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.

Figure 1. The 444 chickens from five F₂ families and18 chickens from the parental lines (P. female and P. male - N = 10) and F₁ generation (N = 8) shown in the 2D plane spanned by their first two principal components.

Figure 2. SNPs associated with feed conversion adj35.

(a) and body weight at 35 days (b) are presented by Manhattan (left side) and QQ (right side) plots. The y-axis is shown as -log10 (p-value). On the left, the red line indicates genome-wise association (P < 7.86E-07) and the blue line, suggestive genome-wise association (P < 1.57E-05) with the respective trait. On the right side, the QQ-plots show the relation of normal theoretical quantiles of the probability distributions between expected (x-axis) and observed (y-axis) p-values from each respective associated trait (feed conversion adj35 and body weight at 35 days).

Figure 3. Haplotype blocks obtained by the solid spine of LD and family structure using Haploview 4.2.

The header represents the physical position of each 94 SNPs selected on chicken genome (Gallus gallus 4.0, NCBI). The family structure is disposed as maternal CC (a) and paternal TT (b) parental pure lines, F₁ (c) and F₂ (d) generations. The black filled squares indicate r² = 1 and square numbers represents r²*100 with black color gradient accordingly.

Figure 4. Karyotype of the QTLs (from Animal QTLdb) distribution regions of the chicken genome overlapping suggestive and significant SNPs associated with performance traits (black marks).

These QTLs were mapped for body weight (bw), postnatal growth (grow), feed intake (f.intake), feed conversion (f.conv), and feed efficiency (effic). The colors becoming denser according to the number of QTL previously mapped superposing each other.