A worldwide correlation of lactase persistence phenotype and genotypes

Abstract

BackgroundThe ability of adult humans to digest the milk sugar lactose - lactase persistence - is a dominant Mendelian trait that has been a subject of extensive genetic, medical and evolutionary research. Lactase persistence is common in people of European ancestry as well as some African, Middle Eastern and Southern Asian groups, but is rare or absent elsewhere in the world. The recent identification of independent nucleotide changes that are strongly associated with lactase persistence in different populations worldwide has led to the possibility of genetic tests for the trait. However, it is highly unlikely that all lactase persistence-associated variants are known. Using an extensive database of lactase persistence phenotype frequencies, together with information on how those data were collected and data on the frequencies of lactase persistence variants, we present a global summary of the extent to which current genetic knowledge can explain lactase persistence phenotype frequency.ResultsWe used surface interpolation of Old World lactase persistence genotype and phenotype frequency estimates obtained from all available literature and perform a comparison between predicted and observed trait frequencies in continuous space. By accommodating additional data on sample numbers and known false negative and false positive rates for the various lactase persistence phenotype tests (blood glucose and breath hydrogen), we also apply a Monte Carlo method to estimate the probability that known lactase persistence-associated allele frequencies can explain observed trait frequencies in different regions.ConclusionLactase persistence genotype data is currently insufficient to explain lactase persistence phenotype frequency in much of western and southern Africa, southeastern Europe, the Middle East and parts of central and southern Asia. We suggest that further studies of genetic variation in these regions should reveal additional nucleotide variants that are associated with lactase persistence.

Fine-scale human genetic structure in Western France

“…[38][39][40] Both the lactase and the HLA regions are known to harbor prominent geographic variation in Europe and the increase in the lactase persistence allele in Brittany fits within the overall increase that is found when moving from southeastern to northwestern Europe. 41 In particular, the frequency of the lactase persistent allele is high in Ireland (95%). 41 The variation of lactasepersistence frequency is in line with the different admixture coefficients found for the Breton individuals pointing to something more than isolation-by-distance because of common ancestry between Bretons and individuals from the British isles.…”

“…41 In particular, the frequency of the lactase persistent allele is high in Ireland (95%). 41 The variation of lactasepersistence frequency is in line with the different admixture coefficients found for the Breton individuals pointing to something more than isolation-by-distance because of common ancestry between Bretons and individuals from the British isles. However, we acknowledge that admixture is not the only process that may have generated particular allele frequencies in Brittany; processes of positive selection that arose because of biological adaptation to agricultural practice can also explain spatial variation of gene frequencies.…”

Associations of the lactase persistence allele and lactose intake with body composition among multiethnic children

“…Finally, we have only tested one of several LP alleles. Other LP alleles have arisen independently in other groups (Imtiaz et al 2007;Ingram et al 2007Ingram et al , 2009Tishkoff et al 2007;Büning et al 2004;Itan et al 2010). It is possible that not all individuals who lack the particular LP allele tested are in fact lactose intolerant.…”

“…The frequency of the lactase persistence (LP) allele is most common in people of European ancestry as well as some African, Middle Eastern, and Southern Asian groups; however, it is nearly absent in the rest of the world (Itan et al 2010). There is strong evidence that the selective pressures that led to the LP allele being common in these geographic regions originated from the dairying practices begun by early European and West Asian farmers \10,000 years ago (Bersaglieri et al 2004;Scrimshaw and Murray 1988).…”

Milk Consumption is Not Affected by C/T-13910 Single Nucleotide Polymorphism in a Tajik Population in a Southern Region of Uzbekistan

“…It is one of the most common enzyme deficiencies among mammals, and has a homozygous recessive inheritance trait [2,3]. Most of the adult human populations have high prevalence of hypolactasia and intolerance to milk [4].…”