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MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection

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Abstract

Saltwater crocodiles are in high demand for the production of luxury fashion items. However, their susceptibility to disease incurs substantial losses and it is hoped to be able to genetically select these animals for disease resistance. So far, this has only been enabled by phenotypic selection. Investigating the major histocompatibility complex (MHC) could provide insight into the ability of an individual to respond to pathogens acting as a selective pressure on the host. Here, we assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 3 among 42 saltwater crocodiles from nine river basins in the Northern Territory, Australia. We generated 640 sequences using cloning and sequencing methods and identified 43 MHC variants among them. Phylogenetic analyses clustered these variants into two major clades, which may suggest two gene lineages. We found the number of variants within an individual varying between one and seven, indicating that there are at least four gene loci in this species. Selection detection analyses revealed an elevated ratio of nonsynonymous to synonymous substitutions (mean = 1.152 per codon), suggesting balancing selection. Population differentiation analyses revealed that the MHC did not show structuring among the river basins, and there were some shared variants among them. This may be a result of possible gene flow and/or similar selection pressures among populations. These findings provide background knowledge to identify potential MHC markers, which could be used for selecting genetically variable individuals for future disease associations. All MHC class I exon 3 sequences reported in this paper were submitted to the GenBank database with following accession numbers: HQ008785–HQ008789, HQ008791–HQ008798, HQ008808–HQ008815, HQ008824, HQ008826–HQ008830, HQ008835, HQ008839, HQ008842–HQ008850, and JX023536–JX023540.

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Acknowledgments

We would like to thank staff at Darwin Crocodile Farm for allowing access to the animals and for their assistance with sampling and data collection. All research took place at the University of Sydney, Australia. Blood samples were provided by Darwin Crocodile Farm, NT, Australia. Capturing, handling, and blood sampling of crocodiles were approved by the Australian Animal Ethics Committee, permit no. N00/5-2009/3/5057. We are also grateful to Dr. Camilla Whittington, Dr. Karma Nidup, and Quintin Lau for copyediting early drafts of the manuscript.

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Authors and Affiliations

  1. Faculty of Veterinary Science, RMC Gunn Building, University of Sydney, Sydney, New South Wales, 2006, Australia

    Weerachai Jaratlerdsiri, Sally R. Isberg & Jaime Gongora

  2. Porosus Pty. Ltd., P.O. Box 86, Palmerston, Northern Territory, 0831, Australia

    Sally R. Isberg

  3. Faculty of Veterinary Science, McMaster Building, University of Sydney, Sydney, New South Wales, 2006, Australia

    Damien P. Higgins

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  1. Weerachai Jaratlerdsiri
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Correspondence to Jaime Gongora.

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Jaratlerdsiri, W., Isberg, S.R., Higgins, D.P. et al. MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection. Immunogenetics 64, 825–838 (2012). https://doi.org/10.1007/s00251-012-0637-x

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