QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus)

Summary The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylusporosus) has now made it possible to carry out the systematic searches necessary for theidentification of quantitative trait loci (QTL) affecting traits of economic, as well as evolu-tionary, importance in crocodilians. In this study, we conducted genome-wide scans for twocommercially important traits, inventory head length (which is highly correlated withgrowth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in acommercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Terri-tory, Australia. To account for the uncommonly large difference in sex-specific recombi-nation rates apparent in the saltwater crocodile, a duel mapping strategy was employed.This strategy employed a sib-pair analysis to take advantage of our full-sib pedigreestructure, together with a half-sib analysis to account for, and take advantage of, the largedifference in sex-specific recombination frequencies. Using these approaches, two putativeQTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeedfor any non-avian member of the Class Reptilia. Mapping of QTL is an important firststep towards the identification of genes and causal mutations for commercially importanttraits and the development of selection tools for implementation in crocodile breedingprogrammes for the industry.Keywords crocodilian, QTL, quantitative trait loci, reptile, saltwater crocodile.