Parental influences on expression of glucose-6-phosphate dehydrogenase, G6pd, in the mouse; a case of imprinting

Glucose-6-phosphate dehydrogenase (G6PD) activity was measured in blood from heterozygotes for the normal allele G6pda and the low activity allele G6pda-mlNeu. In adult mice lower activity was found in G6pda/G6pda-mlNeu than in the reciprocal heterozygote G6pda-mlNeu/G6pda (the maternal allele being listed first). Thus, either the paternally derived allele was over-expressed or the maternally derived allele was under-expressed. By contrast, in younger mice the difference in G6PD activity in reciprocal crosses was less marked. The findings are interpreted in terms of differential imprinting of maternally and paternally inherited information. The explanation offered for age related differences is that, as a consequence of imprinting, either the paternal X-chromosome is preferentially reactivated, or cells in which the paternally derived allele is active are at a selective advantage, and proliferate better than those in which the maternally inherited allele is active.     

Predicting the consequences of selecting on PrP genotypes on PrP frequencies,performance and inbreeding in commercial meat sheep populations

Selection programmes based on prion protein (PrP) genotypes are being implemented for increasing resistance to scrapie. Commercial meat sheep populations participating in sire-referencing schemes were simulated to investigate the effect of selection on PrP genotypes on ARR and VRQ allele frequencies, inbreeding and genetic gain in a performance trait under selection. PrP selection strategies modelled included selection against the VRQ allele and in favour of the ARR allele. Assuming realistic initial PrP frequencies, selection against the VRQ allele had a minimal impact on performance and inbreeding. However, when selection was also in favour of the ARR allele and the frequency of this allele was relatively low, there was a loss of up to three to four years of genetic gain over the 15 years of selection. Most loss in gain occurred during the first five years. In general, the rate of inbreeding was reduced when applying PrP selection. Since animals were first selected on their PrP genotype before being selected on the performance trait, the intensity of selection on performance was weaker under PrP selection (compared with no PrP selection). Eradication of the VRQ allele or fixation of the ARR allele within 15 years of selection was possible only with PrP selection targeting all breeding animals.     

Deficiency in mitochondrial aldehyde dehydrogenase increases the risk for late-onset Alzheimer's disease in the Japanese population

Mitochondrial aldehyde dehydrogenase 2 (ALDH2) deficiency is caused by a mutant allele in the Mongoloids. To examine whether genetic constitutions affecting aldehyde metabolism influence the risk for late-onset Alzheimer's disease (LOAD), we performed a case-control study in the Japanese population on the deficiency in ALDH2 caused by the dominant-negative mutant allele of the ALDH2 gene (ALDH2*2). In a comparison of 447 patients with sex, age, and region matched nondemented controls, the genotype frequency carrying the ALDH2*2 allele was significantly higher in the patients than in the controls (48.1% vs 37.4%, P = 0.001). Logistic regression analysis indicates that carriage of the ALDH2*2 allele is an independent risk for LOAD of the epsilon4 allele of the apolipoprotein E gene (APOE-epsilon4) (P = 0.002). Moreover, the odds ratio for LOAD in carriers of the ALDH2*2 allele was almost twice that in noncarriers, irrespective of status with regard to the APOE-epsilon4 allele. Among patients homozygous for the APOE-epsilon4 allele, age at onset of LOAD was significantly lower in those with than without the ALDH2*2 allele. In addition, dosage of the ALDH2*2 allele significantly affected age at onset of patients homozygous for the APOE-epsilon4 allele. These results indicate that the ALDH2 deficiency is a risk for LOAD, synergistically acting with the APOE-epsilon4 allele.     

New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa

Lactase persistence (LP), the ability to digest lactose into adulthood, is strongly associated with the cultural traits of pastoralism and milk-drinking among human populations, and several different genetic variants are known that confer LP. Recent studies of LP variants in Southern African populations, with a focus on Khoisan-speaking groups, found high frequencies of an LP variant (the C-14010 allele) that also occurs in Eastern Africa, and concluded that the C-14010 allele was brought to Southern Africa via a migration of pastoralists from Eastern Africa. However, this conclusion was based on indirect evidence; to date no study has jointly analyzed data on the C-14010 allele from both Southern African Khoisan-speaking groups and Eastern Africa. Here, we combine and analyze published data on the C-14010 allele in Southern and Eastern African populations, consisting of haplotypes with the C-14010 allele and four closely-linked short tandem repeat loci. Our results provide direct evidence for the previously-hypothesized Eastern African origin of the C-14010 allele in Southern African Khoisan-speaking groups. In addition, we find evidence for a separate introduction of the C-14010 allele into the Bantu-speaking Xhosa. The estimated selection intensity on the C-14010 allele in Eastern Africa is lower than that in Southern Africa, which suggests that in Eastern Africa the dietary changes conferring the fitness advantage associated with LP occurred some time after the origin of the C-14010 allele. Conversely, in Southern Africa the fitness advantage was present when the allele was introduced, as would be expected if pastoralism was introduced concomitantly. Am J Phys Anthropol 156:661–664, 2015. © 2014 Wiley Periodicals, Inc.     

Inheritance of the equine Tf F3 allele

The inheritance of the equine Tf F3 allele was examined in 39 parent-offspring combinations. For 26 of the cases the allele inherited by the offspring from the heterozygous parent could be determined. The proportion of individuals that inherited the F3 variant compared to the alternative allele was exactly 1:1. In five cases the parental phenotype was identical to that of the offspring. For the remaining eight cases the parent was homozygous for the F3 allele and all offspring had the F3 allele. The results were consistent with Mendelian inheritance.     

猪几个血清蛋白质位点的等位基因频率在选育中的变化趋势

采用淀粉凝胶电泳测定了杜洛克猪的转铁蛋白(Tf)、前白蛋白(Pa)、血液结合素(Hpx)、铜兰蛋白(Cp)和淀粉酶(Am)多态性,统计和计算了表现型数和等位基因频率,并同1968年测得的基因频率进行了比较,揭示了杜洛克猪几个血清蛋白质位点的等位基因频率在长期选育中的变化趋势,即随着人们有目的地进行选育,这些血清蛋白质位点的等位基因数减少,基因频率向某个等位基因集中,形成优势等位基因。目前的优势等位基因是Tf^B、Pa^A、Hpx^3、Cp^B、Am^8。此外,将杜洛克猪的基因频率同湖南部分地方猪进行了比较,计算了它们的平均杂合度、遗传相似系数和遗传距离系数,并做了聚类分析。     

Restriction polymorphism in patients with lipid metabolism disorders and ischemic heart disease

Using the RELP analysis we studied the frequency of X2 allele of apoB gene in three groups of patients: 1) men at the age of 20-59 with lipid metabolism disorders revealed in population inspection of Oktyabrsky district in Moscow; 2) men with ischaemic heart disease and 3) healthy men. It was established that in individuals suffering from type IIa hyperlipidemia the frequency of X2 allele was significantly higher than in healthy donors from Moscow population. Homozygotes for X2 allele of XbaI RELP had 7-9% higher serum cholesterol levels, than homozygotes for X1 allele. The study suggests the X2 allele of the apoB gene to be associated with the development of high plasma cholesterol level. No significant difference in X2 allele frequencies was found between patients with ischaemic heart disease and healthy donors. There was also no association found between cholesterol and triglyceride levels and the presence of X2 allele in this group of patients.     

黔北人群TGFα基因多态性与非综合征性唇腭裂的相关性研究

本研究旨在探讨黔北地区人群TGFα基因3个SNP位点的多态性及其与非综合征性唇腭裂的相关性。采用PCR和测序方法对86个对照儿童(其中核心家系41例)和116个NSCL/P儿童(其中核心家系52例)的TGFα基因rs11466297、rs473698和rs115055578 3个SNP位点进行扩增和测序;对样本群体进行Hardy-weinberg平衡检测,对2组人群进行基因型频率、等位基因频率比较及OR分析;对病例组核心家系进行HHRR和TDT检验。对照组与病例组人群rs11466297基因型均为AA野生型,rs473698位点包含GG型、GC型和CC型,rs115055578位点基因型均为GG野生型。对于rs473698位点,对照组和病例组均符合Hardy-Weinberg平衡法则(p>0.05),2组人群的基因型和等位基因频率分布差异均无统计学意义(p<0.05);rs473698位点未发现传递不平衡现象(p>0.05)。黔北地区人群TGFα基因rs11466297和rs115055578位点以野生纯合型为主,rs473698位点具有多态性,但其多态性与黔北地区人群区非综合征性唇腭裂的发生可能没有相关性。     

(AC) dinucleotide repeat polymorphism in intron 1 of human EGFR shows ethnic specificities and high evidence for association with breast cancer

A polymorphic AC repeat in intron 1 of the EGFR gene was genotyped on 352 healthy individuals and 118 women with breast cancer sampled from the Kuwaiti and Tunisian populations. We compared allele frequencies in these populations with published data on various ethnic groups. We found very close similarity between Tunisian and Kuwaiti populations for both allelic and genotypic frequencies and in both control and patient groups. Our analysis revealed clear interethnic differences between populations; in Europeans, allele 16 occurred predominantly, whereas in Tunisia and Kuwait allele 17 was the most frequent and allele 20 predominated in Asians. One hundred twenty-three healthy women, matched with the 118 breast cancer patients, were used as controls to test for associations between AC repeat and cancer risk. Strong evidence for such an association was found for allele 18 when considered alone (chi2=27.04, corrected p=0.0000016, OR=3.94) or with longer alleles (>17 repeats) (chi2=20.21, p=0.0005, OR=2.30). This contrasts with Asian populations where allele 16 was identified as the risk allele, showing allele heterogeneity depending on ethnicity.     

Marker-assisted introgression using non-unique marker alleles I: selection on the presence of linked marker alleles

This paper investigates marker-assisted introgression of a major gene into an outbred line, where identification of the introgressed gene is incomplete because marker alleles are not unique to the base populations (the same marker allele can occur in both donor and recipient population). Those markers are used to identify the introgressed allele as well as the background genotype. The effect of using those markers, as if they were completely informative on the retention of the introgressed allele, was examined over five generations of backcrossing by using a single marker or a marker bracket for different starting frequencies of the marker alleles. Results were calculated by using both a deterministic approach, where selection is only for the desired allele, and by a stochastic approach, where selection is also on background genotype. When marker allele frequencies in donor and recipient population diverged from 1 and 0 (using a diallelic marker), the ability to retain the desired allele rapidly declined. Marker brackets performed notably better than single markers. If selection on background marker genotype was applied, the desired allele could be lost even more quickly than expected at random because the chance that the allele, which is common in the donor line, is present on the locus identifying the introgressed allele and is surrounded by alleles common in the recipient line on the background marker loci, will descend from the donor line (double recombination has taken place), is a lot smaller than the chance that this allele will stem from the recipient line (in which the allele occurs in low frequency). Marker brackets again performed better. Preselection against marker homozygotes (producing uninformative gametes) gave a slightly better retention of the introgressed allele.     

Simulating genealogies of selected alleles in a population of variable size

An importance-sampling method is presented that allows the simulation of the history of a selected allele in a population of variable size. A sample path describing the number of copies of an allele that arose as a single mutant is generated by simulating backwards from the current frequency until the allele is lost. The mathematical expectation of a quantity or statistic is then estimated by taking averages over replicate simulations, weighting each replicate by the ratio of its probabilities under the Markov chains for the forward and backwards processes. This method was used to find the average age of a selected allele in an exponentially growing population. In terms of the effect on average allele age, selection in favour of an allele is not equivalent to exponential growth. To generate gene genealogies of a sample of copies of a selected allele, the neutral coalescent model is simulated for the subpopulation containing only the selected allele. From the resulting intra-allelic genealogy, it is possible to calculate the likelihood of the selection intensity as a function of the observed level of variability at marker loci closely linked to the selected allele. This method was used to estimate the intensity of selection affecting the delta 32 allele at the CCR5 locus in Europeans and a mutant at the MLH1 locus associated with colorectal cancer in the Finnish population.     

Identifying the ptilopody (feathered shank) loci of the chicken.

A series of crosses was made involving lightly-, and heavily-, and non-feather-shanked chickens in an attempt to clear up the confusion in the literature concerning the inheritance of feathered shanks in chickens. The Langshan and Brahma breeds were both shown to possess the same single shank-feathering locus, but because of their differences in phenotype and penetrance in the genetic crosses it was suggested that they possessed different alleles at this locus. This locus was designated as Pti-1, with Pti-1L being the Langshan allele and Pti-1B the Brahma allele. The Brahma allele was shown to be dominant over the Langshan allele. Both the Sultan and Cochin breeds were shown to possess two shank-feathering loci, and the data suggested that one of the loci in the Sultan contained the Pti-1L allele. It is hypothesized that the comparable allele in the Cochin breed was Pti-1B. It is proposed that the second locus in both of these breeds is similar, and the symbol Pti-2 is suggested.     

The growth hormone 1 GH1:c.457C>G mutation is associated with intramuscular and rump fat distribution in a large sample of Australian feedlot cattle

The GH1:c.457C>G exon 5 missense mutation in the bovine growth hormone 1 (GH1) gene that causes the replacement of leucine (L) with valine (V) was investigated in 1027 cattle with primarily Angus and Shorthorn breeding from Australian feedlots. The allele frequency of the GH1:c.457C allele was 0.77 in Angus and 0.76 in Shorthorn. The GH1:c.457C allele was associated with lower marbling (P = 0.0472), and the average effect of allele substitution was -0.22 of a phenotypic standard deviation. This allele was also associated with slightly higher rump fat (P = 0.0541) and the average effect of allele substitution was 0.11 SD. Marbling and rump fat were not strongly correlated (r = 0.097, P < 0.01) in this data set. This mutation had no significant effect on eye muscle area or hot dressed carcass weight (P > 0.1). Given these relationships, the differences between GH1 alleles could be the result of differential deposition of fat in fat depots.     

Genetic analysis and molecular mapping of a pale flower allele at the W4 locus in soybean.

In soybean (Glycine max (L.) Merr.), the w4-mutable line that harbors the w4-m allele was identified in 1983. It was proposed that this line contained an autonomous transposable element at the W4 locus, which is a major locus controlling the biosynthesis of anthocyanin. The w4-m allele can revert to the W4 allele that produces the wild-type phenotype, or sometimes to other alleles that produce intermediate phenotypes. Mutant plants that produce pale flowers were identified among the progeny of a single germinal revertant event from the w4-mutable line. Through genetic analysis, we established that the pale-flower mutation was conditioned by a new allele (w4-p) at the W4 locus. The w4-p allele is dominant to the w4 allele but recessive to the W4 allele, and the w1 allele has an epistatic effect on the w4-p allele. The pale-mutant line (w4-pw4-p) was designated as Genetic Type Collection number T369. An F2 mapping population derived from the cross of Minsoy (W4W4) x T369 (w4-pw4-p) was used to map the W4/w4-p locus, using simple sequence repeat (SSR) markers. The W4 locus was located at one end of molecular linkage group D2, 2.3 cM from the SSR marker Satt386 and close to the nearby telomere.     

Polymorphisms of apolipoproteins A-IV and E in a Turkish population living in Germany

Human apolipoproteins (apo) E and apo A-IV are polymorphic with significantly different allele frequencies among different ethnic groups. Whereas the variation at the apo E gene locus affects plasma cholesterol levels in all populations studied so far and is associated with longevity in Caucasians, the influence of the common apo A-IV polymorphism on plasma lipoproteins has not been unanimously accepted. We have therefore determined the common apo E and apo A-IV polymorphisms by isoelectric focusing, calculated the respective allele frequencies and studied their effects on plasma lipoproteins in a random sample of 240 nonrelated Turkish subjects (141 males, 99 females) living in Germany and originating from central and eastern Anatolia. When compared with the German population and other Caucasians in Europe a prominence of the apo ɛ3 allele frequency (0.885) was accompanied by a decrease in the frequencies of both the apo ɛ2 allele (0.048) and the apo ɛ4 allele (0.067). Thus, the Turkish population studied here clustered with populations mainly from southern Europe and Japan, which have low ɛ2 and ɛ4 allele frequencies. Also, the frequency of the A-IV-1 allele was higher (0.967) and that of the A-IV-2 allele lower (0.033) in the Turkish subjects studied than in other populations. At an average level of total cholesterol of 194.5 ± 45 mg/dl, no significant influence of the A-IV alleles on plasma lipoproteins was seen. However, apo E and apo B differed significantly between apo E phenotypes, with high levels of apo E and low levels of cholesterol and apo B in carriers of the ɛ2 allele, and vice versa for the ɛ4 allele. The average cholesterol excess for the ɛ2 allele was –7.95 mg/dl, for the ɛ3 allele, –1.34, and for the ɛ4 allele, +14.15 mg/dl. Thus, despite the unusual frequency distribution of the apo E alleles, their effects on plasma lipoproteins are within the range reported for other populations in Europe. Received: 10 April 1995 / Revised: 25 March 1996     

Association of Pro12Ala polymorphism in peroxisome proliferator-activated receptor gamma with polycystic ovary syndrome: a meta-analysis

The association between Pro12Ala polymorphism in peroxisome proliferator-activated receptor gamma (PPAR) and polycystic ovary syndrome (PCOS) has been investigated in several studies, whereas results were often incompatible. We conducted a meta-analysis to evaluate the association of Pro12Ala polymorphism in PPAR with PCOS susceptibility. A meta-analysis was performed on the published studies before November, 2011. Meta-analysis was performed for genotypes CG versus CC, CG+GG versus CC and G allele versus C allele in a fixed effect model. The combined odds ratio (OR) with 95?% confidence interval (95?% CI) was calculated to estimate the strength of the association. A total of 13 studies including 1,598 cases and 1,881 controls were enrolled. Ultimately, sensitivity analysis demonstrated that, in total, there was no significant association between Pro12Ala polymorphism and PCOS in the contrast of G allele versus C allele OR?=?0.84 (95?% CI 0.69-1.04) and in Europeans, no significant association in the comparison of G allele versus C allele (OR?=?0.84, 95?% CI 0.67-1.06) was also indicated. In summary, according to the results of our meta-analysis, strictly, the Pro12Ala polymorphism did not significantly associate with PCOS, though the protective trend of G allele existed.     

Failure of a stocking policy, of hatchery reared brown trout, Salmo trutta L., in Asturias, Spain, detected using LDH-5* as a genetic marker

A useful genetic marker exists through the apparent fixation of the LDH-5 * 100 allele in wild populations of brown trout in rivers from Asturias, Spain, contrasted with the near fixation of the LDH-5 * 90 allele in hatchery populations used to stock these rivers. In sampling locations where natural reproduction occurred, the * 100 allele was found exclusively in all areas having no record of hatchery stocking. The * 100 allele also predominated in three stocked areas having natural reproduction; in two of these areas a few individuals of the 0 + age class were homozygous for the * 90 allele. These data indicated that all catchable and reproductive fish originated from indigenous populations and thus the policy of hatchery supplementation was a failure in these areas.     

A MspI polymorphism in the bovine ornithine decarboxylase gene and its possible association with selection for milk production in Holstein bulls

A polymerase chain reaction (PCR)-based method for detection of a MspI-restriction fragment length polymorphism (RFLP) in the bovine ornithine decarboxylase gene was developed, and the allele frequencies of the polymorphism in two groups of Holstein bulls representing progeny-tested bulls during the 1950s-1960s and 1980s, respectively, were estimated. The frequencies of the MspI(-) allele were 0.229 and 0.077 and that of MspI(+) were 0.771 and 0–923 in the progeny-tested bulls of the 1950s-1960s and 1980s, respectively. The difference in allele frequencies between the two groups was statistically significant (P< 0.005). Genetic drift could be responsible for the changes in allele frequencies; however, it could also be possible that selection for milk production was associated with the changes of the allele frequencies in the two bull populations.     

Complementation between uncF alleles affecting assembly of the F1F0-ATPase complex of Escherichia coli.

A mutant affected in the b subunit (coded by the uncF gene) of the F1F0-ATPase in Escherichia coli was isolated by a localized mutagenesis procedure in which a plasmid carrying the unc genes was mutagenized in vivo. The biochemical properties of cells carrying the uncF515 allele were examined in a strain carrying the allele on a multicopy plasmid and a mutator-induced polar unc mutation on the chromosome. The strain carrying the mutant unc allele was uncoupled with respect to oxidative phosphorylation. Membrane-bound ATPase activity was very low or absent, and membranes were somewhat proton permeable. It was concluded that the F0 sector was assembled. Determination of the DNA sequence of the uncF515 allele showed it differed from wild type in that a G----A substitution occurred at position 392, resulting in glycine being replaced by aspartate at position 131. Genetic complementation tests indicated that the uncF515 allele complemented the uncF476 allele (Gly 9----Asp). Two-dimensional gel electrophoresis of membrane preparations indicated that the uncF515 and uncF476 alleles interrupted assembly of the F1F0-ATPase at different stages.     

Association of a missense mutation in the bovine leptin gene with carcass fat content and leptin mRNA levels

Previously, we have shown that alleles of the BM1500 microsatellite, located 3.6 kb downstream of the leptin gene in cattle, were associated with carcass fat measures in a population of 154 unrelated beef bulls. Subsequently, a cytosine (C) to thymine (T) transition that encoded an amino acid change of an arginine to a cysteine was identified in exon 2 of the leptin gene. A PCR-RFLP was designed and allele frequencies in four beef breeds were correlated with levels of carcass fat. The T allele was associated with fatter carcasses and the C allele with leaner carcasses. The frequencies of the SNP alleles among breeds indicated that British breeds have a higher frequency of the T allele whereas the continental breeds have a higher occurrence of the C allele. A ribonuclease protection assay was developed to quantify leptin mRNA in a separate group of animals selected by genotype. Animals homozygous for thymine expressed higher levels of leptin mRNA. This may suggest that the T allele, which adds an extra cysteine to the protein, imparts a partial loss of biological function and hence could be the causative mutation.