Phase-unknown linkage mapping in ants

To create a genetic linkage map of an ant genome, the phase of a marker (i.e., which marker/allele came from the grandmother and which came from the grandfather of the individuals used for linkage mapping) must be known. However, field colonies contain only two generations: the queen(s) and their offspring. Normally, virgin queens disperse from their nest, mate with one or multiple males who die after mating, and start a new colony. A new reproductive brood (i.e., virgin queens and males) is usually produced after colony establishment, which can take from 6 mo to 3-5 yr. Hence, determining the phase of markers from field samples is impossible because the grandparents of a reproductive queen are no longer available for genetic analysis. Ants raised in the laboratory are likewise unsuitable for such analyses, because most ants cannot be bred regularly in the laboratory, and attempts to inseminate ant queens artificially have not been successful. However, three features facilitate "phase-unknown" linkage mapping for any ant (or other social hymenopteran) species, which is described here: (1) Mature colonies usually produce many reproductive offspring during a short period of time, which allows for the collection of a good-sized mapping population (>100 males) from a field colony; (2) Ants have a haplodiploid sex determination system (i.e., males are haploid and females diploid); (3) Queens produce males parthenogenetically. Thus, because they have no father, only those markers for which the queen is heterozygous are expected to segregate 1:1 in her male offspring.