Genome-wide association study for performance traits in chickens using genotype by sequencing approach

Abstract

Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F2 chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.

Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

“…The means and standard deviations of the internal organ weights and percentages reported herein differ from those reported by Venturini et al [36] and Gaya et al [8], however, they used meat-type chickens from broiler lines selected over many generations for rapid growth and meat production [8, 36, 37]. Those differences are expected since the F2 population used herein was founded from reciprocal crosses between grandparental broiler and layer lines, that exhibit different phenotypic abilities [6, 38–40].…”

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes

“…For SNP calling, default filtering parameters were applied except for the use of 5% for mnMAF, 70% of mnTCov, and 70% for mnScov. These parameters were applied in accordance with similar studies ( Pértille et al, 2016 , 2017a , b ). An Archaeopteryx tree ( Han and Zmasek, 2009 ) was then plotted using a cladogram generated by a Neighbor Joining distance matrix using the Tassel v.3.0 software.…”

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

“…Locating single nucleotide polymorphisms (SNPs) in functional and positional candidate genes allowed testing for associations with the trait itself [21–30]. With the advent of whole genome next generation sequencing, however, either through the intermediate of a SNP chip, or more recently (as technology has become cheaper) by sequencing individuals directly, genome-wide association studies (GWASs) are discovering new loci associated with specific traits [31–34].…”