scholarly journals Transcriptome profiles of hypothalamus and adrenal gland linked to haplotype related to coping behavior in pigs

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kevin Gley ◽  
Eduard Murani ◽  
Nares Trakooljul ◽  
Manuela Zebunke ◽  
Birger Puppe ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Candidate Genes ◽  
Hpa Axis ◽  
Genome Wide Association Study ◽  
Coping Behavior ◽  
Positional Candidate ◽  
Genome Wide ◽  
Ngf Signaling ◽  
And Coping ◽  
Haplotype Information

Abstract The hypothalamic-pituitary-adrenal (HPA) axis is an important component of neuroendocrine stress regulation and coping behavior. Transcriptome profiles of the hypothalamus and adrenal gland were assessed to identify molecular pathways and candidate genes for coping behavior in pigs. Ten each of high- (HR) and low- (LR) reactive pigs (n = 20) were selected for expression profiling based haplotype information of a prominent QTL-region on SSC12 discovered in our previous genome-wide association study (GWAS) on coping behavior. Comparing the HR and LR pigs showed 692 differentially expressed genes (DEGs) in the adrenal gland and 853 DEGs in the hypothalamus, respectively. Interestingly, 47% (17 out of 36) of DEGs found in both tissues were located in GWAS regions identified on SSC12, indicating that there are significant functional positional candidate genes for coping behaviour. Pathway analysis assigned DEGs to glucocorticoid receptor signaling in the adrenal gland. Furthermore, oxidative phosphorylation, mitochondrial dysfunction, and NGF signaling as well as cholecystokinin/Gastrin-mediated were identified in the hypothalamus. We narrowed the list of candidate genes in GWAS regions by analyzing their DEGs in the HPA axis. The top identified transcripts, including ATP1B2, AURKB, MPDU1 and NDEL1 provide evidence for molecular correlates of coping behavior in GWAS regions.

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 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.

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 Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marie-Pierre Sanchez ◽  
Dominique Rocha ◽  
Mathieu Charles ◽  
Mekki Boussaha ◽  
Chris Hozé ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Binding Sites ◽  
Mineral Content ◽  
Genome Wide Association Study ◽  
Bovine Milk ◽  
Positional Candidate ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Regulatory Snps

AbstractThe mineral composition of bovine milk plays an important role in determining its nutritional and cheese-making value. Concentrations of the main minerals predicted from mid-infrared spectra produced during milk recording, combined with cow genotypes, provide a unique opportunity to decipher the genetic determinism of these traits. The present study included 1 million test-day predictions of Ca, Mg, P, K, Na, and citrate content from 126,876 Montbéliarde cows, of which 19,586 had genotype data available. All investigated traits were highly heritable (0.50–0.58), with the exception of Na (0.32). A sequence-based genome-wide association study (GWAS) detected 50 QTL (18 affecting two to five traits) and positional candidate genes and variants, mostly located in non-coding sequences. In silico post-GWAS analyses highlighted 877 variants that could be regulatory SNPs altering transcription factor (TF) binding sites or located in non-coding RNA (mainly lncRNA). Furthermore, we found 47 positional candidate genes and 45 TFs highly expressed in mammary gland compared to 90 other bovine tissues. Among the mammary-specific genes, SLC37A1 and ANKH, encoding proteins involved in ion transport were located in the most significant QTL. This study therefore highlights a comprehensive set of functional candidate genes and variants that affect milk mineral content.

scholarly journals The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

2017 ◽  
Vol 7 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Amanda S Lobell ◽  
Rachel R Kaspari ◽  
Yazmin L Serrano Negron ◽  
Susan T Harbison
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Natural Populations ◽  
Direct Role ◽  
Genome Wide ◽  
A Genome ◽  
Fitness Trait ◽  
Sleep Parameters ◽  
Activity Behavior ◽  
Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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.

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