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Background  In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the  ASIP  locus. The aim of our study was to characterize the structural modifications within this locus that explain the  yellow  mutation (large deletion) and the  fawn -2/ beige  mutation (assumed to be caused by a different structural modification).    Results  For the yellow phenotype, we identified a complex mutation that involves a 141,162-bp long deletion. For the fawn-2/beige phenotype, we identified a 71-kb tandem duplication that comprises one unchanged copy of  ASIP  and one copy present in the  ITCH - ASIP  fusion gene, which leads to a transcript coding for a normal ASIP protein. Although this agrees with previous reports that reported an increased level of ASIP transcripts in the skin of mutant animals, we show that in the skin from fawn-2/beige embryos, this level is higher than expected with a simple duplication of the  ASIP  gene. Thus, we hypothesize that the 5′ region of the  ITCH - ASIP  fusion gene leads to a higher transcription level than the 5′ region of the  ASIP  gene.    Conclusions  We were able to conclude that the fawn-2 and beige phenotypes are caused by the same allele at the  ASIP  locus. Both of the associated mutations  fawn - 2/beige  and  yellow  lead to the formation of a fusion gene, which encodes a transcript for the ASIP protein. In both cases, transcription of  ASIP  depends on the promoter of a different gene, which includes alternative up-regulating sequences. However, we cannot exclude the possibility that the loss of the 5′ region of the  ASIP  gene itself has additional impacts, especially for the  fawn - 2/beige  mutation. In addition, in several other species including mammals, the existence of other dominant gain-of-function structural modifications that are localized upstream of the  ASIP  coding sequences has been reported, which supports our hypothesis that repressors in the 5′ region of  ASIP  are absent in the  fawn -2/ beige  mutant.    Electronic supplementary material  The online version of this article (10.1186/s12711-019-0458-6) contains supplementary material, which is available to authorized users.

Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail