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Araucana chickens are known for their rounded, tailless rumps and tufted ears. Inheritance studies have shown that the rumpless ( Rp ) and ear-tufted ( Et ) loci each act in an autosomal dominant fashion, segregate independently, and are associated with an increased rate of embryonic mortality. To find genomic regions associated with  Rp  and  Et , we generated genome-wide SNP profiles for a diverse population of 60 Araucana chickens using the 60 K chicken SNP BeadChip. Genome-wide association studies using 40 rumpless and 11 tailed birds showed a strong association with rumpless on Gga 2 ( P   raw  = 2.45×10 −10 ,  P   genome  = 0.00575), and analysis of genotypes revealed a 2.14 Mb haplotype shared by all rumpless birds. Within this haplotype, a 0.74 Mb critical interval containing two  Iroquois  homeobox genes,  Irx1  and  Irx2 , was unique to rumpless Araucana chickens.  Irx1  and  Irx2  are central for developmental prepatterning, but neither gene is known to have a role in mechanisms leading to caudal development. A second genome-wide association analysis using 30 ear-tufted and 28 non-tufted birds revealed an association with tufted on Gga 15 ( P   raw  = 6.61×10 −7 ,  P   genome  = 0.0981). We identified a 0.58 Mb haplotype common to tufted birds and harboring 7 genes. Because homozygosity for  Et  is nearly 100% lethal, we employed a heterozygosity mapping approach to prioritize candidate gene selection. A 60 kb region heterozygous in all Araucana chickens contains the complete coding sequence for  TBX1  and partial sequence for  GNB1L .  TBX1  is an important transcriptional regulator of embryonic development and a key genetic determinant of human DiGeorge syndrome. Herein, we describe localization of  Rp  and  Et  and identification of positional candidate genes.

Genome-Wide Association Mapping and Identification of Candidate Genes for the Rumpless and Ear-tufted Traits of the Araucana Chicken