ABSTRACT: BACKGROUND: Scaleless (sc/sc) chickens carry a single recessive mutation that causes a lack of almost allbody feathers, as well as foot scales and spurs, due to a failure of skin patterning duringembryogenesis. This spontaneous mutant line, first described in the 1950s, has been usedextensively to explore the tissue interactions involved in ectodermal appendage formation inembryonic skin. Moreover, the trait is potentially useful in tropical agriculture due to theability of featherless chickens to tolerate heat, which is at present a major constraint toefficient poultry meat production in hot climates. In the interests of enhancing ourunderstanding of feather placode development, and to provide the poultry industry with astrategy to breed heat-tolerant meat-type chickens (broilers), we mapped and identified the scmutation. RESULTS: Through a cost-effective and labour-efficient SNP array mapping approach using DNA fromsc/sc and sc/+ blood sample pools, we map the sc trait to chromosome 4 and show that anonsense mutation in FGF20 is completely associated with the sc/sc phenotype. Thismutation, common to all sc/sc individuals and absent from wild type, is predicted to lead toloss of a highly conserved region of the FGF20 protein important for FGF signalling. In situhybridisation and quantitative RT-PCR studies reveal that FGF20 is epidermally expressedduring the early stages of feather placode patterning. In addition, we describe a dCAPSgenotyping assay based on the mutation, developed to facilitate discrimination between wildtype and sc alleles. CONCLUSIONS: This work represents the first loss of function genetic evidence supporting a role for FGFligand signalling in feather development, and suggests FGF20 as a novel central player in thedevelopment of vertebrate skin appendages, including hair follicles and exocrine glands. Inaddition, this is to our knowledge the first report describing the use of the chicken SNP arrayto map genes based on genotyping of DNA samples from pooled whole blood. Theidentification of the sc mutation has important implications for the future breeding of thispotentially useful trait for the poultry industry, and our genotyping assay can facilitate itsrapid introgression into production lines.