Defensins are important components of the innate immune system, where they are involved in protection against invading microorganisms. Very little is known about allelic variation in these genes in birds, particularly waterfowl. Waterfowl are an important reservoir host for a variety of pathogens, including zoonosis such as avian influenza. Therefore a more complete understanding of their immune system is very important.

To assess cross-species amplification and allelic variation of β-defensin genes in different Anatidae species, 11 loci were characterized in 43 different species via PCR and sequencing, using primers designed to amplify defensin genes in Mallard. All defensins amplified in at least some species, and all species amplified for at least some defensins. Species with a closer phylogenetic relationship to Mallards were significantly more likely to amplify. High levels of allelic variation were found, both at DNA and protein level, including many alleles that never have been characterized before. Highest allelic variation was found in AvBD3b and lowest variation was found in AvBD4. Even though the amplified sequences were short (~250bp), many of these defensin genes were able to reconstruct similar broad phylogenetic relationships that are found with more comprehensive genetic analyses of the Anatidae. This study has contributed with new knowledge of the avian immune system; defensin alleles and their evolution.