzer ◽  
Manish L. Raorane ◽  
Björn Junker ◽  
...  
Keyword(s):  
Association Study ◽  
Stress Responses ◽  
Genome Wide Association Study ◽  
Wild Barley ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
Metabolite Accumulation

Metabolites play a key role in plants as they are routing plant developmental processes and are involved in biotic and abiotic stress responses. Their analysis can offer important information on the underlying processes. Regarding plant breeding, metabolite concentrations can be used as biomarkers instead of or in addition to genetic markers to predict important phenotypic traits (metabolic prediction). In this study, we applied a genome-wide association study (GWAS) in a wild barley nested association mapping (NAM) population to identify metabolic quantitative trait loci (mQTL). A set of approximately 130 metabolites, measured at early and late sampling dates, was analysed. For four metabolites from the early and six metabolites from the late sampling date significant mQTL (grouped as 19 mQTL for the early and 25 mQTL for the late sampling date) were found. Interestingly, all of those metabolites could be classified as sugars. Sugars are known to be involved in signalling, plant growth and plant development. Sugar-related genes, encoding mainly sugar transporters, have been identified as candidate genes for most of the mQTL. Moreover, several of them co-localized with known flowering time genes like Ppd-H1, HvELF3, Vrn-H1, Vrn-H2 and Vrn-H3, hinting on the known role of sugars in flowering. Furthermore, numerous disease resistance-related genes were detected, pointing to the signalling function of sugars in plant resistance. An mQTL on chromosome 1H in the region of 13 Mbp to 20 Mbp stood out, that alone explained up to 65% of the phenotypic variation of a single metabolite. Analysis of family-specific effects within the diverse NAM population showed the available natural genetic variation regarding sugar metabolites due to different wild alleles. The study represents a step towards a better understanding of the genetic components of metabolite accumulation, especially sugars, thereby linking them to biological functions in barley.

scholarly journals A Genome-Wide Association Study Identifies Candidate Genes Associated With Shell Color in Bay Scallop Argopecten irradians irradians

2021 ◽  
Vol 8 ◽  
Author(s):  
Xinghai Zhu ◽  
Junhao Zhang ◽  
Xiujiang Hou ◽  
Pingping Liu ◽  
Jia Lv ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Argopecten Irradians ◽  
Shell Color ◽  
Genome Wide ◽  
A Genome ◽  
Bay Scallop

Molluscan shell color has consistently drawn attention for its abundant diversity and commercial use in shellfish breeding projects. Recently, two new strains of bay scallop (Argopecten irradians irradians) with different shell colors as marked phenotypic traits have been artificially bred to improve their economic values; however, the inheritance mechanism of their shell pigmentation is still unclear. In this study, a genome-wide association study (GWAS) was conducted to determine the genetic basis of shell color in bay scallops utilizing 29,036 high-quality single-nucleotide polymorphisms (SNPs) derived from 80 purple-red (PP) and 80 black-brown (BP) shell color individuals. The result of the GWAS showed that 469 SNPs (p <1.72E−6) significantly associated with shell color were mainly distributed in chromosome 7. The top three SNPs (i.e., chr7-12764003, chr7-13213864, and chr7-11899306) are located in the genic region of G-protein-coupled receptor-like 101 (GRL101), polyketide synthase 1 (PKS1), and phosphoinositide phospholipase C (PLC1), which have been widely reported to be involved in pigmentation. Successfully, the top three SNPs were verified in another non-breeding bay scallop population. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses obtained 38 GO terms covering 297 genes and aggregating pathways involving 252 annotated genes. Specifically, the expression profiles of the top three identified candidate genes were detected in mantles of PP and BP individuals by real-time quantitative reverse transcription PCR. The significantly higher expression levels of GRL101 (6.43-fold) and PLC1 (6.48-fold) in PP, and PKS1 (12.02-fold) in BP implied that GRL101 and PLC1 potentially functioned in PP shell coloration, and black pigmentation in BP might be principally regulated by PKS1. Our data provide valuable information for deciphering the phenotype differences of shell color in the bay scallop.

scholarly journals Genome-Wide Association Study for Plant Architecture and Bioenergy Traits in Diverse Sorghum and Sudangrass Germplasm

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1602
Author(s):  
Feng Luo ◽  
Zhongyou Pei ◽  
Xiongwei Zhao ◽  
Huifen Liu ◽  
Yiwei Jiang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Sweet Sorghum ◽  
Plant Architecture ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide ◽  
A Genome

Sorghum is an important grain, forage, and bioenergy crop. The objective of this study was to identify genetic signals associated with plant architecture and bioenergy traits in sorghum and sudangrass germplasm through a genome-wide association study (GWAS). Plant height (HT), tiller number (TN), internode number (IN), stem diameter (SD), panicle length (PL), panicle weight (PW), reducing sugar (RS) content, Brix, and protein (PRO) content were assessed in 300 germplasm consisting of grain sorghum, sweet sorghum, sudangrass, sweet sorghum-sweet sorghum recombinant inbred lines (RILs) and sudangrass-sudangrass RILs grown in three different environments over two years. Large variations of phenotypic traits were observed in the population panel. The heritability of traits were all higher than 0.5, ranging from 0.52 (PRO) to 0.92 (HT) with an average of 0.76. The population exhibited three population structures (Q) and minor relative kinship (K), assessed by using 7982 single-nucleotide polymorphisms (SNPs). After controlling Q and K, GWAS identified 24 SNPs that were significantly associated with traits, including three SNPs with HT, four with TN, four with PL, three with Brix, and ten with RS. Of them, seven SNPs were novel signals that were not identified previously, including one for HT, one for TN, one for Brix, and four for RS. The putative candidate genes involved in brassinosteroid regulatory pathway, auxin biosynthesis, carbohydrate metabolism, and sugar transport were identified underlying the significant SNPs. Identification of SNP signals and related candidate genes would enrich the current genomic resource for further molecular breeding aimed at improvement of food, feed, and biofuel productions of sorghum.

scholarly journals Genome-wide association study of Alzheimer’s disease CSF biomarkers in the EMIF-AD Multimodal Biomarker Discovery dataset

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shengjun Hong ◽  
◽  
Dmitry Prokopenko ◽  
Valerija Dobricic ◽  
Fabian Kilpert ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Biomarker Discovery ◽  
Case Control ◽  
Genome Wide Association ◽  
Great Promise ◽  
Phenotypic Traits ◽  
Genome Wide

AbstractAlzheimer’s disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Susceptibility to AD is considerably determined by genetic factors which hitherto were primarily identified using case–control designs. Elucidating the genetic architecture of additional AD-related phenotypic traits, ideally those linked to the underlying disease process, holds great promise in gaining deeper insights into the genetic basis of AD and in developing better clinical prediction models. To this end, we generated genome-wide single-nucleotide polymorphism (SNP) genotyping data in 931 participants of the European Medical Information Framework Alzheimer’s Disease Multimodal Biomarker Discovery (EMIF-AD MBD) sample to search for novel genetic determinants of AD biomarker variability. Specifically, we performed genome-wide association study (GWAS) analyses on 16 traits, including 14 measures derived from quantifications of five separate amyloid-beta (Aβ) and tau-protein species in the cerebrospinal fluid (CSF). In addition to confirming the well-established effects of apolipoprotein E (APOE) on diagnostic outcome and phenotypes related to Aβ42, we detected novel potential signals in the zinc finger homeobox 3 (ZFHX3) for CSF-Aβ38 and CSF-Aβ40 levels, and confirmed the previously described sex-specific association between SNPs in geminin coiled-coil domain containing (GMNC) and CSF-tau. Utilizing the results from independent case–control AD GWAS to construct polygenic risk scores (PRS) revealed that AD risk variants only explain a small fraction of CSF biomarker variability. In conclusion, our study represents a detailed first account of GWAS analyses on CSF-Aβ and -tau-related traits in the EMIF-AD MBD dataset. In subsequent work, we will utilize the genomics data generated here in GWAS of other AD-relevant clinical outcomes ascertained in this unique dataset.

scholarly journals Genome-Wide Association Study and QTL Mapping Revealed Genetic Loci for Fusarium Head Blight Resistance in Chinese Hexaploid Wheat

2021 ◽  
Author(s):  
Chaonan Shi ◽  
Junyou Geng ◽  
Yan Ren ◽  
Yueting Zheng ◽  
Chunyi Liu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Wheat Yield ◽  
Fusarium Head Blight Resistance ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Genetic Loci ◽  
Head Blight ◽  
Genome Wide ◽  
Fhb Resistance

Abstract Fusarium Head Blight (FHB) greatly affects wheat yield worldwide and could also downgrade quality. In this study, a total of 406 wheat cultivars were investigated for FHB disease index (DI). Results indicated that the FHB DI of 95% of the tested cultivars showed more than scale 2. Genome-wide association study (GWAS) identified 321 SNPs significantly related to FHB resistance on all chromosomes with 2.71–13.32% phenotypic variance explained (PVE). An important genetic locus gFHB-5A (329,828,930 to 595,372,995 bp) was identified to modulate FHB resistance in two panels, and the incidence of resistant alleles at the gFHB-5A1a locus were increasing with time in the tested cultivars. Two loci of gFHB-2B (9,740,162 to 68,200,954 bp) with PVE values of 2.73–3.57% and gFHB-7A (515,126,041 to 537,557,064 bp) with PVE values of 2.71–7.04% were identified to be significantly associated with FHB resistance. Linkage analysis in a bi-parental population identified the QTL FHB.hau-4D flanked by markers wPt-8836 and wPt-4572 with PVE value of 8.9%. This study identified new genetic loci to control FHB resistance and provided useful information of marker-assist selection in wheat FHB resistance breeding.

Genome wide association study on memory in schizophrenia patients and unaffected probands

2009 ◽  
Vol 42 (05) ◽  
Author(s):  
B Konte ◽  
I Giegling ◽  
AM Hartmann ◽  
H Konnerth ◽  
P Muglia ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide
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