Autozygosity

Autozygosity refers to the genetic condition in which both copies of a gene or locus in an individual are identical by descent, owing to inheritance of a common ancestral chromosomal segment. It commonly arises through inbreeding, consanguinity, or population bottlenecks that increase the chance that related individuals contribute the same ancestral alleles. In contrast to allozygosity, where alleles are identical in state but not inherited from a recent common ancestor, autozygosity indicates alleles that are identical by descent.

The extent of autozygosity in a genome can be summarized by measures such as runs of homozygosity (ROH) or the inbreeding coefficient F. ROH are uninterrupted stretches of homozygous genotypes detected from SNP data or sequence data. Long ROH suggest recent parental relatedness, whereas shorter ROH reflect more ancient shared ancestry. Various software tools, including those designed for SNP arrays and whole-genome sequencing data, identify ROH to estimate an individual’s autozygosity.

Applications of autozygosity analysis include mapping recessive disease genes, assessing levels of inbreeding in populations and individuals, and inferring demographic history in humans and other species. It is also used in breeding programs for livestock and crops to manage genetic diversity and in conservation genetics to understand population viability.

Limitations arise from marker density, sequencing quality, and complex demographic histories, which can influence ROH detection and F estimates. Accurate interpretation typically requires integrating ROH results with recombination rates, effective population size, and pedigree information when available.