scholarly journals Genetic basis of transgressive segregation in rice heading phenotypes

2018 ◽  
Author(s):  
Yohei Koide ◽  
Takashi Uchiyama ◽  
Yuya Ota ◽  
Shuntaro Sakaguchi ◽  
Ayumi Tezuka ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Epistatic Effect ◽  
Transgressive Segregation ◽  
Snp Analysis ◽  
Single Nucleotide ◽  
Genome Wide ◽  
High Latitude Region ◽  
Extreme Phenotypes ◽  
Latitude Region ◽  
The One

ABSTRACTTransgressive segregation produces hybrid progeny phenotypes that exceed parental phenotypes. Unlike heterosis, extreme phenotypes caused by transgressive segregation are heritably stable. We examined transgressive phenotypes of flowering time in rice. Our previous study examined days to flowering (heading; DTH) in six F2 populations for which the parents had distal DTH, and found very few transgressive phenotypes. Here, we demonstrate that transgressive segregation in F2 populations occurred between parents with proximal DTH. DTH phenotypes of the A58 × Kitaake F2 progenies frequently exceeded those of both parents. Both A58 and Kitaake are japonica rice cultivars adapted to Hokkaido, Japan, which is a high-latitude region, and have short DTH. Among the four known loci required for short DTH, three loci had common alleles in A58 and Kitaake, and only the one locus had different alleles. This result indicates that there is a similar genetic basis for DTH between the two varieties. We identified five new quantitative trait loci (QTLs) associated with transgressive DTH phenotypes by genome-wide single nucleotide polymorphism (SNP) analysis. Each of these QTLs showed different degrees of additive effects on DTH, and two QTLs had epistatic effect on each other. These results demonstrated that genome-wide SNP analysis facilitated detection of genetic loci associated with the extreme phenotypes and revealed that the transgressive phenotypes were produced by exchanging complementary alleles of a few minor QTLs in the similar parental genotypes.

scholarly journals Common Susceptibility Loci for Male Breast Cancer

2020 ◽  
Author(s):  
Sarah Maguire ◽  
Eleni Perraki ◽  
Katarzyna Tomczyk ◽  
Michael E Jones ◽  
Olivia Fletcher ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Association Study ◽  
Genetic Correlation ◽  
Male Breast Cancer ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Susceptibility Loci ◽  
Single Nucleotide ◽  
Genome Wide

Abstract Background The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. Methods We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10–06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. Results The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10–08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor–positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10–30). Conclusions These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.

scholarly journals COPHYLOGENETIC ANALYSES OF TRACHYMYRMEX ANT-FUNGAL SPECIFICITY: ‘ONE TO ONE WITH SOME EXCEPTIONS’

2021 ◽  
Author(s):  
Katherine Beigel ◽  
Alix Matthews ◽  
Katrin Kellner ◽  
Christine Pawlik ◽  
Matthew Greenwold ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Marker Genes ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Native Populations ◽  
Symbiotic Fungi ◽  
Fungal Specificity

Over the past few decades, large-scale phylogenetic analyses of fungus-gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is somewhat widespread among unrelated ant lineages. These symbioses are thought to be explained by a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange was indeed symbiont sharing or an issue of employing relatively uninformative molecular markers, samples of Trachymyrmex arizonensis and Trachymyrmex pomonae and their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome-wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence between Trachymyrmex species and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange. These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.

Wnt receptor gene FZD1 was associated with schizophrenia in genome-wide SNP analysis of the Australian Schizophrenia Research Bank cohort

2019 ◽  
Vol 54 (9) ◽  
pp. 902-908 ◽  
Author(s):  
Xiaoman Liu ◽  
Siew-Kee Low ◽  
Joshua R Atkins ◽  
Jing Qin Wu ◽  
William R Reay ◽  
...  
Keyword(s):  
Association Study ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Receptor Gene ◽  
Genome Wide Association ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide

Objectives: Large-scale genetic analysis of common variation in schizophrenia has been a powerful approach to understanding this complex but highly heritable psychotic disorder. To further investigate loci, genes and pathways associated more specifically in the well-characterized Australian Schizophrenia Research Bank cohort, we applied genome-wide single-nucleotide polymorphism analysis in these three annotation categories. Methods: We performed a case–control genome-wide association study in 429 schizophrenia samples and 255 controls. Post-genome-wide association study analyses were then integrated with genomic annotations to explore the enrichment of variation at the gene and pathway level. We also examine candidate single-nucleotide polymorphisms with potential function within expression quantitative trait loci and investigate overall enrichment of variation within tissue-specific functional regulatory domains of the genome. Results: The strongest finding ( p = 2.01 × 10−6, odds ratio = 1.82, 95% confidence interval = [1.42, 2.33]) in genome-wide association study was with rs10252923 at 7q21.13, downstream of FZD1 (frizzled class receptor 1). While this did not stand alone after correction, the involvement of FZD1 was supported by gene-based analysis, which exceeded the threshold for genome-wide significance ( p = 2.78 × 10−6). Conclusion: The identification of FZD1, as an independent association signal at the gene level, supports the hypothesis that the Wnt signalling pathway is altered in the pathogenesis of schizophrenia and may be an important target for therapeutic development.

scholarly journals Selection on a pleiotropic color gene block underpins early differentiation between two warbler species

2019 ◽  
Author(s):  
Silu Wang ◽  
Sievert Rohwer ◽  
Devin R. de Zwaan ◽  
David P. L Toews ◽  
Irby J. Lovette ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Basis ◽  
Early Stage ◽  
Population Substructure ◽  
Carotenoid Pigment ◽  
Single Nucleotide ◽  
Gene Block ◽  
Genome Wide ◽  
Genomic Regions ◽  
Divergence With Gene Flow

AbstractWhen one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsend’s (Setophaga townsendi) and Hermit warblers (S. occidentalis). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the ‘divergence with gene flow’ model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.

scholarly journals The genetic basis of the human-cannabis relationship

2018 ◽  
Author(s):  
Philippe Henry
Keyword(s):  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Diagnostic Process ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Single Nucleotide ◽  
Web Based ◽  
Genome Wide ◽  
A Genome ◽  
Shed Light

AbstractCannabis can elicit various reactions in different consumers. In order to shed light on the mechanisms underlying the human-cannabis relationship, we begin to investigate the genetic basis of this differential response. The web-based platform OpenSNP was used to collect selfreported genetic and phenotypic data. Participants either reported a positively or negative affinity to cannabis. A total of 26 individuals were retained, 10 of which indicated several negative responses and the remaining 16 indicating strong affinity for Cannabis. A total of 325’895 single nucleotide polymorphisms (SNPs) were retained. The software TASSEL 5 was used to run a genome-wide association study (GWAS), with a generalized liner model (GLM) and1000 permutations. The analysis yielded a set of 45 SNPs that were significantly associated with the reported affinity to cannabis, including one strong outlier found in the MYO16 gene. A diagnostic process is proposed by which individuals can be assessed for their affinity to cannabis. We believe this type of tool may be helpful in alleviating some of the stigma associated with cannabis use in individuals sensitive to THC and other cannabis constituents such as myrcene, which may potentiate negative responses.

scholarly journals Genetic source tracking of human plague cases in Inner Mongolia-Beijing, 2019

2021 ◽  
Vol 15 (8) ◽  
pp. e0009558
Author(s):  
Jianyun Li ◽  
Yumeng Wang ◽  
Fang Liu ◽  
Xiaona Shen ◽  
Yiting Wang ◽  
...  
Keyword(s):  
Inner Mongolia ◽  
Meriones Unguiculatus ◽  
Source Tracking ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Genetic Source ◽  
Inner Mongolia Autonomous Region ◽  
Relationship Of

On 12 November 2019, one couple from the Sonid Left Qi (County) in the Inner Mongolia Autonomous Region was diagnosed with pneumonic plague in Beijing. The wife acquired the infection from her husband. Thereafter, two bubonic plague cases were identified in Inner Mongolia on November 16th and 24th. In this study, genome-wide single nucleotide polymorphism (SNP) analysis was used to identify the phylogenetic relationship of Yersinia pestis strains isolated in Inner Mongolia. Strains isolated from reservoirs in 2018 and 2019 in Inner Mongolia, together with the strain isolated from Patient C, were further clustered into 2.MED3m, and two novel lineages (2.MED3q, 2.MED3r) in the 2.MED3 population. According to the analysis of PCR-based molecular subtyping methods, such as the MLVA 14 scheme and seven SNP allele sequencing, Patients A/B and D were classified as 2.MED3m. In addition, strains from rodents living near the patients’ residences were clustered into the same lineage as patients. Such observations indicated that human plague cases originated from local reservoirs. Corresponding phylogenetic analysis also indicated that rodent plague strains in different areas in Inner Mongolia belong to different epizootics rather than being caused by spreading from the same epizootic in Meriones unguiculatus in 2019.

Whole Genome Association Study in Acute Myeloid Leukemia with a Normal Karyotype, Using a Single-Nucleotide Polymorphism (SNP) Analysis.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4253-4253
Author(s):  
Yongjun Cha ◽  
Kwang-Sung Ahn ◽  
Juwon Park ◽  
Byung-Su Kim ◽  
Soo-Mee Bang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Myeloid Leukemia ◽  
Normal Karyotype ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Significant Difference ◽  
Acute Myeloid

Abstract As a result of numerous genetic aberrations, acute myeloid leukemia (AML) present with very heterogeneous clinical features. Moreover, structural and numerical chromosome aberrations currently comprise the most important basis for predicting these heterogeneous outcomes. However, 30 to 50 percent of AML patients have cytogenetically normal karyotypes. Though submicroscopic genetic alterations (such as NPM1, CEBPA, MLL-PTD) are increasingly being used for clinical purposes, additional markers with prognostic or predictive value are still lacking in this group. In this study, we performed a genome-wide, single-nucleotide polymorphism (SNP) study in order to identify novel genomic regions of interest in normal karyotype AML. 54 untreated AML patients with normal karyotypes were analyzed with an Illumina infinium 317K SNP chip assay. SNP genotype call rate was 99.8 percent, resulting in a resolution of 1 SNP/Mb. In a genome-wide SNP analysis, 317 SNP loci, having a significant difference between AML and normal control, were found. In addition, about 300 loci were also identified, showing a significant difference between patients who achieved CR and those who did not. Some of these were found to be related with drug metabolism and MDR family. Also we used the SNP assay to screen a loss of heterozygosity (LOH), suggesting possible involvement of tumor suppressor genes. In summary, 38 LOH regions larger than 1Mb were observed in 23 cases (43%) among 54 AML patients having normal karyotypes. Most (55%) of them were copy-neutral events and the most frequently identified alterations were located at 3p, 8p, 13q and 22q. 11 (29%) out of 38 LOH regions had overlapping parts among them. Some LOHs were correlated with response to chemotherapy. Various genetic changes were discovered by use of an SNP-based chip array in normal karyotype AML patients. Moreover, some of these were related with CR acquisition and drug metabolism. These results can be used to differentiate normal karyotype AML and warrant further study.

scholarly journals SNP Alleles Associated With Low Bolting Tendency in Sugar Beet

2021 ◽  
Vol 12 ◽  
Author(s):  
Samathmika Ravi ◽  
Giovanni Campagna ◽  
Maria Cristina Della Lucia ◽  
Chiara Broccanello ◽  
Giovanni Bertoldo ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Allelic Status ◽  
The One ◽  
Detection Technologies

The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet (Beta vulgaris L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study. An elaborate 3-year field trial comprising 13 sugar beet lines identified L14 as the one exhibiting the lowest bolting tendency along with an increased survival rate after autumnal sowing. For SNP discovery following phenotyping, contrasting phenotypes of 24 non-bolting and 15 bolting plants of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq). An association model was established with a set of 10,924 RAD-based single nucleotide polymorphism (SNP) markers. The allelic status of the most significantly associated SNPs ranked based on their differential allelic status between contrasting phenotypes (p < 0.01) was confirmed on three different validation datasets comprising diverse sugar beet lines and varieties adopting a range of SNP detection technologies. This study has led to the identification of SNP_36780842 and SNP_48607347 linked to low bolting tendency and can be used for marker-assisted breeding and selection in sugar beet.

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