Abstract
BackgroundFeed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations.ResultsFeed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens.ConclusionsThe use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
Highlights
Feed efficiency and growth rate have been targets for selection to improve chicken production
The aims of this study were to estimate the genomic heritability for performance traits, and to identify genomic regions and positional candidate genes associated with these traits in a Brazilian F2 Chicken Resource population that was derived from a reciprocal cross between a broiler and a layer line
Descriptive statistics The number of animals, means and standard errors, variance components, and estimated genomic heritabilities are given in Table 1 for: feed intake between 35 and 41 days of age (FI), feed conversion ratio between 35 and 41 days of age (FC), feed efficiency between 35 and 41 days of age (FE), weight gain between 35 and 41 days of age (WG), body weight at hatch (BW1), body weight at 35 days of age (BW35) and body weight at 41 days of age (BW41)
Summary
Feed efficiency and growth rate have been targets for selection to improve chicken production. 1637 QTL have been reported for growth traits (including average daily gain and body weight at different days of age) Many of these QTL have only been coarsely mapped (i.e., they have very broad confidence intervals for location). QTL mapping studies were previously conducted on this Brazilian experimental population (Embrapa F2 Chicken Resource Population) for feeding, growth and carcass traits [8, 9]. Those studies utilized up to 127 microsatellite markers, which resulted in the identification of QTL that span large regions of the genome. The average length of interval of the QTL reported by Nones et al [9] and Ambo et al [8] were 5.46 Mb and 11.9 Mb, respectively
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