scholarly journals Genome-wide Association Study for Noise-induced Cochlear Synaptopathy

2018 ◽  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Noise Exposure ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Positional Candidate ◽  
Genome Wide ◽  
Hybrid Mouse Diversity Panel ◽  
Susceptibility To Noise ◽  
Cell Synapse

Article SummaryIn order to elucidate the genetic architecture of the auditory hair cell synapse and the susceptibility to noise-induced cochlear synaptopathy, we are providing the first genome-wide association study with 111 strains (n=695) of the Hybrid Mouse Diversity Panel based upon the strain variation of the wave 1 P1-N1 amplitude of the auditory brainstem responses both before and after noise exposure. Based on this association analysis and our cochlear gene expression data, we identified several novel loci and prioritized positional candidate genes related to cochlear synaptopathy, especially after exposure to noise.AbstractThis is the first genome-wide association study (GWAS) with the Hybrid Mouse Diversity Panel (HMDP) to define the genetic landscape of the auditory hair cell synapse and the susceptibility to noise-induced cochlear synaptopathy. We tested 5-week old female mice (n=695) from 111 HMDP strains (n= 6-7/strain) at baseline and post noise exposure using ABR wave 1 suprathreshold amplitudes (P1-N1 at 80 dB SPL) at 8, 12, 16, 24 and 32 kHz tone burst stimuli. Mice were exposed for 2 hours to 10 kHz octave band noise (OBN) at 108 dB SPL. A broad range of suprathreshold ABR wave 1 amplitude were detected across the HMDP strains. At the genome-wide significance threshold (-logP = 5.39), associations on Chr. 3 and Chr. 16 were identified at baseline. Also, association peaks on Chr. 2 and Chr. 13 were determined post noise exposure. In order to prioritize candidate genes, we generated gene expression microarray profiles using RNA isolated from cochleae in 64 HMDP strains (n =3 arrays per strain). We then used EMMA to perform an association analysis between all SNPs and array probes mapping within each region. A total of 17 genes (2 within Chr. 3 association, 6 within Chr. 2 association and 9 within Chr. 13 association) of these 3 loci were identified with at least 1 probe whose expression was regulated by a significant cis eQTL in the cochlea. Also, the genetic architecture of noise induced cochlear synaptopathy is distinct from that of baseline auditory nerve/synapse integrity. In summary, from this GWAS and our eQTL data, we identified 4 novel loci and prioritized positional candidate genes related to cochlear synaptopathy at baseline and after exposure to noise.

Genome-wide Association Study Identifies Positional Candidate Genes Affecting Carcass Weight Trait in Pigs

2017 ◽  
Vol 51 (2) ◽  
pp. 127-134
Author(s):  
Jae-Bong Lee ◽  
◽  
Hee-Bok Park ◽  
Jun-Ho Shin ◽  
Chae-Kyoung Yoo ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Carcass Weight ◽  
Genome Wide Association ◽  
Positional Candidate ◽  
Genome Wide ◽  
Weight Trait

Genome-wide Association Study Identifies Positional Candidate Genes Affecting Birth Weight Trait in Purebred Landrace

2018 ◽  
Vol 52 (3) ◽  
pp. 55-62
Author(s):  
Ho-Chan Kang ◽  
◽  
Jae-Bong Lee ◽  
Chae-Kung Yoo ◽  
Tae-Jeong Choi ◽  
...  
Keyword(s):  
Birth Weight ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Positional Candidate ◽  
Genome Wide ◽  
Weight Trait

scholarly journals Genome-wide association study identifies new loci associated with noise-induced tinnitus in Chinese populations

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chengyong Xie ◽  
Yuguang Niu ◽  
Jie Ping ◽  
Yahui Wang ◽  
Chenning Yang ◽  
...  
Keyword(s):  
Association Study ◽  
Noise Exposure ◽  
Genome Wide Association Study ◽  
Acoustic Stimulus ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Chinese Populations ◽  
Genome Wide ◽  
Susceptibility To Noise

Abstract Background Tinnitus is an auditory phantom sensation in the absence of an acoustic stimulus, which affects nearly 15% of the population. Excessive noise exposure is one of the main causes of tinnitus. To now, the knowledge of the genetic determinants of susceptibility to tinnitus remains limited. Results We performed a two-stage genome-wide association study (GWAS) and identified that two single nucleotide polymorphisms (SNPs), rs2846071 located in the intergenic region at 11q13.5 (odds ratio [OR] = 2.14, 95% confidence interval [CI] = 1.96–3.40, combined P = 4.89 × 10− 6) and rs4149577 located in the intron of TNFRSF1A gene at 12p13.31 (OR = 2.05, 95% CI = 1.89–2.51, combined P = 6.88 × 10− 6), are significantly associated with the susceptibility to noise-induced tinnitus. Furthermore, the expression quantitative trait loci (eQTL) analyses revealed that rs2846071 is significantly correlated with the expression of WNT11 gene, and rs4149577 with the expression of TNFRSF1A gene in multiple brain tissues (all P < 0.05). The newly identified candidate gene WNT11 is involved in Wnt pathway, and TNFRSF1A in the tumor necrosis factor pathway, respectively. Pathway enrichment analyses also showed that these two pathways are closely relevant to tinnitus. Conclusions Our findings highlight two novel loci at 11q13.5 and 12p13.31 conferring susceptibility to noise-induced tinnitus. and suggest that the WNT11 and TNFRSF1A genes might be the candidate causal targets of 11q13.5 and 12p13.31 loci, respectively.

scholarly journals Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joon-Ki Hong ◽  
Jae-Bong Lee ◽  
Yuliaxis Ramayo-Caldas ◽  
Si-Dong Kim ◽  
Eun-Seok Cho ◽  
...  
Keyword(s):  
Animal Model ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Single Step ◽  
Genetic Effects ◽  
Genome Wide Association ◽  
Positional Candidate ◽  
Network Analyses ◽  
Genome Wide

Abstract In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.

scholarly journals A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Gabriel Costa Monteiro Moreira ◽  
Clarissa Boschiero ◽  
Aline Silva Mello Cesar ◽  
James M. Reecy ◽  
Thaís Fernanda Godoy ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Broiler Chickens ◽  
Genome Wide Association Study ◽  
Fat Deposition ◽  
Genome Wide Association ◽  
Positional Candidate ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

scholarly journals Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Bingru Zhao ◽  
Hanpeng Luo ◽  
Xixia Huang ◽  
Chen Wei ◽  
Jiang Di ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Improvement ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Fibre Diameter ◽  
Single Step ◽  
Genome Wide Association ◽  
Six Traits ◽  
Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

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