scholarly journals Estimated Genetic Variance Explained by Single Nucleotide Polymorphisms of Different Minor Allele Frequencies for Carcass Traits in Japanese Black Cattle

2016 ◽  
Vol 04 (05) ◽  
pp. 89-97 ◽  
Author(s):  
Shinichiro Ogawa ◽  
Hirokazu Matsuda ◽  
Yukio Taniguchi ◽  
Toshio Watanabe ◽  
Yoshikazu Sugimoto ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variance ◽  
Carcass Traits ◽  
Minor Allele ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Japanese Black Cattle ◽  
Single Nucleotide ◽  
Variance Explained

scholarly journals Correlating single nucleotide polymorphisms in the myostatin gene with performance traits in rabbit

2016 ◽  
Vol 24 (3) ◽  
pp. 213 ◽  
Author(s):  
E.M. Abdel-Kafy ◽  
S.F. Darwish ◽  
D. ElKhishin
Keyword(s):  
Body Weight ◽  
Weight Gain ◽  
Single Nucleotide Polymorphisms ◽  
Untranslated Region ◽  
Carcass Traits ◽  
Reproductive Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Mstn Gene ◽  
Positive Effects

The Myostatin (MSTN), or Growth and Differentiation Factor 8 (GDF8), gene has been implicated in the double muscling phenomenon, in which a series of mutations render the gene inactive and unable to properly regulate muscle fibre deposition. Single nucleotide polymorphisms (SNPs) in the MSTN gene have been correlated to production traits, making it a candidate target gene to enhance livestock and fowl productivity. This study aimed to assess any association of three SNPs in the rabbit MSTN gene (c.713T>A in exon 2, c.747+34C>T in intron 2, and c.*194A>G in 3’-untranslated region) and their combinations, with carcass, production and reproductive traits. The investigated traits included individual body weight, daily body weight gain, carcass traits and reproductive traits. The 3 SNPs were screened using PCR-restriction fragment length polymorphism (RFLP)-based analysis and the effects of the different SNP genotypes and their combinations were estimated in a rabbit population. Additionally, additive and dominance effects were estimated for significant traits. The results found no significant association between the c.713 T>A SNP and all the examined traits. Allele T at the c.747+34C>T SNP was only significantly associated (P<0.05) with increased body weight at 12 wk of age. However, for the SNP residing in the 3’ untranslated region (c.*194A>G), allele G was significantly associated (P<0.05) with increased body weight and high growth rate. Genotype GG at the c.*194A>G SNP also had positive effects on most carcass traits. The estimated additive genetic effect for the c.*194A>G SNP was significant (P<0.05) with most body weight, daily gain and carcass traits. No significant association was obtained between any MSTN SNPs and reproductive traits. In the combinations analysis, regardless of the genotypes of SNPs at c.713T>A and c.747+34C>T, GG at the c.*194A>G SNP correlated with highest values in body weight and daily weight gain. In conclusion, the ‘G’ allele at the c.*194A>G SNP had positive effects on growth and carcass traits and so could be used as a favourable allele in planning rabbit selection. Further population-wide studies are necessary to test the association of the c.*194A>G SNP with carcass traits. We also recommend evaluation of the potential effects of the c.*194A>G SNP on MSTN gene expression.

scholarly journals Estimating the Genetic Variance of Major Depressive Disorder Due to All Single Nucleotide Polymorphisms

2012 ◽  
Vol 72 (8) ◽  
pp. 707-709 ◽  
Author(s):  
Gitta H. Lubke ◽  
Jouke Jan Hottenga ◽  
Raymond Walters ◽  
Charles Laurin ◽  
Eco J.C. de Geus ◽  
...  
Keyword(s):  
Major Depressive Disorder ◽  
Single Nucleotide Polymorphisms ◽  
Depressive Disorder ◽  
Genetic Variance ◽  
Nucleotide Polymorphisms ◽  
Major Depressive ◽  
Single Nucleotide

Multiple marker effects of single nucleotide polymorphisms in three genes,AKIRIN2,EDG1andRPL27A, for marbling development in Japanese Black cattle

2013 ◽  
Vol 85 (3) ◽  
pp. 193-197 ◽  
Author(s):  
Shin Sukegawa ◽  
Takeshi Miyake ◽  
Takayuki Ibi ◽  
Yoichi Takahagi ◽  
Hiroshi Murakami ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Japanese Black Cattle ◽  
Single Nucleotide

scholarly journals Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds

2006 ◽  
Vol 6 (4) ◽  
pp. 992-997 ◽  
Author(s):  
I. CAPPUCCIO ◽  
L. PARISET ◽  
P. AJMONE-MARSAN ◽  
S. DUNNER ◽  
O. CORTES ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequencies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals OR24-05 Identifying Regulatory Elements Within a Novel Enhancer of FSHB Containing Two PCOS-Associated Single Nucleotide Polymorphisms

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Stephanie C Bohaczuk ◽  
Varykina G Thackray ◽  
Pamela L Mellon
Keyword(s):  
Transcription Factor ◽  
Single Nucleotide Polymorphisms ◽  
Regulatory Elements ◽  
Minor Allele ◽  
Specific Marker ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Alcoholic Fatty Liver ◽  
Conserved Region

Abstract Polycystic ovary syndrome (PCOS) is the most common cause of female infertility, affecting approximately 10 percent of women by Rotterdam criteria, and is comorbid with obesity, type II diabetes, hypertension, and non-alcoholic fatty liver disease. As twin studies reveal that genetics account for approximately 70% of PCOS risk, genome-wide association studies (GWAS) can provide powerful insight into PCOS etiology. PCOS GWAS studies from several populations identified a risk locus containing the FSHB gene, which encodes the beta subunit of follicle-stimulating hormone (FSH). As FSH supplementation can restore ovulation in some PCOS patients, deficient FSH signaling could be a causative factor of anovulation and potentially other facets of PCOS. Two of the lead single nucleotide polymorphisms (SNPs) in association with PCOS, rs11031005 and rs11031006, fall within a highly conserved genomic region in mammals. We hypothesized that the conserved region (~450 base pairs) enhances FSHB transcription, and that one or both PCOS-related SNPs alter its function. We have shown that the conserved region from both human and mouse can act as an enhancer of FSHB in LβT2 cells, an immortalized, mouse-derived, mature pituitary gonadotrope cell line, and that its function is altered by the rs11031006 minor allele through modification of an SF1 consensus site. As elimination of the SF1 site reduced but did not completely abolish the function of the enhancer, we continued our investigation to identify additional regulatory sites. Transient transfection of LβT2 cells revealed a possible role for the rs11031005 SNP in FSHB regulation, with the minor allele decreasing enhancer-mediated FSHB transcription. This effect may be due to decreased binding of an unidentified transcription factor, as gel shift revealed that the rs11031005 minor allele reduced the intensity of a binding complex. Using truncations and sliding deletions, we identified three additional putative transcription factor binding sites with consensus sequences for ZEB1, PTX1, and SMAD. To support a role for the conserved region as an enhancer in native chromatin, we assessed the histone status in LβT2 chromatin. Compared to the proximal Fshb promoter, the enhancer-specific marker, H3K4me1, was enriched near the conserved region. Neither promoter/enhancer markers of active (H3K27Ac) or repressed (H3K27me3) chromatin were enriched near the conserved region, although levels of both modifications were consistent with the Fshb proximal promoter. Overall, our data support the role of this conserved region as a novel regulator of FSHB/Fshb transcription and reveal a possible mechanism to explain the contribution of PCOS-associated SNPs through FSHB regulation.

Sign in / Sign up

Export Citation Format

Share Document