Major histocompatibility I gene diversity in the critically endangered Laysan duck (Anas laysanensis).

Abstract

Quantifying the genetic composition of founder populations is important to the success of reintroduction programmes, especially for bottlenecked and/or specialized species, such as island endemics. By implementing admixture schemes based on genetic variability, captive breeding programmes can minimize the detrimental effects of bottlenecking, inbreeding depression, outbreeding depression, etc. Particular attention has been given to genes within the major histocompatibility complex (MHC) due to their direct correlation to an individual’s immunity. However, isolating and amplifying MHC haplotypes remains difficult owing to the high diversity and paralogous nature. We describe a method of MHC I haplotype isolation based on an iterative process of primer design for the endangered island endemic, the Laysan duck (Anas laysanensis). Ultimately, haplotype-specific primers allow for direct genotyping after gel electrophoresis based on the presence/absence of their respective amplicons. Using the developed techniques, a total of eight unique haplotypes were isolated and assayed across 21 Laysan duck individuals from Laysan Island (N = 10) and Midway Atoll (N = 11). The presence/absence of seven haplotypes were variable across individuals with three haplotypes present in 95% of individuals, three in 38% of individuals, and one in 90% of individuals. The protocols described herein provide a simple, cost-effective method for isolating haplotypes and monitoring existing MHC variation in Laysan ducks, and the general approach can be applied to other molecular markers and species with low genetic diversity.