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

Rooksana E Noorai,Leigh Anne Clark,Lindsay M Wright,Susan C Chapman,Nowlan H Freese,Berta Alsina

doi:10.1371/journal.pone.0040974

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.

Highlights

There are hundreds of domestic chicken breeds worldwide [1]
A total of 191 SNPs were associated with the rumpless phenotype (Praw #0.0001), 72 of which were located on Gga 2 (Figure 2b)
We took advantage of the fact that both traits segregate independently in the population by using a single data set to carry out an association analysis for each trait

Summary

Introduction

There are hundreds of domestic chicken breeds worldwide [1]. Breeds were generally developed for meat and egg production, but morphological traits, plumage color, and other distinctive characteristics were selected. Araucana chickens are known for two other distinguishing traits: a rounded, tailless rump and protruding ear-tufts. These traits segregate in the population, the United States Araucana breed standard requires show birds to possess both phenotypes. Wherein some caudal vertebrae are present but irregularly fused together, is thought to result from a modifier gene introduced through crosses with non-Araucana tailed chickens [3,4]. The non-tufted chicks from the Et/Et male produced tufted progeny when crossed with an et+/ et+ White Leghorn, indicating that their predicted genotype does not match their phenotype, providing further evidence for variable penetrance. The aim of our investigation was to localize the genetic bases for the rumpless and tufted phenotypes of the Araucana chicken. Using a genome-wide association approach, we elucidate the chromosomal regions harboring Rp and Et and identify strong candidate genes for each trait

Results

Discussion

Materials and Methods