The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history

Background  

The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed.     

ADH1B Arg47His polymorphism is associated with esophageal cancer risk in high-incidence Asian population: evidence from a meta-analysis

Background and Objectives

Incidence of Esophageal squamous cell carcinoma (ESCC) is prevalent in Asian populations, especially in the ones from the “Asian esophageal cancer belt” along the Silk Road and the ones from East Asia (including Japan). Silk Road and Eastern Asia population genetics are relevant to the ancient population migration from central China. The Arg47His (rs1229984) polymorphism of ADH1B is the highest in East Asians, and ancient migrations along the Silk Road were thought to be contributive to a frequent ADH1B*47His allele in Central Asians. This polymorphism was identified as responsible for susceptibility in the first large-scale genome-wide association study of ESCC and that''s explained by its modulation of alcohol oxidization capability. To investigate the association of ADH1B Arg47His with ESCC in Asian populations under a common ancestry scenario of the susceptibility loci, we combined all available studies into a meta-analysis.

Methods

A dataset composed of 4,220 cases and 8,946 controls from twelve studies of Asian populations was analyzed for ADH1B Arg47His association with ESCC and its interactions with alcohol drinking and ALDH2 Glu504Lys. Heterogeneity among studies and their publication bias were also tested.

Results

The ADH1B*47Arg allele was found to be associated to increased risk of ESCC, with the odds ratios (OR) being 1.62 (95% CI: 1.49–1.76) and 3.86 (2.96–5.03) for the His/Arg and the Arg/Arg genotypes, respectively. When compared with the His/His genotype of non-drinkers, the Arg/Arg genotype can interact with alcohol drinking and greatly increase the risk of ESCC (OR = 20.69, 95%CI: 5.09–84.13). Statistical tests also showed gene-gene interaction of ADH1B Arg+ with ALDH2 Lys+ can bring more risk to ESCC (OR  = 13.46, 95% CI: 2.32–78.07).

Conclusion

Revealed by this meta-analysis, ADH1B*47Arg as a common ancestral allele can significantly increase the risk of ESCC in Asians, especially when coupled with alcohol drinking or the ALDH2*504Lys allele.     

Polymorphism of alcohol dehydrogenase gene ADH1B in eastern Slavic and Iranian-speaking populations

Frequencies of alleles and genotypes for alcohol dehydrogenase gene ADH1B (arg47his polymorphism), associated with alcohol tolerance/sensitivity, were determined. It was demonstrated that the frequency of allele ADH1B*47his, corresponding to atypical alcohol dehydrogenase variant in Russians, Ukrainians, Iranians, and mountain-dwellers of the Pamirs constituted 3, 7, 24, and 22%, respectively. The frequencies established were consistent with the allele frequency distribution pattern among the populations of Eurasia. Russians and Ukrainians were indistinguishable from other European populations relative to the frequency of allele ADH1B*47his, and consequently, relative to specific features of ethanol metabolic pathways. The data obtained provide refinement of the geographic pattern of ADH1B*47his frequency distribution in Eurasia.     

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984^∗T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease.     

High frequency of CYP1A1*2C allele in Brazilian populations

The genetic variability of the CYP1A1 I462V polymorphism (CYP1A1*2C) was investigated in four Brazilian populations: three groups of African descent and one group of European descent. The CYP1A1 polymorphism was analyzed by two different procedures, first by the allele-specific polymerase chain reaction (PCR) method and then by the PCR-restricted fragment length polymorphism (PCR-RFLP) method before digestion with BsrDI. The frequency of CYP1A1 *2C was 11% in Brazilians of European descent, a frequency that is slightly higher but not statistically different from that observed in European populations. In Brazilians of African ancestry this value was very high (12% to 15%). This allele was not observed in the only two African populations investigated thus far. By themselves, the two factors of interethnic admixture (with populations of European descent and/or Amerindian populations) and genetic drift cannot explain the high values observed here. Our findings suggest that the CYP1A1 *2C allele may possibly be present in Africa, but restricted to some ethnic groups not yet investigated. Environmental factors in South America might also have acted as selective factors increasing the CYP1A1 *2C gene frequency. Our data also suggest that the CYP1A1 *2C allele might possibly have originated in Africa.     

Molecular analysis of the ADH1-C m allele of maize

The Adh1-C ^mallele and each gene in the Adh1-FC ^mduplication have been cloned and restriction-mapped. Of the C ^mallele 6 kb was sequenced. A single amino acid substitution of aspartate for tyrosine at residue 52 accounts for the altered enzymatic properties of the C ^mprotein. Comparison of the nucleotide sequence to that of Adh1-1F and Adh1-1S shows structural and restriction site polymorphisms in the 3 flanking DNA. C ^mlacks the insertion sequence present in 1F and 1S and contains a complex sequence composed of two direct repeats and an inverted repeat. The two genes of the duplication allele have similar restriction maps to C ^mand each other.     

Ethnic differences in allele distribution for the IL8 and IL1B genes in populations from eastern India

Populations from eastern India have been examined for the allele distribution at polymorphic sites in the IL8 and IL1B genes. Significant differences in allele frequencies between caste and tribal population groups were observed. However, there are no differences in allele frequencies among various subpopulations within caste or tribal groups. We argue that different caste populations from the same geographic location can be pooled for the purpose of population association studies.     

Alcohol dehydrogenases ADH1B and ADH7 gene polymorphism in Russian population from the Siberian region

The Allele and genotype didtributions of the two alcohol dehydrogenase genes ADH1B (polymorphism A/G in exon 3, detected with restrictase MslI) and ADH7 (polymorphism G/C in intron 5, detected with restrictase StyI) was studied in three Russian populations from the Siberian region. The absence of interpopulation and intersexual differences in the allele frequency was determined. The allele ADH1B*G (+MslI, A2) was found in low frequency (3.6-7.5%), the mutant allele ADH7 (-StyI, B2) frequency in total population (n = 339) was 46.02%. The genotype distributions of the ADH1B and ADH7 in these populations were agreed with the Hardy-Weinberg equilibrium and linkage equilibrium. Increased frequency of ADH7 B2 allele was revealed in elder group (after 40 years) in the total sample and in the Tomsk city inhabitants (n = 113) on 11% (P = 0.001) and 9% (P = 0.017) accordingly. ADH7 and ADH1B genes polymorpisms did not show association with antioxidant activity, which was determined from the blood plasma ability to reduce the yield of products interacting with thiobarbituric acid in the lecitin-Fe2+ ions model system. The statistically significant decrease of serum very low density lipoproteins (LPVLD) level (on 9.95%, P = 0.045) and close to statistically significant decrease systolic pressure (on 6.80%, P = 0.068) and serum triglycerides level (on 6.16 of %, P = 0.058) were revealed among the A2 allele ADH1B gene carriers in Tomsk population.     

Variation in the ADH1B proximal promoter affects expression

The primary pathway of metabolism of dietary alcohol is via its oxidation in liver by alcohol dehydrogenases (ADH). Differences in the ADH enzyme activity or levels of enzyme present could affect the risk for alcoholism. Regulatory variations have been shown to affect the promoter activity and thereby affect the risk for alcoholism. In this study the functional effects of the two SNPs (rs1159918 and rs1229982) in the proximal promoter region of ADH1B that were associated with alcoholism were explored. We examined the effects of five naturally occurring haplotypes on the promoter activity. We observed that a C to A change at rs1229982 increased promoter activity 1.4-fold.     

Extremely high prevalence of DNASE1*1 allele in African populations

The single nucleotide polymorphism (SNP) at deoxyribonuclease I (DNase I), designated as DNASE1 (NCBI SNP number; 1053874), in exon 8 (A2317G) has been shown to be associated with liver disease, colorectal carcinoma, and gastric carcinoma in Japanese patients. In this study, we investigated the frequency of the DNASE1 polymorphism in Ghanaian (n = 96) and Xhosa (n = 78) populations and compared the results with those of other studies. The single nucleotide polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The frequencies of DNASE1*1 in the Ghanaian and Xhosa populations were 0.90 and 0.88, respectively. These two African populations had an extremely high frequency of DNASE1*1, similar to that of the Ovambos living in Namibia. Caucasians and Asians had a lower frequency of DNASE1*1 than the African groups. This study is the first to reveal an extremely high frequency of DNASE1*1 among African populations.     

ADH allele frequency changes in olive fruit flies shift from olives to artificial larval food and vice versa, effect of temperature

When field collected olive fruit flies, Dacus oleae Gmelin (Diptera: Tephritidae), were maintained on an artificial larval medium or on ripe (black) olives in the laboratory for four consecutive generations, the frequency of alcohol dehydrogenase (ADH) allozymes changed (impressively) only in the flies kept on artifical larval food. When flies reared in the laboratory for about 2 years (allele frequencies of artificially reared flies in equilibrium) were provided ripe olives for oviposition for three consecutive generations, the ADH allozyme frequencies changed substantially within only one generation, remaining stable thereafter. The change was towards the frequency levels of natural populations of flies. Finally, when field collected flies were reared artificially under three different daily temperature regimes (i.e. 17, 17–25 and 25 °C), the general pattern of ADH allozyme frequency changes was not affected by the different temperature regimes. The only difference was that the stable temperatures, especially the high one, exhibited more rapid changes of allele frequencies than the daily fluctuating temperature regime.

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Résumé Quand des lots de Dacus oleae Gmelin (Dipt. Tephritidae) ont été conservés pendant plusieurs générations au laboratoire sur des olives mûres (noires) ou sur un substrat alimentaire larvaire artificiel, la fréquence des allozymes de l'alcohol déshydrogénase n'a changé fortement que chez les mouches élevées sur substrat artificiel. Quand les mouches élevées pendant deux ans sur substrat artificiel (fréquences alléliques en équilibre) sont ensuite pourvues en olives mûres (noires) pendant 3 générations pour pondre, les fréquences des allozymes de l'alcool deshydrogénase ont changé nettement en une génération, restant stable ensuite. Le changement rapprochait les fréquences obtenues de celles des populations naturelles.Quand les mouches récoltés à l'extérieur étaient élevées artificiellement dans trois conditions de températures (17° constant, 17/25 et 25° constant), les modifications des fréquences étainent semblables; cependant, le changement était plus rapide aux températures constantes, surtout la plus élevée.

     

A new DRB1 * 1202 allele (DRB1 * 12022) found in association with DQA1 * 0102 and DQB1 * 0602 in two Black narcoleptic subjects

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number L34353. The name listed for this sequence has been officially assigned by the WHO Nomenclature Committee in August 1994. This follows the agreed policy that subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al 1994), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report