Structural and functional characterisation of the αS1-casein (CSN1S1) gene and association studies with milk traits in Assaf sheep breed

Prolactin (PRL) and its receptor (PRLR) were considered as potential genetic markers for milk production and quality traits in cattle. However, little information is available regarding PRLR genetic diversity and association studies with milk traits in Egyptian water buffaloes. Therefore, the present study was conducted to search for mutations in PRLR and determine their associations with milk performance in these animals. Exon3 (E3) and E10 of PRLR were screened for polymorphisms using single strand conformation polymorphism (SSCP) and sequencing in 400 buffaloes. The associations between haplotypes and milk production (fat%, protein%, lactose%, and solid%) traits as well as mRNA and protein levels of PRL and PRLR were studied. Two single nucleotide polymorphisms (SNPs) in E10 were detected: g.11685G>A (p.Ala494Thr) and g.11773T>C (p.Val523Aal). The G and T alleles were wild (ancestral) alleles, while the A and C alleles were mutant alleles. These SNPs resulted in four haplotypes; AC, AT, GC, and GT. Buffaloes with wild GT haplotypes showed significantly higher milk yield, fat% and protein%, mRNA and protein levels of PRL and PRLR in milk somatic cells than other animals. Animals carrying mutant AC haplotype had inferior milk traits and lowest levels of associated mRNAs and proteins. With these results, we could conclude that the selection of buffaloes with wild GT haplotypes for g.11685G>A and g.11773T>C SNPs of the PRLR gene might improve the milk production traits of Egyptian water buffaloes.

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ASSOCIATION OF GENETIC VARIANTS OF β-LACTOGLOBULIN GENE WITH MILK TRAITS OF JEZEROPIVSKA SHEEP BREED

The Journal Agriculture and Forestry ◽

10.17707/agricultforest.66.3.02 ◽

2020 ◽

Vol 66 (3) ◽

Author(s):

Milena DJOKIC ◽

Bozidarka MARKOVIC ◽

Vesna GANTNER ◽

Milan MARKOVIC

Keyword(s):

Genetic Variants ◽

Sheep Breed ◽

Milk Traits ◽

Β Lactoglobulin

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Genome-wide association studies for reproductive seasonality traits in Rasa Aragonesa sheep breed

Theriogenology ◽

10.1016/j.theriogenology.2017.05.011 ◽

2017 ◽

Vol 99 ◽

pp. 21-29 ◽

Cited By ~ 4

Author(s):

Albert Martinez-Royo ◽

José Luis Alabart ◽

Pilar Sarto ◽

Magdalena Serrano ◽

Belén Lahoz ◽

...

Keyword(s):

Association Studies ◽

Sheep Breed ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Reproductive Seasonality ◽

Genome Wide

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Genetic polymorphism of Pit-1|HinfI gene in Grati-Ongole Grade cattle at Indonesian Beef Cattle Research Station

Journal of the Indonesian Tropical Animal Agriculture ◽

10.14710/jitaa.43.4.315-322 ◽

2018 ◽

Vol 43 (4) ◽

pp. 315

Author(s):

H. Hartati ◽

S. Anwar ◽

B.D.P. Soewandi

Keyword(s):

Transcription Factor ◽

Genetic Polymorphism ◽

Gene Polymorphism ◽

Beef Cattle ◽

Genomic Dna ◽

Association Studies ◽

Research Station ◽

Milk Traits ◽

Genotype Frequencies ◽

Pcr Rflp

The pituitary transcription factor (Pit-1) gene is one of the considered genes that responsible to growth in cattle. A specific Pit-1|HinfI gene polymorphism located within exon 6(g.1256G>A) has been shown to be associated with growth and milk traits in cattle. This study aimed to identify the Pit-1|Hinf1 gene polymorphism in Grati-Ongole Grade cattle (Grati-OG cattle). A total of 107 genomic DNA of Grati-OG cattle were used in this study. The detection of polymorphism was performed by PCR-RFLP method. Only AB and BB genotypes were succesfully identified with the frequency of 0.009 and 0.991, respectively. Whereas, the frequency of A and B alleles were 0.005 and 0.995, respectively. The observed genotype frequencies in this population do not deviated from HWE. The value of Ho, He and PIC were 0.009, 0.009 and 0.009, respectively.In conclusion, the Pit-1|HinfI gene polymorphism in Grati-OG cattle is monomorphic and hence it should not be used in further association studies.

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Genome-wide association studies for sperm traits in Assaf sheep breed

animal ◽

10.1016/j.animal.2020.100065 ◽

2020 ◽

pp. 100065

Author(s):

M. Serrano ◽

M. Ramón ◽

J.H. Calvo ◽

M.Á. Jiménez ◽

F. Freire ◽

...

Keyword(s):

Association Studies ◽

Sheep Breed ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Sperm Traits

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gwasrapidd: an R package to query, download and wrangle GWAS Catalog data

10.1101/643940 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ramiro Magno ◽

Ana -Teresa Maia

Keyword(s):

Association Studies ◽

R Package ◽

Genome Wide Association Studies ◽

Server Side ◽

Functional Characterisation ◽

Genome Wide ◽

Rest Api ◽

Integrate Data ◽

Programmatic Access ◽

Gwas Catalog

AbstractMotivationThe NHGRI Catalog of Published Genome-Wide Association Studies (GWAS) Catalog has collected, curated, and made available data from over 3 900 studies. The recently developed GWAS Catalog REST API is the only method allowing programmatic access to this resource.ResultsHere, we describe gwasrapidd, an R package that provides a client interface to the GWAS Catalog REST API, representing an important software counterpart to the server-side component. gwasrapidd enables users to quickly retrieve, filter and integrate data with comprehensive bioinformatics analysis tools, which is particularly critical for those looking into functional characterisation of risk loci.Availabilitygwasrapidd is freely available under an MIT License, and can be accessed from https://github.com/ramiromagno/gwasrapidd.

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Alternative splicing regulation by GWAS risk loci for breast cancer

10.1101/766394 ◽

2019 ◽

Author(s):

Juliana Machado ◽

Ramiro Magno ◽

Joana M Xavier ◽

Ana-Teresa Maia

Keyword(s):

Breast Cancer ◽

Alternative Splicing ◽

Target Genes ◽

Cancer Susceptibility ◽

Association Studies ◽

Normal Breast ◽

Genome Wide Association Studies ◽

Functional Characterisation ◽

Genome Wide ◽

Gene Isoforms

ABSTRACTRecent genome-wide association studies (GWAS) have revealed the association of hundreds of single nucleotide polymorphisms (SNPs) with breast cancer (BC) risk, which mostly locate in non-coding regions, suggesting regulatory roles to the causal variants. Functional characterisation of GWAS loci has been biased towards the effect of regulatory SNPs on transcription factor binding. Here we set out to determine the extent of the contribution of breast cancer risk-associated SNPs to alternative splicing (AS).We screened genome-wide significant (P ≤ 5 × 10−8) BC risk SNPs for association with AS, using expression and genotype data from normal breast samples, from the GTEx project. We identified four splicing quantitative trait loci (sQTL). In locus 6p22.1, rs6456883 is a significant cis-sQTL for the expression of ZNF311 gene isoforms. Three SNPs in locus 8p23.3, rs6682326, rs3008282 and rs2906324, were also identified as significant cis-sQTLs/svQTLs for the expression of RPL23AP53 gene isoforms. In-silico functional analysis revealed that these variants can potentially alter enhancer splicing elements within the target genes.Our work shows that BC risk-associated variants at two loci are associated with AS isoforms in normal breast tissue, thus demonstrating that AS plays an important role in breast cancer susceptibility. Furthermore, it supports that all cis-regulatory mechanisms should be considered in the functional characterisation of risk loci.

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Serotonergic Genes and Suicidality

Crisis ◽

10.1027//0227-5910.22.2.54 ◽

2001 ◽

Vol 22 (2) ◽

pp. 54-60 ◽

Cited By ~ 42

Author(s):

Lisheng Du ◽

Gabor Faludi ◽

Miklos Palkovits ◽

David Bakish ◽

Pavel D. Hrdina

Keyword(s):

Suicidal Ideation ◽

Suicidal Behavior ◽

Tryptophan Hydroxylase ◽

Association Studies ◽

Receptor Gene ◽

Brain Regions ◽

Depressive Illness ◽

Control Group ◽

Serotonergic Activity ◽

Completed Suicide

Summary: Several lines of evidence indicate that abnormalities in the functioning of the central serotonergic system are involved in the pathogenesis of depressive illness and suicidal behavior. Studies have shown that the number of brain and platelet serotonin transporter binding sites are reduced in patients with depression and in suicide victims, and that the density of 5-HT2A receptors is increased in brain regions of depressed in suicide victims and in platelets of depressed suicidal patients. Genes that code for proteins, such as tryptophan hydroxylase, 5-HT transporter, and 5-HT2A receptor, involved in regulating serotonergic neurotransmission, have thus been major candidate genes for association studies of suicide and suicidal behavior. Recent studies by our group and by others have shown that genetic variations in the serotonin-system-related genes might be associated with suicidal ideation and completed suicide. We have shown that the 102 C allele in 5-HT2A receptor gene was significantly associated with suicidal ideation (χ2 = 8.5, p < .005) in depressed patients. Patients with a 102 C/C genotype had a significantly higher mean HAMD item #3 score (indication of suicidal ideation) than T/C or T/T genotype patients. Our results suggest that the 102T/C polymorphism in 5-HT2A receptor gene is primarily associated with suicidal ideation in patients with major depression and not with depression itself. We also found that the 5-HT transporter gene S/L polymorphism was significantly associated with completed suicide. The frequency of the L/L genotype in depressed suicide victims was almost double of that found in control group (48.6% vs. 26.2%). The odds ratio for the L allele was 2.1 (95% CI 1.2-3.7). The association between polymorphism in serotonergic genes and suicidality supports the hypothesis that genetic factors can modulate suicide risk by influencing serotonergic activity.

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