White striping (WS) is one of the most common myopathies identified in broiler chickens leading to substantial production losses, where the incidence reaches 12% in commercial chickens. It occurs primarily in heavier chickens being a modification of the breast muscle characterized by the presence of pale parallel streaks in the same orientation of the muscle fibers. Since the WS etiology remains unclear, we aimed to identify the biological and genetic mechanisms involved in its occurrence through the whole transcriptome analysis of WS in affected and unaffected chicken breast muscles. A total of 11,177 genes were expressed in the pectoralis major muscle. Out of those, 1,441 genes were differentially expressed (FDR ≤ 0.01) between the two analyzed groups, being, respectively, 772 genes upregulated and 669 downregulated in the WS affected group. A total of 36 significantly overrepresented GO terms related to WS myopathy were enriched, and the most relevant biological processes were activation of immune system, angiogenesis, hypoxia, cell death, and striated muscle contraction. The unbalance of those biological processes may trigger the occurrence of the WS phenotype in broilers. The possible lack of capillary blood supply homogeneously in the muscle triggers the hypoxia, following the activation of glycolysis, calcium signaling and apoptosis related genes facilitating the tissue damage and WS incidence.

BackgroundGenetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (Fx) and genomic information using runs of homozygosity (FROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (FSNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (Ne) were also estimated.ResultsEstimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller Ne. Estimates of Ne based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed.ConclusionsThe use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.

Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (N e ), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The N e of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.

ABSTRACT. The objective of this study was to estimate the genetic and environmental parameters for carcass, carcass part, and organ weights in a paternal strain of broiler chickens that was selected mainly for body weight at 42 days of age (BW42) to provide support for poultry genetic improvement programs. A total of 1448 chickens were used that resulted from the expansion of a pure paternal strain named TT, which was developed by Embrapa Suínos e Aves. The following weights were evaluated: BW42, chilled carcass, wing, drumstick meat, thigh meat, breast meat, breast fillet, back, liver, heart (HRT), and gizzard (GIZ). The variance component was estimated by the restricted maximum likelihood method using a multi-trait animal model. The general model included the additive genetic and residual random effects and the fixed effect of the sex-hatch group (10 levels). The heritability estimates ranged from 0.27 ± 0.06 for HRT to 0.44 ± 0.08 for GIZ. These results indicated that all the traits have enough additive genetic variability to respond to selection. The genetic correlation estimates between BW42 and the carcass and carcass part weights were high and positive. However, the genetic correlation estimates between BW42 and organ weights were Genetic parameters of economic traits in broiler chickens low. In this population, the carcass traits might respond indirectly to selection applied to BW42. It can be concluded that selection to increase BW42 is not effective in improving broiler organ weight. Therefore, to obtain suitable genetic improvement for these traits, the selection indexes for broilers should include organ weight-based criteria.

Genetic selection for production traits has resulted in a rapid improvement in animal performance and development. Previous studies have mapped quantitative trait loci for body weight at 35 and 41 days, and drum and thigh yield, onto chicken chromosome 4. We investigated this region for single nucleotide polymorphisms and their associations with important economic traits. Three positional candidate genes were studied: KLF3 (Krüeppel-like factor 3), SLIT2 (Slit homolog 2), and PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha). Fragment sequencing of these genes was conducted in 11 F1 animals, and one polymorphism in each gene was selected and genotyped in an F2 population (N = 276) and a paternal broiler line TT (N = 840). Associations were identified with growth, carcass, and fat traits in the F2 and the paternal line (P < 0.05). Using single markers in both the F2 and the TT line, KLF3 was associated with weight gain (P < 0.05), PPPARGC1A was associated with liver and wing-parts weights and yields (P < 0.05), and SLIT2 was associated with back yield (P < 0.05) and fat traits (P < 0.05). Using multiple markers, KLF3 lost its significance in both populations, and SLIT2 was associated with feed conversion only in the TT population (P < 0.05). The QTLs mapped in the F2 population could be partly explained by PPARGC1A and SLIT2, which were associated with body weight at 35 and 41 days, respectively, and with drum and thigh yield in the same population. The results of this study indicate the importance of these genes for production traits.