Articles de revues : « SNP candidati »

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Seoane, José A., Vanessa Aguiar Pulido, Alba Cabarcos, Sonsoles Quintela, Juan Ramon Rabuñal et Julián Dorado. « SNP locator : a candidate SNP selection tool ». International Journal of Data Mining, Modelling and Management 5, n^o 3 (2013) : 193. http://dx.doi.org/10.1504/ijdmmm.2013.055863.

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Souche, E. L., B. Hellemans, J. K. J. Van Houdt, A. Canario, S. Klages, R. Reinhardt et F. A. M. Volckaert. « Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags of European Sea Bass ». Journal of Integrative Bioinformatics 4, n^o 3 (1 décembre 2007) : 158–67. http://dx.doi.org/10.1515/jib-2007-73.

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Abstract As a multitude of sequence data are published, discovering polymorphisms bioinformatically becomes a valid option. In silico Single Nucleotide Polymorphism (SNP) detection is based on the analysis of multiple alignments. Each column of an alignment is considered a slice containing one base of every sequence aligned. If a mismatch is detected, the slice is further analysed and the mismatch may be reported as a candidate SNP.About 30,000 Expressed Sequence Tags (ESTs) of the fish European sea bass have been sequenced and processed. Since ESTs are redundant, they provide a resource for in silico SNP discovery. To prevent the detection of sequencing errors, a redundancy of two is chosen in order for a mismatch to be considered a candidate SNP. Among the various tools available to detect candidate SNPs, three software packages were tested: SNPServer, PolyBayes and PolyFreq. Candidate SNPs were validated in the laboratory by cloning and sequencing. From preliminary results PolyFreq outperforms both PolyBayes and SNPServer in terms of positive predictive value and SNPServer is the most sensitive tool. PolyFreq and SNPServer non-default identify respectively the fewest and highest number of candidates. Considering candidates detected by several tools seems to enhance both positive predictive value and sensitivity. Out of the 69 loci sequenced, only four were monomorphic, leading to a total of 91.3% polymorphic loci. Randomly chosen contigs will be sequenced to know whether SNP discovery tools tend to predict polymorphic fragments. Polymorphisms will be mapped, used for selection in aquaculture and the study of adaptation in natural populations.

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Um, Nam-Hyun. « Effectiveness of Celebrity Endorsement Of Political Candidates ». Social Behavior and Personality : an international journal 46, n^o 10 (4 octobre 2018) : 1585–96. http://dx.doi.org/10.2224/sbp.6757.

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I examined the effects of celebrity endorsement of political candidates, drawing on third-person effect theory, social identification theory, and political efficacy theory. Participants were 283 students at an American university who took part in a web-based survey that explored attitudes using actual presidential candidates and real celebrities. Study findings suggest that people view such endorsements as having no impact on their own voting behavior yet influencing that of others by encouraging them to vote for the endorsed candidate. In addition, people positively evaluate the endorsed political candidate when they hold a high level of identification with the celebrity endorser and are likely to vote for the candidate. Lastly, whereas political efficacy does influence people's intention to vote, it does not appear to influence their evaluation of the candidate. Limitations of the study and future research are discussed.

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Harlid, Sophia, Malin I. L. Ivarsson, Salma Butt, Shehnaz Hussain, Ewa Grzybowska, Jorunn Erla Eyfjörd, Per Lenner et al. « A candidate CpG SNP approach identifies a breast cancer associated ESR1-SNP ». International Journal of Cancer 129, n^o 7 (11 mars 2011) : 1689–98. http://dx.doi.org/10.1002/ijc.25786.

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Taylor, Jacquelyn Y., Deborah Sampson, Andre D. Taylor, Dennis Caldwell et Yan V. Sun. « Genetic and BMI Risks for Predicting Blood Pressure in Three Generations of West African Dogon Women ». Biological Research For Nursing 15, n^o 1 (22 août 2011) : 105–11. http://dx.doi.org/10.1177/1099800411419026.

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The study of genetic polymorphisms and body mass index (BMI) among African women in Africa and in the United States contributes to our understanding of the genetic and environmental risk factors for hypertension. African American women have the highest prevalence of hypertension and obesity compared to other ethnic groups in the United States. Using a cross-sectional research design, we examined the effects of genetic and environmental risks of single nucleotide polymorphisms (SNPs) and BMI on blood pressure (BP) among three generations of West African Dogon women ( N = 199). We genotyped six SNPs located in the candidate genes known to be related to hypertension. We tested the associations between these SNPs and systolic BP (SBP) and diastolic BP (DBP) with Fisher’s exact tests, chi-square tests for independence, and multivariable linear mixed models. The SNP rs8179526 (SLC4A5) was significantly associated with SBP adjusted for age, age2, and BMI ( p = .02). The “C” allele variant of rs8179526 (allele frequency of 0.445) was associated with higher SBP. This SNP did not deviate from the Hardy–Weinberg equilibrium (HWE) with p value of .772. The SNP × BMI interaction effects associated with SBP and DBP were not significant. rs8179526 is located on the SLC4A5 gene on chromosome 2. SLC4A5 encodes a protein that transports sodium and bicarbonate across cell membranes while regulating cellular pH and contains several SNPs linked to elevated BP. Knowledge of the SNP’s effect on hypertension among West African women can help health practitioners educate their patients about genetic risks of developing hypertension.

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Stone, Brad, Scott Graves, Arnold Kas, Alexander Ford, Nathan Standifer, Crystal Rawlings, Steven Rosinski, Susan Masewicz, Maynard Olson et Rainer F. Storb. « Direct Genotyping of Coding Non-Synonymous SNPs for Identification of Novel Minor Histocompatibility Antigens. » Blood 108, n^o 11 (16 novembre 2006) : 3237. http://dx.doi.org/10.1182/blood.v108.11.3237.3237.

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Abstract Traditional methods for identifying minor histocompatibility antigens (mHags) are technically challenging and biased against discovery of mHags not expressed in the peripheral blood. In this work, we propose a rapid, unbiased, genetic approach for identification minor antigens resulting from disparities in coding non-synonymous SNPs (“C SNPS”). This approach is capable of testing for responses to candidate minor antigens expressed in virtually any tissue, including those expressed exclusively in tissues targeted by GVHD. The first step in our approach begins with comparison of donor and recipient C SNP genotypes generated using C SNP microarrays. These arrays interrogate approximately 80% of human C SNPs predicted to occur in greater than 5% of the population. Comparison of C SNP genotypes directly identifies protein-altering alleles present in the recipient but not the donor (hereafter referred to as “recipient-restricted” alleles), thereby identifying a transplant-specific set of candidate minor antigens. The second step utilizes conventional HLA-class I epitope prediction performed on all linear peptides that include amino-acid residues defined by a recipient-restricted allele. This two step filtering process identifies a small, “testable” number candidate minor peptide epitopes for an individual expressed HLA-class I allele. Candidate epitopes can then be synthesized, pooled and tested at diagnosis of GVHD using a commercial Granzyme B ELISPOT assay. As proof-of-principal for a direct genotyping approach, we have analyzed C SNP genotypes, performed epitope prediction and generated T-cell lines specific for candidate minor antigens using DNA and PBL from a pair of disease-free HLA-identical siblings. Analysis of 10,000 C SNPs shows that approximately 2,000 C SNP alleles are restricted to one sibling within the pair. BIMAS epitope prediction of short unique peptide sequences determined by each sibling-restricted allele identifies approximately 100 candidate minor epitopes predicted to bind HLA-A*0201. These candidate minor epitopes were ranked using expression microarrays performed on EBV-transformed LCL derived from each sibling, with candidates derived from highly expressed genes ranked above those from genes with lower expression levels. A pool of 12 candidate minor epitopes that were both unique to sibling “A” and derived from genes highly expressed in LCL were synthesized and used to generate CD8+ T-cell lines from sibling “B”. Stimulation utilized autologous (sibling “B”-derived) mature dendritic cells loaded with candidate minor epitopes. After several rounds of in-vitro stimulation, each T-cell line was tested for responses to EBV-LCL from sibling “B” and sibling “A” using a Granzyme B ELISPOT kit. Five out of sixteen lines responded to LCL from sibling A while no line responded to autologous LCL. Thus we show that this approach frequently generates CD8+ T-cell lines specific for sibling-derived target cells, suggesting that this approach efficiently identifies genuine, novel, endogenously processed and presented minor epitopes. Deconvolution of the peptide pool suggests that at least two out of the twelve candidate minor epitopes are naturally processed and presented.

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Laird, Eamon, Aisling M. O’halloran, Artur Fedorowski, Olle Melander, Ann Hever, Marketa Sjögren, Daniel Carey et Rose Anne Kenny. « Orthostatic Hypotension and Novel Blood Pressure Associated Gene Variants in Older Adults : Data From the TILDA Study ». Journals of Gerontology : Series A 75, n^o 11 (10 décembre 2019) : 2074–80. http://dx.doi.org/10.1093/gerona/glz286.

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Abstract Orthostatic hypotension (OH) is associated with increased risk of trauma and cardiovascular events. Recent studies have identified new genetic variants that influence orthostatic blood pressure (BP). The aim of this study was to investigate the associations of candidate gene loci with orthostatic BP responses in older adults. A total of 3,430 participants aged ≥50 years from The Irish Longitudinal Study on Ageing (TILDA) with BP measures and genetic data from 12 single-nucleotide polymorphism (SNP) linked to BP responses were analyzed. Orthostatic BP responses were recorded at each 10 s interval and were defined as OH (SBP drop ≥20 mmHg or DBP drop ≥10 mmHg) at the time-points 40, 90, and 110 s. We defined sustained OH (SOH) as a drop that exceeded consensus BP thresholds for OH at 40, 90, and 110 s after standing. Logistic regression analyses modeled associations between the candidate SNP alleles and OH. We report no significant associations between OH and measured SNPs after correction for multiple comparisons apart from the SNP rs5068 where proportion of the minor allele was significantly different between cases and controls for SOH 40 (p = .002). After adjustment for covariates in a logistic regression, those with the minor G allele (compared to the A allele) had a decreased incidence rate ratio (IRR) for SOH 40 (IRR 0.45, p = .001, 95% CI 0.29–0.72). Only one SNP linked with increased natriuretic peptide concentrations was associated with OH. These results suggest that genetic variants may have a weak impact on OH but needs verification in other population studies.

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Levin, Irwin P., Robert M. Rouwenhorst et Heather M. Trisko. « SEPARATING GENDER BIASES IN SCREENING AND SELECTING CANDIDATES FOR HIRING AND FIRING ». Social Behavior and Personality : an international journal 33, n^o 8 (1 janvier 2005) : 793–804. http://dx.doi.org/10.2224/sbp.2005.33.8.793.

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A two-stage procedure (consideration set formation and final choice) was used to track the emergence of gender biases in hiring and firing decisions. Participants were allowed to select their own strategy for narrowing choice options (which candidates to retain or which candidates to delete). Each of the two experiments included a condition where job candidates were considered for hiring and a condition where current employees were considered for firing. Candidate features varied across experiments but the initial set always included 18 females and 18 males with comparable credentials. In both experiments male and female respondents selected candidates of their own sex for hiring and both males and females selected mostly male candidates for firing. In each experiment the bias showed up only in the final-choice stage.

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Pun, F., C. Zhao, W. Lo, S. Ng, S. Tsang, V. Nimgaonkar, W. Chung, G. Ungvari et H. Xue. « Imprinting in the schizophrenia candidate gene GABRB2 ». European Psychiatry 26, S2 (mars 2011) : 823. http://dx.doi.org/10.1016/s0924-9338(11)72528-7.

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Imprinting, characterized by unequal expression of the offspring's genes in a parent-of-origin dependent manner, has been functionally implicated in brain development and in psychiatric disorders. In this study, unambiguous distortion in paternal but not maternal transmission of the disease-associated single-nucleotide polymorphism (SNP) rs6556547 (T/G) clearly indicated the presence of parent-of-origin effect (POE) in the GABAA receptor β2 subunit gene (GABRB2). ‘Flipping’ of allelic mRNA expression in heterozygotes of SNP rs2229944 (C/T) and the observed two-tiered distribution of mRNA expression levels in heterozygotes of the disease-associated SNP rs1816071 (G/A) furnished important support for the occurrence of imprinting at GABRB2. Imprinting in effect introduced heterozygotes from different parents-of-origin endowed with dissimilar mRNA expression capabilities. The deficit of upper-tiered expressions accounted for the lowered mRNA expression levels in the schizophrenic heterozygotes. This pointed to the necessity of differentiating between two kinds of heterozygotes of different parental origins in disease association studies on GABRB2. Bisulfite sequencing revealed hypermethylation in the neighborhood of SNP rs1816071, and methylation differences between controls and schizophrenia patients. Notably, allele-specific methylation was observed at the disease-associated SNPs rs6556547 and rs1816071. These findings raised the possibility that CpG methylation status of these sites could have an impact on the expression of GABRB2 and the risk of schizophrenia. Furthermore, the occurrence of imprinting and allele-specific methylation in the schizophrenia candidate gene GABRB2 was compatible with the epigenetic hypothesis for schizophrenia pathophysiology, thereby calling for the need to explore the role of epigenetic factors in mediating susceptibility to schizophrenia.

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Song, Long, Jing Qin Wu, Chong Mei Dong et Robert F. Park. « Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina ». Genes 11, n^o 9 (21 septembre 2020) : 1107. http://dx.doi.org/10.3390/genes11091107.

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The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt (‘Pt104’) as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27–40 candidates and CNV analysis identified 14–31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.

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Raschetti, Marta, Bianca Castiglioni, Anna Caroli, Denis Guiatti, Giulio Pagnacco et Stefania Chessa. « SNP identification in swine candidate genes for meat quality ». Livestock Science 155, n^o 2-3 (août 2013) : 165–71. http://dx.doi.org/10.1016/j.livsci.2013.05.008.

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Wu, Michael C., Arnab Maity, Seunggeun Lee, Elizabeth M. Simmons, Quaker E. Harmon, Xinyi Lin, Stephanie M. Engel, Jeffrey J. Molldrem et Paul M. Armistead. « Kernel Machine SNP-Set Testing Under Multiple Candidate Kernels ». Genetic Epidemiology 37, n^o 3 (7 mars 2013) : 267–75. http://dx.doi.org/10.1002/gepi.21715.

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Zhou, Chengcheng, Yingtian Guo, Yali Chen, Hongbin Zhang, Yousry A. El-Kassaby et Wei Li. « Genome Wide Association Study Identifies Candidate Genes Related to the Earlywood Tracheid Properties in Picea crassifolia Kom. » Forests 13, n^o 2 (18 février 2022) : 332. http://dx.doi.org/10.3390/f13020332.

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Picea crassifolia Kom. is one of the timber and ecological conifers in China and its wood tracheid traits directly affect wood formation and adaptability under harsh environment. Molecular studies on P. crassifolia remain inadequate because relatively few genes have been associated with these traits. To identify markers and candidate genes that can potentially be used for genetic improvement of wood tracheid traits, we examined 106 clones of P. crassifolia, and investigated phenotypic data for 14 wood tracheid traits before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the studied traits. We developed 4,058,883 SLAF-tags and 12,275,765 SNP loci, and our analyses identified a total of 96 SNP loci that showed significant correlations with three earlywood tracheid traits using a mixed linear model (MLM). Next, candidate genes were screened in the 100 kb zone (50 kb upstream, 50 kb downstream) of each of the SNP loci, whereby 67 candidate genes were obtained in earlywood tracheid traits, including 34 genes of known function and 33 genes of unknown function. We provide the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in wood traits improvement and candidate genes for the development of earlywood tracheid in P. crassifolia.

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Melo, Thaise P., Marina R. S. Fortes, Gerardo A. Fernandes Junior, Lucia G. Albuquerque et Roberto Carvalheiro. « RAPID COMMUNICATION : Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1 ». Journal of Animal Science 97, n^o 7 (11 avril 2019) : 3027–33. http://dx.doi.org/10.1093/jas/skz121.

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Abstract An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10–4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10–3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.

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Wu, Ruiming, Jingxuan Bao, Mansu Kim, Andrew J. Saykin, Jason H. Moore et Li Shen. « Mining High-Level Imaging Genetic Associations via Clustering AD Candidate Variants with Similar Brain Association Patterns ». Genes 13, n^o 9 (24 août 2022) : 1520. http://dx.doi.org/10.3390/genes13091520.

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Brain imaging genetics examines associations between imaging quantitative traits (QTs) and genetic factors such as single nucleotide polymorphisms (SNPs) to provide important insights into the pathogenesis of Alzheimer’s disease (AD). The individual level SNP-QT signals are high dimensional and typically have small effect sizes, making them hard to be detected and replicated. To overcome this limitation, this work proposes a new approach that identifies high-level imaging genetic associations through applying multigraph clustering to the SNP-QT association maps. Given an SNP set and a brain QT set, the association between each SNP and each QT is evaluated using a linear regression model. Based on the resulting SNP-QT association map, five SNP–SNP similarity networks (or graphs) are created using five different scoring functions, respectively. Multigraph clustering is applied to these networks to identify SNP clusters with similar association patterns with all the brain QTs. After that, functional annotation is performed for each identified SNP cluster and its corresponding brain association pattern. We applied this pipeline to an AD imaging genetic study, which yielded promising results. For example, in an association study between 54 AD SNPs and 116 amyloid QTs, we identified two SNP clusters with one responsible for amyloid beta clearances and the other regulating amyloid beta formation. These high-level findings have the potential to provide valuable insights into relevant genetic pathways and brain circuits, which can help form new hypotheses for more detailed imaging and genetics studies in independent cohorts.

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Vaidyanathan, Venkatesh, Vijay Naidu, Nishi Karunasinghe, Anower Jabed, Radha Pallati, Gareth Marlow et Lynnette R. Ferguson. « SNP-SNP interactions as risk factors for aggressive prostate cancer ». F1000Research 6 (3 mai 2017) : 621. http://dx.doi.org/10.12688/f1000research.11027.1.

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Prostate cancer (PCa) is one of the most significant male health concerns worldwide. Single nucleotide polymorphisms (SNPs) are becoming increasingly strong candidate biomarkers for identifying susceptibility to PCa. We identified a number of SNPs reported in genome-wide association analyses (GWAS) as risk factors for aggressive PCa in various European populations, and then defined SNP-SNP interactions, using PLINK software, with nucleic acid samples from a New Zealand cohort. We used this approach to find a gene x environment marker for aggressive PCa, as although statistically gene x environment interactions can be adjusted for, it is highly impossible in practicality, and thus must be incorporated in the search for a reliable biomarker for PCa. We found two intronic SNPs statistically significantly interacting with each other as a risk for aggressive prostate cancer on being compared to healthy controls in a New Zealand population.

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Anderson, Katherine, Malcolm Wright et Meagan Wheeler. « Snap Judgement Polling : Street Interviews Enabled by New Technology ». International Journal of Market Research 53, n^o 4 (juillet 2011) : 463–78. http://dx.doi.org/10.2501/ijmr-53-4-463-478.

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We took a promising new method of political polling – snap judgements of political candidates' facial appearance – from the lab to the real world with internet-enabled mobile phones. Using iPhones and online multimedia-rich surveys, we collected over 6000 snap judgements of political candidates' faces, providing proof of concept for a new method of candidate pre-testing and political polling. Consistent with prior research, we find that snap judgements by small samples (178) of politically naive respondents can accurately predict election outcomes. Further, we advance this method of research by testing design elements and providing practical details about the use of mobile technology to aid data collection.

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Wang, Yan, Li, Li, Zhao, Yuan, Sun et Shan. « GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies ». Genes 10, n^o 10 (12 octobre 2019) : 803. http://dx.doi.org/10.3390/genes10100803.

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Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

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Chuluun-Erdene, Ariunbold, Orgil Sengeragchaa, Tsend-Ayush Altangerel, Purevjal Sanjmyatav, Batnaran Dagdan, Solongo Battulga, Lundiamaa Enkhbat, Nyamjav Byambasuren, Munkhzol Malchinkhuu et Munkhtstetseg Janlav. « Association of Candidate Gene Polymorphism with Metabolic Syndrome among Mongolian Subjects : A Case-Control Study ». Medical Sciences 8, n^o 3 (2 septembre 2020) : 38. http://dx.doi.org/10.3390/medsci8030038.

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Metabolic syndrome (MetS) is complex and determined by the interaction between genetic and environmental factors and their influence on obesity, insulin resistance, and related traits associated with diabetes and cardiovascular disease risk. Some dynamic markers, including adiponectin (ADIPOQ), brain-derived neurotrophic factor (BDNF), and lipoprotein lipase (LPL), are implicated in MetS; however, the influence of their genetic variants on MetS susceptibility varies in racial and ethnic groups. We investigated the association of single nucleotide polymorphism (SNP)-SNP interactions among nine SNPs in six genes with MetS’s genetic predisposition in Mongolian subjects. A total of 160 patients with MetS for the case group and 144 healthy individuals for the control group were selected to participate in this study. Regression analysis of individual SNPs showed that the ADIPOQ + 45GG (odds ratio (OR) = 2.09, p = 0.011) and P+P+ of LPL PvuII (OR = 2.10, p = 0.038) carriers had an increased risk of MetS. Conversely, G allele of LPL S447X (OR = 0.45, p = 0.036) and PGC-1α 482Ser (OR = 0.26, p = 0.001) allele were estimated as protective factors, respectively. Moreover, a haplotype containing the G-P+-G combination was related to MetS. Significant loci were also related to body mass index (BMI), systolic blood pressure (SBP), serum high-density lipoprotein cholesterol (HDL-C), triglyceride (TG), and fasting blood glucose (FBG), adipokines, and insulin as well as insulin resistance (p < 0.05). Our results confirm that ADIPOQ + 45T > G, LPL PvII, and PGC-1α Gly482Ser loci are associated with MetS in Mongolian subjects.

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Lee, Kai Wei, Siew Mooi Ching, Vasudevan Ramachandran, Maiza Tusimin, Noraihan Mohd Nordin, Seng Choi Chong et Fan Kee Hoo. « Association Analysis of 14 Candidate Gene Polymorphism with Depression and Stress among Gestational Diabetes Mellitus ». Genes 10, n^o 12 (30 novembre 2019) : 988. http://dx.doi.org/10.3390/genes10120988.

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The association of candidate genes and psychological symptoms of depression, anxiety, and stress among women with gestational diabetes mellitus (GDM) in Malaysia was determined in this study, followed by the determination of their odds of getting psychological symptoms, adjusted for socio-demographical background, maternal, and clinical characteristics. Single nucleotide polymorphisms (SNPs) recorded a significant association between SNP of EPHX2 (rs17466684) and depression symptoms (AOR = 7.854, 95% CI = 1.330–46.360) and stress symptoms (AOR = 7.664, 95% CI = 1.579–37.197). Associations were also observed between stress symptoms and SNP of OXTR (rs53576) and (AOR = 2.981, 95% CI = 1.058–8.402) and SNP of NRG1 (rs2919375) (AOR = 9.894, 95% CI = 1.159–84.427). The SNP of EPHX2 (rs17466684) gene polymorphism is associated with depression symptoms among Malaysian women with GDM. SNP of EPHX2 (rs17466684), OXTR (rs53576) and NRG1 (rs2919375) are also associated with stress symptoms.

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Berry, D. P., N. McHugh, E. Wall, K. McDermott et A. C. O’Brien. « Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population ». Irish Journal of Agricultural and Food Research 58, n^o 1 (1 mars 2019) : 1–12. http://dx.doi.org/10.2478/ijafr-2019-0001.

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Abstract The generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome.

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Belous, Anna A., Alexander A. Sermyagin et Natalia A. Zinovieva. « PSXI-5 Genome-wide association study of feed efficiency in Russian Duroc boars ». Journal of Animal Science 99, Supplement_3 (8 octobre 2021) : 247. http://dx.doi.org/10.1093/jas/skab235.451.

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Abstract The cost of fodder is the major part in expenditure in pork industry. In this regard, improving the feed efficiency is the main goal of breeding programs for the most of pig breeds. Residual feed intake (RFI) is an alternative measure for feed efficiency, which is accepted in different livestock species including pigs. RFI is defined as the difference between the observed and predicted feed intake based on average daily gain and (additionally) back fat thickness. Our aim was to find the candidate genes responsible for RFI in Russian Duroc boars. RFI values for individual boars (n = 766) were calculated using linear regression of daily feed intake on metabolic mid-test weight and average daily gain. The SNP genotyping was carried out using Porcine GGP HD BeadChip (GeneSeek/Neogene). After data quality control, performed in PLINK 1.9, 43,199 SNPs were selected for genome-wide association studies (GWAS). The average daily gain in studied boars was 957 g with variation in individual animals from 424 to 1508 g. Feed conversion rates averaged to 2.21 kg/kg with variation from 1.8 to 3.7 kg/kg. GWAS results showed the presence of 48 SNPs, which were significantly (P < 0.00001) associated with RFI, including 15 SNPs on SSC2, 9 SNP – SSC4, 2 SNPs – SSC6, 21 SNPs – SSC9, and 1 SNP – SSC17. A search for genes located within 0.4 Mb window (0.2 Mb down-stream to 0.2 Mb up-stream from identified SNP) revealed several putative candidates. Functional annotation of the obtained candidates showed the presence of genes involved in protein metabolism (ADAMTS2,UIMC1 on SSC2; NTNG1 on SSC4), regulation of glucose and bile acid metabolism (FGFR4 on SSC2), neuronal development (ENC1 on SSC2; NTRK1, MEF2D on SSC4), vitamin D and K pathways (BGLAP on SSC4). The study was funded by the Russian Ministry of Science and Higher Education No.0445-2019-0029.

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Wang, Charlotte, Fabrizio Ruggeri, Chuhsing K. Hsiao et Raffaele Argiento. « Bayesian nonparametric clustering and association studies for candidate SNP observations ». International Journal of Approximate Reasoning 80 (janvier 2017) : 19–35. http://dx.doi.org/10.1016/j.ijar.2016.07.014.

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Forche, Anja, P. T. Magee, B. B. Magee et Georgiana May. « Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans ». Eukaryotic Cell 3, n^o 3 (juin 2004) : 705–14. http://dx.doi.org/10.1128/ec.3.3.705-714.2004.

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ABSTRACT Single-nucleotide polymorphisms (SNPs) are essential tools for studying a variety of organismal properties and processes, such as recombination, chromosomal dynamics, and genome rearrangement. This paper describes the development of a genome-wide SNP map for Candida albicans to study mitotic recombination and chromosome loss. C. albicans is a diploid yeast which propagates primarily by clonal mitotic division. It is the leading fungal pathogen that causes infections in humans, ranging from mild superficial lesions in healthy individuals to severe, life-threatening diseases in patients with suppressed immune systems. The SNP map contains 150 marker sequences comprising 561 SNPs and 9 insertions-deletions. Of the 561 SNPs, 437 were transition events while 126 were transversion events, yielding a transition-to-transversion ratio of 3:1, as expected for a neutral accumulation of mutations. The average SNP frequency for our data set was 1 SNP per 83 bp. The map has one marker placed every 111 kb, on average, across the 16-Mb genome. For marker sequences located partially or completely within coding regions, most contained one or more nonsynonymous substitutions. Using the SNP markers, we identified a loss of heterozygosity over large chromosomal fragments in strains of C. albicans that are frequently used for gene manipulation experiments. The SNP map will be useful for understanding the role of heterozygosity and genome rearrangement in the response of C. albicans to host environments.

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Goertsches, Robert, Sergio E. Baranzini, Carlos Morcillo, Carlos Nos, Montse Camiña, Jorge R. Oksenberg, Xavier Montalban et Manuel Comabella. « Evidence for association of chromosome 10 open reading frame (C10orf27) gene polymorphisms and multiple sclerosis ». Multiple Sclerosis Journal 14, n^o 3 (avril 2008) : 412–14. http://dx.doi.org/10.1177/1352458507083780.

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A recent association study has provided evidence that chromosome 10q22.1 may contain candidate genes for multiple sclerosis (MS). We analysed two intronic and a non-synonymous single nucleotide polymorphism (SNP) of the C10orf27 gene in 571 patients with MS (relapsing remitting and primary progressive) and healthy controls. Adjusted comparisons revealed significant association with disease susceptibility for one intronic SNP in RRMS individuals and the amino acid modifying SNP for PPMS cases; the latter may also contribute to faster disease progression. Transcript expression in brain lesions from MS patients was increased. These findings suggest C10orf27 as a candidate gene for MS susceptibility and pathogenesis. Multiple selerosis 2008; 14: 412—414. http://msj.sagepub.com

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Paredes-Sánchez, Francisco Alejandro, Ana María Sifuentes-Rincón, Edgar Eduardo Lara-Ramírez, Eduardo Casas, Felipe Alonso Rodríguez-Almeida, Elsa Verónica Herrera-Mayorga et Ronald D. Randel. « Identificación de genes candidatos y SNP relacionados con el temperamento del ganado utilizando un análisis GWAS junto con un análisis de redes interactuantes ». Revista Mexicana de Ciencias Pecuarias 14, n^o 1 (27 décembre 2022) : 1–22. http://dx.doi.org/10.22319/rmcp.v14i1.6077.

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The objective of this study was to identify in Angus and Brangus breed animals with extreme temperament, measured as exit velocity, genomic regions and candidate genes associated with bovine temperament. The population was genotyped with the Genomic Profiler HD 150K chip and after the genome-wide association analysis, the SNPs rs133956611 (P=2.65 E-06) and rs81144933 (P=9.58 E-06) were associated with temperament. The mapping analysis of the regions close to the SNP rs81144933 identified the SNCA (alpha-synuclein) and MMRN1 (multimerin-1) genes at 222.8 and 435.9 Kb downstream respectively, while for the rs133956611 loci the gene GPRIN3 (GPRIN family-member-3) was identified at 245.7 Kb upstream, all three genes are located on the BTA6 chromosome. The analysis of SNCA protein-protein interactions allowed the identification of the genes APP (β-amyloid precursor protein), PARK7 (parkinsonism-associated-deglycase), UCHL1 (ubiquitin-C-terminal-hydrolase-L1), PARK2 (parkin-RBR- E3-ubiquitin-protein-ligase), and genes of the SLC family as candidates to be associated with bovine temperament. All these candidate genes and their interacting were resequenced, which allowed the discovery of new SNPs in the SNCA and APP genes. Of these, the SNPs located in introns 5, 8 and 11 of the APP gene affect splicing site motifs. These results indicate that SNCA and its interacting genes are candidates to be related to bovine temperament.

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Sani, Morteza Bitaraf, Zahra Roudbari, Omid Karimi, Mohammad Hossein Banabazi, Saeid Esmaeilkhanian, Nader Asadzadeh, Javad Zare Harofte, Ali Shafei Naderi et Pamela Anna Burger. « Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries ». Animals 12, n^o 2 (13 janvier 2022) : 184. http://dx.doi.org/10.3390/ani12020184.

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Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, but in dromedaries, the number of studies is very low. This project aimed to find biological themes affecting growth in dromedaries. In the first step, 99 candidate SNPs were chosen from a previously established set of SNPs associated with body weight, gain, and birth weight in Iranian dromedaries. Next, 0.5 kb upstream and downstream of each candidate SNP were selected from NCBI (assembly accession: GCA_000803125.3). The annotation of fragments with candidate SNPs regarding the reference genome was retrieved using the Blast2GO tool. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant biological themes were identified to be related to growth in dromedaries. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via JAK-STAT, and cytokine activity. EFCAB5, MTIF2, MYO3A, TBX15, IFNL3, PREX1, and TMOD3 genes are candidates for improving growth in camel breeding programs.

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Karaesmen, Ezgi, Abbas A. Rizvi, Leah M. Preus, Philip L. McCarthy, Marcelo C. Pasquini, Kenan Onel, Xiaochun Zhu et al. « Replication and validation of genetic polymorphisms associated with survival after allogeneic blood or marrow transplant ». Blood 130, n^o 13 (28 septembre 2017) : 1585–96. http://dx.doi.org/10.1182/blood-2017-05-784637.

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Key Points Candidate SNP associations with survival outcomes after URD transplant are most likely false-positive findings. Over 85% of candidate SNPs are not linked to a biochemical function; of those that are, about half are not linked to the candidate gene.

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Schosser, A., M. Y. Ng, A. W. Butler, S. Cohen-Woods, N. Craddock, M. Owen, I. Craig, A. E. Farmer, C. M. Lewis et P. McGuffin. « COMT in major depression - UK candidate gene association study ». European Psychiatry 26, S2 (mars 2011) : 813. http://dx.doi.org/10.1016/s0924-9338(11)72518-4.

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Catechol-O-methyltransferase (COMT) has a central role in brain dopamine, noradrenalin and adrenalin signaling, and has been suggested to be involved in the pathogenesis and pharmacological treatment of affective disorders. The functional single nucleotide polymorphism (SNP) in exon 4 (Val158Met, rs4680) influences the COMT enzyme activity. The Val158Met polymorphism is a commonly studied variant in psychiatric genetics, and initial studies in schizophrenia and bipolar disorder presented evidence for association with the Met allele. In unipolar depression, while some of the investigations point at an association between the Met/Met genotype and others have found a link between the Val/Val genotype and depression, most of the studies cannot detect any difference in Val158Met allele frequency between depressed individuals and controls.In the present study, we further elucidated the impact of COMT polymorphisms including the Val158Met in MDD. We investigated 1,250 subjects with DSM-IV and/or ICD-10 diagnosis of major depression (MDD), and 1,589 control subjects from UK. A total of 24 SNPs spanning the COMT gene were successfully genotyped using the Illumina HumaHap610-Quad Beadchip (22 SNPs), SNPlex™ genotyping system (1 SNP), and Sequenom MassARRAY® iPLEX Gold (1 SNP). Statistical analyses were implemented using PASW Statistics18, FINETTI (http://ihg.gsf.de/cgi-bin/hw/hwa1.pl), UNPHASED version 3.0.10 program and Haploview 4.0 program.Neither single-marker nor haplotypic association was found with the functional Val158Met polymorphism or with any of the other SNPs genotyped. Our findings do not provide evidence that COMT plays a role in MDD or that this gene explains part of the genetic overlap with bipolar disorder.

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Nodzenski, Michael, Min Shi, Juno M. Krahn, Alison S. Wise, Yuanyuan Li, Leping Li, David M. Umbach et Clarice R. Weinberg. « GADGETS : a genetic algorithm for detecting epistasis using nuclear families ». Bioinformatics 38, n^o 4 (12 novembre 2021) : 1052–58. http://dx.doi.org/10.1093/bioinformatics/btab766.

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Abstract Motivation Epistasis may play an etiologic role in complex diseases, but research has been hindered because identification of interactions among sets of single nucleotide polymorphisms (SNPs) requires exploration of immense search spaces. Current approaches using nuclear families accommodate at most several hundred candidate SNPs. Results GADGETS detects epistatic SNP-sets by applying a genetic algorithm to case-parent or case-sibling data. To allow for multiple epistatic sets, island subpopulations of SNP-sets evolve separately under selection for evident joint relevance to disease risk. The software evaluates the identified SNP-sets via permutation testing and provides graphical visualization. GADGETS correctly identified epistatic SNP-sets in realistically simulated case-parent triads with 10 000 candidate SNPs, far more SNPs than competitors can handle, and it outperformed competitors in simulations with many fewer SNPs. Applying GADGETS to family-based oral-clefting data from dbGaP identified SNP-sets with possible epistatic effects on risk. Availability and implementation GADGETS is part of the epistasisGA package at https://github.com/mnodzenski/epistasisGA. Supplementary information Supplementary data are available at Bioinformatics online.

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Göllner, Tobias, et Martin Fieder. « Selection in the dopamine receptor 2 gene : a candidate SNP study ». PeerJ 3 (11 août 2015) : e1149. http://dx.doi.org/10.7717/peerj.1149.

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Fleming, Alissa C., Hanna Hlebasko, Sarah C. Adams, Krystal N. Roach et Neil D. Christiansen. « Effects of sexism and job–applicant match on leadership candidate evaluations ». Social Behavior and Personality : an international journal 48, n^o 9 (2 septembre 2020) : 1–8. http://dx.doi.org/10.2224/sbp.8452.

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In the lack of fit model and role congruity theory it is suggested that mismatch between female candidates and agentic, male-typed jobs is responsible for discrimination when women apply for leadership positions. In 2 studies we examined the effects of job–applicant mismatch and evaluator sexism on candidate evaluations. In Study 1 (participant evaluators N = 306), mismatch between a female applicant and an agentic job was beneficial for hireability and competence when the evaluator was male and scored low in sexism. However, we were surprised by the result that female evaluators who scored high in sexism rated female applicants for communal jobs lower on competence, likeability, and hireability than did female evaluators who scored low in sexism. In Study 2 (participant evaluators N = 619), evaluator sexism was related to hireability through competence but not through likeability. Further research should be conducted to explore why sexist women devalue a female candidate who is applying for a communal position.

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Warren, Christopher R., Mona Zanhour, Mark Washburn et Brianna Odom. « Helping or hurting ? Effects of sexism and likeability on third party perceptions of women ». Social Behavior and Personality : an international journal 48, n^o 10 (7 octobre 2020) : 1–13. http://dx.doi.org/10.2224/sbp.9315.

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Hostile and benevolent sexism continue to have adverse impacts on opportunities for advancement of women in organizations. In this study we examined the relationship between observer assessments and male interviewer sexism, emphasizing sexism's impact on perceptions of female candidates' hireability and competence. The sample included 266 male and female participants randomized as observers across interview scenarios. Scenario conditions varied between hostile, benevolent, and neutral interviewers, but the female candidate remained neutral. We found that benevolent sexism implies a positive outcome of enhanced observer perception of hireability with little stigma associated with the female candidate's competence, whereas hostile sexism had an overall negative effect, which was offset by observer impressions of likeability of the female job candidate who maintained a neutral composure. Our study findings suggest that observers' perceptions of sexism, benevolence, and a woman candidate's likeability differ and may change with experience. Perception of likeability, in particular, may provide a positive relational strategy for mitigating the effect of benevolent sexism without the tradeoff of perceived diminished competence.

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Weisz, F., T. Urban, P. Chalupová et A. Knoll. « Association analysis of seven candidate genes with performance traits in Czech Large White pigs ». Czech Journal of Animal Science 56, No. 8 (18 août 2011) : 337–44. http://dx.doi.org/10.17221/169/2010-cjas.

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 In this study association analyses were performed between genes tagged SNP (IGF2, NAMPT, DGAT1, MYF4, MC3R, MC4R and MYOD1), performance traits (backfat thickness, lean meat content, average daily gain from birth to the end of the test, average daily gain in test) and estimated breeding values (EBVs) in a population of Czech Large White sows (n = 101). Genotyping of all SNPs was performed by SNapShot with the exception of SNP within NAMPT gene for which HpaII PCR-RFLP assay was used. The following significant associations between genes tagged SNPs and traits or EBVs were found out: DGAT1 – lean meat content (AG > AA, P ≤ 0.05), MC4R – EBV for lean meat content (GG > AA, P ≤ 0.05; GG > AG, P ≤ 0.05), IGF2 – EBV for reproduction (piglets born alive in the second and subsequent parity) (AG > AA, P ≤ 0.05) and total EBV (AG > AA, P ≤ 0.01) and MC3R – EBV for average daily gain (CT > TT, P ≤ 0.05).

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Karimian, Seyedeh Sara, Mohammad Taghi Akbari, Seyed Saeed Sadr et Gholamreza Javadi. « Association of Candidate Single Nucleotide Polymorphisms Related to Candidate Genes in Patients With Schizophrenia ». Basic and Clinical Neuroscience Journal 11, n^o 5 (1 septembre 2020) : 595–608. http://dx.doi.org/10.32598/bcn.9.10.470.

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Introduction: Schizophrenia is a chronic heterogenic neurodevelopment disorder. Many genes interfere in the development of SCZ. All four genes, NrCAM, PRODH, ANK3, and ANKK1, which were evaluated in this study, were previously reported to be associated with Schizophrenia. The NrCAM contributes to creating cognitive deficiencies through the CAM’s signaling pathway. PRODH plays a vital role in creating SCZ negative symptoms through the signaling pathway of glutamatergic and NMDA receptors. ANK3 affects ion channel and molecular adhesion in Ranvier and initial segments of axons, leading to mental retardation, sleep disorder, and SCZ. ANKK1 encodes a protein kinase and was reported to be associated with alcohol addiction, Attention Deficit Hyperactivity Disorder (ADHD), and SCZ. Methods: The subjects were selected from Schizophrenic patients referring to the Psychiatric Ward of Imam-Hussein Hospital and Schizophrenic Patients Support Institution (AHEBBA). 95 (30 Schizoaffective patients, 57 Paranoid patients, and 8 disorganized) patients were recruited as the subjects in the present case-control association study. 120 healthy subjects were recruited from the Tehran Medical Genetics Laboratory staff and a group of students from the Islamic Azad University of Science and Research in Tehran. The genotypes were determined with molecular genotyping techniques of PCR-RFLP, ARMS-PCR, and Cycle sequencing. Results were analyzed by the Chi-Square test using SPSS V. 24 and R, SNP STATE Package to investigate significant differences between cases and controls. Results: The incidence of schizophrenia was 68% and 32% among men and women, respectively. The evaluation of the allelic association between schizophrenia and all the candidate SNPs showed a significant association between NrCAM's SNP rs10235968 and SCZ (P=0.001). Haplotype T, T, C in rs10235968, rs6967368, rs3763463, respectively, within the NrCAM gene, showed significant association with schizophrenia disorder (P=0.0001). Conclusion: No association was found between other candidate SNPs and SCZ among the subjects.

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DIEGUEZ-GONZALEZ, REBECA, SERVET AKAR, MANUEL CALAZA, ISIDORO GONZALEZ-ALVARO, BENJAMIN FERNANDEZ-GUTIERREZ, JOSE RAMON LAMAS, ARTURO R. de la SERNA et al. « Lack of Association with Rheumatoid Arthritis of Selected Polymorphisms in 4 Candidate Genes : CFH, CD209, Eotaxin-3, and MHC2TA ». Journal of Rheumatology 36, n^o 8 (30 juin 2009) : 1590–95. http://dx.doi.org/10.3899/jrheum.090022.

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Objective.To investigate associations with rheumatoid arthritis (RA) of single-nucleotide polymorphisms (SNP) in 4 candidate genes, complement factor H (CFH), CD209 or DC-SIGN, eotaxin-3, and the MHC class II Transactivator (MHC2TA) genes. These SNP have been reported as important for RA (eotaxin-3 and MHC2TA) or for other immune-mediated diseases (CFH and CD209).Methods.Genotypes for the 7 selected SNP were obtained from 1587 patients with RA and 1570 controls of Spanish ancestry. Analyses were carried out after stratification for sex, erosions, rheumatoid factor, shared epitope, anti-cyclic citrullinated peptide antibodies, and the R620W PTPN22 SNP.Results.None of the comparisons between patients with RA and controls or between the different strata of patients according to disease features was significant.Conclusion.None of the SNP in CFH and CD209 showed evidence of association with RA. We did not replicate the association of eotaxin-3 with RA described in Koreans, or that of the MHC2T SNP.

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Bhusudsawang, Gunlayarat, Ratchanee Rattanawong, Thitaporn Phumichai, Wirulda Pootakham, Sithichoke Tangphatsornruang et Kittipat Ukoskit. « Identification of Candidate Gene-Based Markers for Girth Growth in Rubber Trees ». Plants 10, n^o 7 (14 juillet 2021) : 1440. http://dx.doi.org/10.3390/plants10071440.

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Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

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Tiwari, Arun K., Clement C. Zai, Gautam Sajeev, Tamara Arenovich, Daniel J. Müller et James L. Kennedy. « Analysis of 34 candidate genes in bupropion and placebo remission ». International Journal of Neuropsychopharmacology 16, n^o 4 (1 mai 2013) : 771–81. http://dx.doi.org/10.1017/s1461145712000843.

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Abstract There is considerable variability in the rate of response and remission following treatment with antidepressant drugs or placebo in depression patients. No pharmacogenetic studies of bupropion response have been done. We investigated 532 tagging single nucleotide polymorphisms (SNPs) in 34 candidate genes for association with remission and response to either bupropion (n=319) or placebo (n=257) in patients with major depressive disorder. Analyses were performed using conditional logistic regression. Significant association (gene-wide correction) was observed for remission following treatment with bupropion for a SNP within the serotonin receptor 2A gene (HTR2A rs2770296, pcorrected=0.02). Response to bupropion treatment was significantly associated with a SNP in the dopamine transporter gene (rs6347, pcorrected=0.013). Among the patients who received placebo, marginal association for remission was observed between a SNP in HTR2A (rs2296972, pcorrected=0.055) as well as in the serotonin transporter gene (5-HTT or SLC6A4 rs4251417, pcorrected=0.050). Placebo response was associated with SNPs in the glucocorticoid receptor gene (NR3C1; rs1048261, pcorrected=0.040) and monoamine oxidase A gene (MAOA; rs6609257, pcorrected=0.046). Although the above observations were significant after gene-wide corrections, none of these would be significant after a more conservative study-wide correction for multiple tests. These results suggest a possible role for HTR2A in remission to bupropion treatment. In accordance with bupropion pharmacology, dopamine transporter may play a role in response. The MAOA gene may be involved in placebo response.

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Ghosh, Sujoy, Juan C. Vivar, Mark A. Sarzynski, Yun Ju Sung, James A. Timmons, Claude Bouchard et Tuomo Rankinen. « Integrative pathway analysis of a genome-wide association study of V̇o2max response to exercise training ». Journal of Applied Physiology 115, n^o 9 (1 novembre 2013) : 1343–59. http://dx.doi.org/10.1152/japplphysiol.01487.2012.

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We previously reported the findings from a genome-wide association study of the response of maximal oxygen uptake (V̇o2max) to an exercise program. Here we follow up on these results to generate hypotheses on genes, pathways, and systems involved in the ability to respond to exercise training. A systems biology approach can help us better establish a comprehensive physiological description of what underlies V̇o2maxtrainability. The primary material for this exploration was the individual single-nucleotide polymorphism (SNP), SNP-gene mapping, and statistical significance levels. We aimed to generate novel hypotheses through analyses that go beyond statistical association of single-locus markers. This was accomplished through three complementary approaches: 1) building de novo evidence of gene candidacy through informatics-driven literature mining; 2) aggregating evidence from statistical associations to link variant enrichment in biological pathways to V̇o2max trainability; and 3) predicting possible consequences of variants residing in the pathways of interest. We started with candidate gene prioritization followed by pathway analysis focused on overrepresentation analysis and gene set enrichment analysis. Subsequently, leads were followed using in silico analysis of predicted SNP functions. Pathways related to cellular energetics (pantothenate and CoA biosynthesis; PPAR signaling) and immune functions (complement and coagulation cascades) had the highest levels of SNP burden. In particular, long-chain fatty acid transport and fatty acid oxidation genes and sequence variants were found to influence differences in V̇o2max trainability. Together, these methods allow for the hypothesis-driven ranking and prioritization of genes and pathways for future experimental testing and validation.

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Ponomarenko, Mikhail, Dmitry Rasskazov, Olga Arkova, Petr Ponomarenko, Valentin Suslov, Ludmila Savinkova et Nikolay Kolchanov. « How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter ». BioMed Research International 2015 (2015) : 1–17. http://dx.doi.org/10.1155/2015/359835.

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The use of biomedical SNP markers of diseases can improve effectiveness of treatment. Genotyping of patients with subsequent searching for SNPs more frequent than in norm is the only commonly accepted method for identification of SNP markers within the framework of translational research. The bioinformatics applications aimed at millions of unannotated SNPs of the “1000 Genomes” can make this search for SNP markers more focused and less expensive. We used our Web service involving Fisher’sZ-score for candidate SNP markers to find a significant change in a gene’s expression. Here we analyzed the change caused by SNPs in the gene’s promoter via a change in affinity of the TATA-binding protein for this promoter. We provide examples and discuss how to use this bioinformatics application in the course of practical analysis of unannotated SNPs from the “1000 Genomes” project. Using known biomedical SNP markers, we identified 17 novel candidate SNP markers nearby: rs549858786 (rheumatoid arthritis); rs72661131 (cardiovascular events in rheumatoid arthritis); rs562962093 (stroke); rs563558831 (cyclophosphamide bioactivation); rs55878706 (malaria resistance, leukopenia), rs572527200 (asthma, systemic sclerosis, and psoriasis), rs371045754 (hemophilia B), rs587745372 (cardiovascular events); rs372329931, rs200209906, rs367732974, and rs549591993 (all four: cancer); rs17231520 and rs569033466 (both: atherosclerosis); rs63750953, rs281864525, and rs34166473 (all three: malaria resistance, thalassemia).

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Ponomarenko, Petr, Dmitry Rasskazov, Valentin Suslov, Ekaterina Sharypova, Ludmila Savinkova, Olga Podkolodnaya, Nikolay L. Podkolodny et al. « Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters ». BioMed Research International 2016 (2016) : 1–21. http://dx.doi.org/10.1155/2016/8642703.

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Variations in human genome (e.g., single nucleotide polymorphisms, SNPs) may be associated with hereditary diseases, their complications, comorbidities, and drug responses. Using Web service SNP_TATA_Comparator presented in our previous paper, here we analyzed immediate surroundings of known SNP markers of diseases and identified several candidate SNP markers that can significantly change the affinity of TATA-binding protein for human gene promoters, with circadian consequences. For example, rs572527200 may be related to asthma, where symptoms are circadian (worse at night), and rs367732974 may be associated with heart attacks that are characterized by a circadian preference (early morning). By the same method, we analyzed the 90 bp proximal promoter region of each protein-coding transcript of each human gene of the circadian clock core. This analysis yielded 53 candidate SNP markers, such as rs181985043 (susceptibility to acute Q fever in male patients), rs192518038 (higher risk of a heart attack in patients with diabetes), and rs374778785 (emphysema and lung cancer in smokers). If they are properly validated according to clinical standards, these candidate SNP markers may turn out to be useful for physicians (to select optimal treatment for each patient) and for the general population (to choose a lifestyle preventing possible circadian complications of diseases).

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Myung, W., J. Kim, S.-W. Lim, S. Shim, H.-H. Won, Seonwoo Kim, Sangha Kim et al. « A genome-wide association study of antidepressant response in Koreans ». Translational Psychiatry 5, n^o 9 (septembre 2015) : e633-e633. http://dx.doi.org/10.1038/tp.2015.127.

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Abstract We conducted a three-stage genome-wide association study (GWAS) of response to antidepressant drugs in an ethnically homogeneous sample of Korean patients in untreated episodes of nonpsychotic unipolar depression, mostly of mature onset. Strict quality control was maintained in case selection, diagnosis, verification of adherence and outcome assessments. Analyzed cases completed 6 weeks of treatment with adequate plasma drug concentrations. The overall successful completion rate was 85.5%. Four candidate single-nucleotide polymorphisms (SNPs) on three chromosomes were identified by genome-wide search in the discovery sample of 481 patients who received one of four allowed selective serotonin reuptake inhibitor (SSRI) antidepressant drugs (Stage 1). In a focused replication study of 230 SSRI-treated patients, two of these four SNP candidates were confirmed (Stage 2). Analysis of the Stage 1 and Stage 2 samples combined (n=711) revealed GWAS significance (P=1.60 × 10-8) for these two SNP candidates, which were in perfect linkage disequilibrium. These two significant SNPs were confirmed also in a focused cross-replication study of 159 patients treated with the non-SSRI antidepressant drug mirtazapine (Stage 3). Analysis of the Stage 1, Stage 2 and Stage 3 samples combined (n=870) also revealed GWAS significance for these two SNPs, which was sustained after controlling for gender, age, number of previous episodes, age at onset and baseline severity (P=3.57 × 10-8). For each SNP, the response rate decreased (odds ratio=0.31, 95% confidence interval: 0.20–0.47) as a function of the number of minor alleles (non-response alleles). The two SNPs significantly associated with antidepressant response are rs7785360 and rs12698828 of the AUTS2 gene, located on chromosome 7 in 7q11.22. This gene has multiple known linkages to human psychological functions and neurobehavioral disorders. Rigorous replication efforts in other ethnic populations are recommended.

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Sarzynski, Mark A., Peter Jacobson, Tuomo Rankinen, Björn Carlsson, Lars Sjöström, Lena M. S. Carlsson et Claude Bouchard. « Association of GWAS-Based Candidate Genes with HDL-Cholesterol Levels before and after Bariatric Surgery in the Swedish Obese Subjects Study ». Journal of Clinical Endocrinology & ; Metabolism 96, n^o 6 (1 juin 2011) : E953—E957. http://dx.doi.org/10.1210/jc.2010-2227.

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Context and Objective: The magnitude of weight loss-induced high-density lipoprotein cholesterol (HDL-C) changes may depend on genetic factors. We examined the associations of eight candidate genes, identified by genome-wide association studies, with HDL-C at baseline and 10 yr after bariatric surgery in the Swedish Obese Subjects study. Methods: Single-nucleotide polymorphisms (SNP) (n = 60) in the following gene loci were genotyped: ABCA1, APOA5, CETP, GALNT2, LIPC, LIPG, LPL, and MMAB/MVK. Cross-sectional associations were tested before (n = 1771) and 2 yr (n = 1583) and 10 yr (n = 1196) after surgery. Changes in HDL-C were tested between baseline and yr 2 (n = 1518) and yr 2 and 10 (n = 1149). A multiple testing corrected threshold of P = 0.00125 was used for statistical significance. Results: In adjusted multivariate models, CETP SNP rs3764261 explained from 3.2–4.2% (P < 10−14) of the variation in HDL-C at all three time points, whereas CETP SNP rs9939224 contributed an additional 0.6 and 0.9% at baseline and yr 2, respectively. LIPC SNP rs1077834 showed consistent associations across all time points (R2 = 0.4–1.1%; 3.8 × 10−6 < P < 3 × 10−3), whereas LPL SNP rs6993414 contributed approximately 0.5% (5 × 10−4 < P < 0.0012) at yr 2 and 10. In aggregate, four SNP in three genes explained 4.2, 6.8, and 5.6% of the HDL-C variance at baseline, yr 2, and yr 10, respectively. None of the SNP was significantly associated with weight loss-related changes in HDL-C. Conclusions: SNP in the CETP, LIPC, and LPL loci contribute significantly to plasma HDL-C levels in obese individuals, and the associations persist even after considerable weight loss due to bariatric surgery. However, they are not associated with surgery-induced changes in HDL-C levels.

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Alhaddad, Hasan, Mona Abdi et Leslie A. Lyons. « Patterns of allele frequency differences among domestic cat breeds assessed by a 63K SNP array ». PLOS ONE 16, n^o 2 (25 février 2021) : e0247092. http://dx.doi.org/10.1371/journal.pone.0247092.

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Cats are ubiquitous companion animals that have been keenly associated with humans for thousands of years and only recently have been intentionally bred for aesthetically appealing coat looks and body forms. The intense selection on single gene phenotypes and the various breeding histories of cat breeds have left different marks on the genomes. Using a previously published 63K Feline SNP array dataset of twenty-six cat breeds, this study utilized a genetic differentiation-based method (di) to empirically identify candidate regions under selection. Defined as three or more overlapping (500Kb) windows of high levels of population differentiation, we identified a total of 205 candidate regions under selection across cat breeds with an average of 6 candidate regions per breed and an average size of 1.5 Mb per candidate region. Using the combined size of candidate regions of each breed, we conservatively estimate that a minimum of ~ 0.1–0.7% of the autosomal genome is potentially under selection in cats. As positive controls and tests of our methodology, we explored the candidate regions of known breed-defining genes (e.g., FGF5 for longhaired breeds) and we were able to detect the genes within candidate regions, each in its corresponding breed. For breed specific exploration of candidate regions under selection, eleven representative candidate regions were found to encompass potential candidate genes for several phenotypes such as brachycephaly of Persian (DLX6, DLX5, DLX2), curled ears of American Curl (MCRIP2, PBX1), and body-form of Siamese and Oriental (ADGRD1), which encourages further molecular investigations. The current assessment of the candidate regions under selection is empiric and detailed analyses are needed to rigorously disentangle effects of demography and population structure from artificial selection.

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Picoult-Newberg, Leslie, Trey E. Ideker, Mark G. Pohl, Scott L. Taylor, Miriam A. Donaldson, Deborah A. Nickerson et Michael Boyce-Jacino. « Mining SNPs From EST Databases ». Genome Research 9, n^o 2 (1 février 1999) : 167–74. http://dx.doi.org/10.1101/gr.9.2.167.

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There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.[The SNPs identified in this study can be found in the National Center of Biotechnology (NCBI) SNP database under submitter handles ORCHID (SNPS-981210-A) and debnick (SNPS-981209-A and SNPS-981209-B).]

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Isubakova, D. S., N. V. Litviakov, O. S. Tsymbal, T. V. Usova, M. Yu Tsyplenkova, I. V. Milto et R. M. Takhauov. « Search for polymorphic variants of candidate genes contributing to individual radiosensitivity ». Bulletin of Siberian Medicine 21, n^o 4 (21 janvier 2023) : 79–87. http://dx.doi.org/10.20538/1682-0363-2022-4-79-87.

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Background. Cytogenetic damage (СD) in lymphocytes induced by low doses (up to 0.1 Sv) of ionizing radiation (IR) is the main cytogenetic sign of individual radiosensitivity of the human body. In addition to DNA repair and cell death, which affect the formation of СD and its elimination, IR effects on the cell can be manifested through changes in proliferation of cells with unrepaired DNA damage. The system of cyclins and cyclin-dependent kinases (CDK), which provide coordination of mitotic events during passage of a cell through the cell cycle, plays a crucial role in regulation of cell proliferation.Aim. To evaluate the relationship of single-nucleotide polymorphisms (SNPs) of cell cycle genes with an increased frequency of СD in workers of a nuclear power plant affected by chronic occupational radiation exposure in the dose range of 100–500 mSv.Materials and methods. The object of the study was blood of 55 conditionally healthy workers of Siberian Chemical Plant (SCP) who were affected by chronic occupational radiation exposure (gamma radiation) in the dose range of 100–500 mSv. A standard cytogenetic analysis of blood lymphocytes was performed for all examined individuals. Genomic DNA was isolated from the blood of the workers using the QIAamp DNA Blood Mini Kit (QIAGEN, Germany). DNA was genotyped using 257 SNPs of cyclin genes and neighboring intergenic regions using DNA microarrays from the high-density CytoScan HD Array (Affymetrix, USA).Results. Taking into account the Bonferroni correction, only statistically significant associations of SNPs with the frequency of dicentric chromosomes were found; all other types of chromosomal aberrations did not show statistical significance. The rs803054 CCNI2 was associated with an increased frequency of dicentric chromosomes arising under the influence of chronic occupational radiation exposure.Conclusion. The discovered SNP (rs803054), whose recessive genotype is associated with an increased frequency of dicentric chromosomes in workers of SCP exposed to radiation at doses of 100–500 mSv over a long time, can be considered as a potential marker of individual radiosensitivity. To confirm the identified associations, further validation studies are needed on an expanded sample of people affected by chronic occupational radiation exposure.

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Green, Nancy S., Katherine Ender, Farzana Pashankar, Catherine Driscoll, Patricia Giardina, Craig A. Mullen, Lorraine Clark et al. « Genetics of HbF and HbF Response to Hydroxyurea In Pediatric Sickle Cell Disease : A Multi-Site Pilot Analysis of Candidate SNP Variants ». Blood 116, n^o 21 (19 novembre 2010) : 2641. http://dx.doi.org/10.1182/blood.v116.21.2641.2641.

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Abstract Abstract 2641 Abstract: Only few genes appear to strongly regulate HbF levels in adults with sickle cell disease (SCD). We aim to: (1) Extend these observations to children with SCD, who likely have better preserved marrow capacity; (2) Assess whether these same genes and other previously identified candidates (Ma et al., 2007) associate with HbF response to HU. Methods: We performed a retrospective analysis from 6 sites (see author affiliations) of children age 5–21 with HbSS or HbS-B thalassemia, untreated with HU or treated for > 6 months at comparable indications and dosing, using %HbF at steady state (baseline) and on HU at or near maximal tolerated dose (MTD), defined as >20mg/kg/day. Subject adherence to HU was assessed by report to their hematology clinician. Siblings were excluded to ensure genetic independence. Candidate 36 SNPs from 2 groups of genes were genotyped: 1) those from reported GWAS: 15 SNPs in BCL11A, 3 in HBS1L-MYB intron, 5' site in B globin, plus sar1; and 2) 15 candidate SNPs exhibiting the largest effect size on HbF with HU treatment (Ma, 2007). SNP genotyping (minor allele frequency (MAF) ranging from 0.10 to 0.50) was performed on the Sequenom MassArray iPLEX platform. (SNP sequences are available.) Duplicate samples assured genotype concordance. Genotype frequency distribution at each SNP was tested for deviations from Hardy-Weinberg equilibrium. MAFs were comparable across our 6 sites, to allele frequencies in HapMap for CEU populations, and CSSCD (Lettre et al., 2008), confirming validity of pooling SNP genotype data from the sites. Using HbF as a continuous trait, genetic associations were assessed from a total of 80 children, 29 of whom are on HU, between each of the 36 SNPs and: a) baseline %HbF; b) %HbF on HU treatment; c) delta %HbF (HU treatment - baseline). For each model, linear regression analysis was used to test quantitative trait and disease trait SNP associations assuming an additive effect for each copy of the minor allele on the phenotype. Resultant p-values were assessed for significance using Bonferroni adjustment for multiple testing. Results: Of the 80 children, comparing the 51 not on HU to those 29 on HU, no significance differences were seen in the distribution and average of baseline %HbF (9.2 vs. 8.9, p=0.820). SNP analyses are summarized in Table 1. 8 SNPs were nominally significantly associated with baseline %HbF. Direction of SNP association differed among these SNPs; some MAF may be reversed in this population compared to those previously reported. For %HbF on HU, the B globin SNP was significantly associated. The delta %HbF on HU is significantly associated with the B globin SNP and nominally so with BCLA11 and SAR1A gene. Our preliminary data begin to extend findings of specific genetic variants regulating HbF to children with SCD. Early data suggest that HbF in response to HU may share some of the mechanisms governing baseline HbF in SCD, not surprising given the commonality of enhanced erythropoiesis. Subject recruitment and analyses are on-going. Disclosure: Off Label Use: Hydroxyurea has not been FDA approved for use in children with sickle cell disease, a topic of the submitted abstract.

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Borel, Patrick, Myriam Moussa, Emmanuelle Reboul, Bernard Lyan, Catherine Defoort, Stéphanie Vincent-Baudry, Matthieu Maillot et al. « Human fasting plasma concentrations of vitamin E and carotenoids, and their association with genetic variants in apo C-III, cholesteryl ester transfer protein, hepatic lipase, intestinal fatty acid binding protein and microsomal triacylglycerol transfer protein ». British Journal of Nutrition 101, n^o 5 (29 juillet 2008) : 680–87. http://dx.doi.org/10.1017/s0007114508030754.

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Plasma concentrations of vitamin E and carotenoids are governed by several factors, including genetic factors. Single nucleotide polymorphisms (SNP) in some genes involved in lipid metabolism have recently been associated with fasting plasma concentrations of these fat-soluble micronutrients. To further investigate the role of genetic factors that modulate the plasma concentrations of these micronutrients, we assessed whether SNP in five candidate genes (apo C-III,CETP,hepatic lipase,I-FABPandMTP) were associated with the plasma concentrations of these micronutrients. Fasting plasma vitamin E and carotenoid concentrations were measured in 129 French Caucasian subjects (forty-eight males and eighty-one females). Candidate SNP were genotyped by PCR amplification followed by restriction fragment length polymorphisms. Plasma γ-tocopherol, α-carotene and β-carotene concentrations were significantly different (P < 0·05) in subjects who carried different SNP variants in hepatic lipase. Plasma α-tocopherol concentrations were significantly different in subjects who had different SNP variants in apo C-III and cholesteryl ester transfer protein (CETP). Plasma lycopene concentrations were significantly different (P < 0·05) in women who had different SNP variants in intestinal fatty acid binding protein (I-FABP). Finally, there was no effect of SNP variants in microsomal TAG transfer protein upon the plasma concentrations of these micronutrients. Most of the observed differences remained significant after the plasma micronutrients were adjusted for plasma TAG and cholesterol. These results suggest that apo C-III, CETP and hepatic lipase play a role in determining the plasma concentrations of tocopherols while hepatic lipase and I-FABP may modulate plasma concentrations of carotenoids.

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Huang, Zhenyu, Fei Shen, Yuling Chen, Ke Cao et Lirong Wang. « Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study ». Plants 10, n^o 2 (27 janvier 2021) : 242. http://dx.doi.org/10.3390/plants10020242.

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Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key genes related to peach pollen fertility trait. The significant association peak was detected at Chr.06: 2,116,368 bp, which was in accordance with the previous genetic mapping results, but displayed largely improved precision, allowing for the identification of nine candidate genes. Among these candidates, gene PpABCG26, encoding an ATP-binding cassette G (ABCG) transporter and harboring the most significantly associated SNP (Single Nucleotide Polymorphism) marker in its coding region, was hypothesized to control peach pollen fertility/sterility based on the results of gene function comparison, gene relative expression, and nucleotide sequence analysis. The obtained results will help us to understand the genetic basis of peach pollen fertility trait, and to discover applicable markers for pre-selection in peach.

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Guo, Fucheng, Liang Ming, Rendalai Si, Li Yi, Jing He et Rimutu Ji. « A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus ». Animals 10, n^o 1 (7 janvier 2020) : 96. http://dx.doi.org/10.3390/ani10010096.

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Bactrian camels (Camelus bactrianus) are one of the few large livestock species that can survive in the Gobi Desert. Animal immunity and disease resistance are related to hematological traits, which are also associated with tolerance observed in Bactrian camels. However, no genome-wide association studies have examined the genetic mechanism of the immune capability of Bactrian camels. In the present study, we used genotyping-by-sequencing data generated from 366 Bactrian camel accessions to perform a genome-wide association study for 17 hematological traits. Of the 256,616 single-nucleotide polymorphisms (SNPs) obtained, 1,635 trait–SNP associations were among the top quantitative trait locus candidates. Lastly, 664 candidate genes associated with 13 blood traits were identified. The most significant were ZNF772, MTX2, ESRRG, MEI4, IL11, FRMPD4, GABPA, NTF4, CRYBG3, ENPP5, COL16A1, and CD207. The results of our genome-wide association study provide a list of significant SNPs and candidate genes, which offer valuable information for further dissection of the molecular mechanisms that regulate the camel’s hematological traits to ultimately reveal their tolerance mechanisms.

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