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

Abstract

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.

A Novel Gain-Of-Function Mutation of the Proneural IRX1 and IRX2 Genes Disrupts Axis Elongation in the Araucana Rumpless Chicken

“…Although IRX4 does not fall within the defined critical region, it is within the same genomic cluster as IRX1 and IRX2 [31], [55]. IRX4 expression is restricted primarily to the heart at these stages, suggesting that the regulatory elements controlling its expression are not as closely shared as for IRX1 and IRX2 [55], [56], [57], [58].…”

Single nucleotide polymorphisms associated with growth traits in Jinghai yellow chickens

“…In chickens, many genome-wide association studies (GWAS) were conducted using the Illumina 60K SNP Beadchip. Using this method, major loci associated with growth (Gu et al, 2011;Xie et al, 2012), egg production Wolc et al, 2012), rumpless and ear-tufted traits (Noorai et al, 2012), body composition and meat quality (Liu et al, 2013), resistance to Marek's disease (Li et al, 2013), and immune responses to Newcastle disease virus (Luo et al, 2013) were identified.…”

Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology

“…In chickens, GWASs have been used to identify major loci associated with growth (Gu et al 2011;Xie et al 2012), egg production (Liu et al 2011;Wolc et al 2012), rumpless and ear-tufted traits (Noorai et al 2012), body composition and meat quality , resistance to Marek's disease ) and immune response to NDV (Luo et al 2013). However, these studies were carried out using SNP chips.…”