scholarly journals Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations

2005 ◽  
Author(s):  
Joel I. Weller ◽  
Harris A. Lewin ◽  
Micha Ron
Keyword(s):  
Mammary Gland ◽  
Dairy Cattle ◽  
Single Gene ◽  
Allele Frequencies ◽  
Causative Mutation ◽  
Economic Traits ◽  
Allelic Frequencies ◽  
Animal Populations ◽  
Israeli Population ◽  
Daughter Design

Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.   

Distribution of drug-metabolizing enzymes coding genes CYP2D6, CYP3A4, CYP3A5 alleles in a group of healthy Turkish population

2018 ◽  
Vol 44 (2) ◽  
pp. 142-146
Author(s):  
İsmail Ün ◽  
İ. Ömer Barlas ◽  
Nisa Uyar ◽  
Bahar Taşdelen ◽  
Naci Tiftik
Keyword(s):  
Drug Therapy ◽  
Adverse Drug Reactions ◽  
Low Frequency ◽  
Turkish Population ◽  
Allele Frequencies ◽  
Drug Reactions ◽  
Metabolizing Enzymes ◽  
Frequency Distributions ◽  
Allelic Frequencies ◽  
Hardy Weinberg Equilibrium

Abstract Objective: Variant alleles in specific ethnic groups are important for personalized drug therapy regimens and adverse drug reactions. Therefore, the aim of this study was to investigate allelic frequencies of the CYP2D6*1, CYP3A4*5, CYP3A4*18, CYP3A5*2 and CYP3A5*4 in a group of Turkish population. Materials and methods: Three hundred and six unrelated healthy subjects who were accepted as blood donors to the Mersin University Blood Bank were included in the study after informed consent. Allelic frequencies of the CYP2D6*1 (rs3892097), CYP3A4*5 (rs55901263), CYP3A4*18 (rs28371759), CYP3A5*2 (rs28365083) and CYP3A5*4 (rs56411402) were determined by using polymerase chain reaction-restriction fragment length polymorphism assays. Results: CYP2D6 allele frequencies in detected group was 100% for CYP2D6*1 (WT/WT). CYP3A4 allele frequencies of subjects were 100% for CYP3A4*5 (C/C) and CYP3A4*18 (T/T). CYP3A5 allele were in Hardy-Weinberg equilibrium for CYP3A5*2 (p=0.142) and frequencies for C and A allele were 91% and 9% respectively. CYP3A5 allele frequencies of subjects was 100% for CYP3A5*4 (WT/WT). Conclusion: Screening of low frequency alleles by pharmacogenetic testing must not be omitted to optimize pharmacotherapy and avoid severe drug toxicities. Frequency distributions of the identified polymorphisms in the present study may contribute to the personalized drug therapy regimens and prediction of possible adverse drug reactions in the Turkish population.

scholarly journals Allele Frequencies of 15 AmpFISTR Identifiler loci in the Nepalese population

2012 ◽  
Vol 10 (10) ◽  
pp. 20-23 ◽  
Author(s):  
Dinesh Kumar Jha ◽  
Luis Javier Martinez Gonzalez ◽  
Jiwan Prasad Rijal ◽  
Bhinu Shova Tuladhar ◽  
Nirajan Thapa Chhetri
Keyword(s):  
Allele Frequencies ◽  
Statistical Parameters ◽  
Weinberg Equilibrium ◽  
Allelic Frequencies ◽  
Str Loci ◽  
Scientific World ◽  
Hardy Weinberg Equilibrium

Allele frequencies for the 15 STR loci in the AmpFlSTR® Identifiler® and statistical parameters were estimated from a sample of 233 unrelated individuals from different area of Nepal. A total of 161 alleles were found, with corresponding allelic frequencies ranging from 0.0021 to 0.4077. The MP, PD, PIC, PE, TPI, Ho and He ranged from 0.0282 to 0.1511, 0.8489 to 0.9717, 0.6478 to 0.8700, 0.4546 to 0.7631, 1.7651 to 4.3148, 0.7167 to 0.8841 and 0.7009 to 0.8833 respectively. Deviations from the Hardy–Weinberg Equilibrium were observed for D16S539, D18S51, D21S11 and TPOX Markers. One new allele has been detected in the process. Scientific World, Vol. 10, No. 10, July 2012 p20-23 DOI: http://dx.doi.org/10.3126/sw.v10i10.6856

Allele frequencies of gene polymorphisms related to economic traits in Bos taurus and Bos indicus cattle breeds

2011 ◽  
Vol 82 (6) ◽  
pp. 717-721 ◽  
Author(s):  
Makoto KANEDA ◽  
Bang Zhong LIN ◽  
Shinji SASAZAKI ◽  
Kenji OYAMA ◽  
Hideyuki MANNEN
Keyword(s):  
Gene Polymorphisms ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Allele Frequencies ◽  
Economic Traits ◽  
Cattle Breeds

Strategies and cost–benefit of selecting for a polled sheep nucleus by using DNA testing

2019 ◽  
Vol 59 (8) ◽  
pp. 1428
Author(s):  
T. Granleese ◽  
S. A. Clark ◽  
N. Duijvesteijn ◽  
P. E. Bradley ◽  
J. H. J. van der Werf
Keyword(s):  
Allele Frequency ◽  
Genetic Gain ◽  
Single Gene ◽  
Cost Benefit ◽  
Economic Loss ◽  
Allele Frequencies ◽  
Production Traits ◽  
Dna Testing ◽  
Dominance Model ◽  
Female Candidates

The present study assessed the effectiveness and cost–benefit of several genotyping strategies for breeding poll Merino sheep in a closed nucleus with different initial allele frequencies and assuming a single-gene responsible for the horn or poll phenotype. We assumed that selection was based on phenotypes or genotypes for a single gene conferring polledness via a complete-dominance model. Under such a model, a complete fixation of the ‘polled allele’ (P) requires genotyping of the ewe-selection candidates. Testing a higher proportion of female candidates resulted in a faster fixation of the P-allele. Fixation ranged from 1 year of selection with a high starting P-allele frequency of 0.9, to 7 years for low starting P-allele frequencies of 0.3. When premiums of AU$50 or AU$100 were paid for rams with a PP genotype, breeding for PP genotypes was not profitable when the starting P-allele frequency was below 0.7. If the starting allele frequency was above 0.7, net profitability was positive over 10 years when premiums of AU$200 were paid for known PP-genotype rams. While fixing the P-allele, genetic gain for production traits was slowed down in the first 5 years of selection by up to 23% and 3% for initial P allele-frequencies of 0.3 and 0.9 respectively. Lost genetic gain due to fixing the P-allele, which can never be recovered in a closed nucleus, incurred 200–800% higher costs than the DNA testing costs. Rates of genetic gain recovered to pre-P-allele selection level rates of genetic gain once the P-allele was fixed. Testing a maximum of 25% ewe-selection candidates was the least expensive strategy across all starting allele frequencies and premiums. To avoid large losses of genetic gain in a closed nucleus with low P-allele starting frequencies, opening the nucleus should be considered to increase starting P-allele frequencies and also to potentially increase rates of genetic gain to offset the economic loss caused by P-selection.

scholarly journals Effect of heat stress during the early and late dry period on mammary gland development of Holstein dairy cattle

2020 ◽  
Vol 103 (9) ◽  
pp. 8576-8586
Author(s):  
Thiago F. Fabris ◽  
Jimena Laporta ◽  
Amy L. Skibiel ◽  
Bethany Dado-Senn ◽  
Stephanie E. Wohlgemuth ◽  
...  
Keyword(s):  
Heat Stress ◽  
Mammary Gland ◽  
Dairy Cattle ◽  
Mammary Gland Development ◽  
Dry Period ◽  
Gland Development

scholarly journals Detection of genes influencing economic traits in three French dairy cattle breeds

2003 ◽  
Vol 35 (1) ◽  
Author(s):  
Didier Boichard ◽  
Cécile Grohs ◽  
Florence Bourgeois ◽  
Frédérique Cerqueira ◽  
Rémi Faugeras ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Economic Traits ◽  
Cattle Breeds

scholarly journals Measures of spatial structure in samples of genotypes for multiallelic loci

1999 ◽  
Vol 73 (3) ◽  
pp. 251-261 ◽  
Author(s):  
B. K. EPPERSON ◽  
Z. HUANG ◽  
T.-Q. LI
Keyword(s):  
Allele Frequencies ◽  
Multiple Alleles ◽  
Sampling Schemes ◽  
Animal Populations ◽  
Wide Range ◽  
Theoretical Population ◽  
Theoretical Population Genetics ◽  
Predicted Values ◽  
Join Count Statistics ◽  
First Time

Various spatial autocorrelation statistics have been widely used both in theoretical population genetics and to study the spatial distribution of diploid genotypes in many plant and animal populations. However, previous simulation studies have considered only diallelic loci. In this paper, we use a large number of space–time simulations to characterize for the first time the parametric and statistical values of Moran's I-statistics for converted individual genotypes as well as for join- count statistics. A wide range of levels of dispersal and numbers of alleles and allele frequencies are modelled and the results reveal the different general effects of each of these factors on these statistics. We also examine the range of appropriate sampling designs and sizes for which predicted values can be interpolated for specific sampling schemes for any given population genetic field survey. Numbers of alleles and allele frequencies each affect some statistics but not others. The results indicate generally low standard deviations. The results also develop precise and efficient methods of estimating gene dispersal, based on the various autocorrelation measures of standing spatial patterns of genetic variation within populations. The results also extend these methods to loci with multiple alleles, typical of those studied through modern molecular methods.

scholarly journals Genetic Analysis of Children with Dravet Syndrome in a Resourcelimited Setting

2021 ◽  
Author(s):  
Sorawit Viravan ◽  
Chutima Meesamarnpong ◽  
Wanna Thongnoppakhun ◽  
Mongkol Chanvanichtrakool
Keyword(s):  
Sanger Sequencing ◽  
Direct Sequencing ◽  
Single Gene ◽  
Gene Mutations ◽  
Large Deletion ◽  
Dravet Syndrome ◽  
Causative Mutation ◽  
Resource Limited ◽  
Therapeutic Decisions ◽  
Scn1a Gene

Objective: To identify the common causal gene mutations in Thai children with the Dravet (DS) phenotype, using single gene analysis.Material and Methods: The study was carried out on 20 DS patients at Siriraj Hospital, Bangkok, Thailand. Sanger sequencing of the Voltage-Gated Sodium Channel Alpha Subunit 1 (SCN1A) gene was conducted in all patients. In SCN1A-negative patients, multiplex ligation-dependent probe amplification of the SCN1A gene was performed in all cases; however, direct sequencing of the Protocadherin-19 (PCDH19) gene was analyzed in girls only.Results: Fourteen (70.0%) DS patients were found to carry pathogenic SCN1A mutations, with 6 novel mutations. In SCN1A-negative patients; 1 of the 4 girl patients (25.0%) had a novel PCDH19 mutation, while none of the 6 patients had a large deletion or duplication in the SCN1A gene.Conclusion: The SCN1A gene is the most common causative mutation in Thai children with DS phenotype. This study emphasizes the benefit of Sanger sequencing of the SCN1A gene in resource-limited countries to aid in making appropriate therapeutic decisions.

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