Are the SSTR alleles stable enough to be considered monophyletic and hence reliable anthropogenetic markers? Linkage disequilibrium study on the (ACT)n COL1A2 SSTR.

ABSTRACT

An extremely low production rate of a polymorphic allele (formally called the mutation rate)--a prerequisite for using the allele as a marker (particularly for anthropogenetic purposes where the alleles must be assumed to be monophyletic)--cannot be taken for granted for alleles of highly polymorphic VNTRs, but a low production rate can be used to identify alleles produced by a single nucleotide substitution. This property was indirectly tested for the (ACT)n COL1A2 (of type I collagen) microsatellite SSTR (degree of heterozygosity H = 0.72) by searching for linkage disequilibria between the SSTR's four common alleles (n = 6, 8, 9, or 10) and three RFLPs of the same gene. A strong linkage disequilibrium between at least three of the four SSTR alleles and two of the three closely linked RFLPs has been demonstrated in a Sardinian population (Italy), a finding that suggests a low production rate of these alleles. Thus it seems that this highly polymorphic system and, by a reasonable extrapolation, other VNTRs with a comparable degree of heterozygosity may be valuable anthropogenetic markers, at least in distinguishing subgroups of a major ethnic group.