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

Abstract

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.

Results: We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000 to approximately 7,000 years ago.

Conclusion: We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.

Figure 1

The distribution of the ADH1B*47His allele and the sites of early rice relics. The contour map of the ADH1B*47His frequency in East Asian populations and the ancient sites of rice domestication in China. The allele frequency data includes the 38 populations in the present study and those published before.[17]. The geographic locations of the rice sites are from the published data [5].

Figure 2

The selection test for the ADH1B gene region. (A) The haplotype-bifurcation diagrams for the core haplotype with at least 9% frequency at the ADH1B gene region in the East Asian populations. The core haplotype CTTCG shows unusual long-range homozygosity. (B) The EHH and REHH plots of the core haplotype covering the candidate SNP (rs1229984) in the East Asian populations. The EHH and REHH values are plotted against the physical distances extending both upstream and downstream of the selected core region. Only the core haplotypes with frequency ≥9% are shown.

Figure 3

The correlation test for ADH1B*47His allele frequencies with the ages of rice domestication. The correlation of the ADH1B*47His allele frequencies with the ages of rice domestication in 14 regions of China. The data of rice domestication was collected from the published study [5]. The correlation analysis was conducted with the use of SPSS13.0, and the statistical significance was accessed by t test.