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BackgroundPisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon.Methods2,601 Atlantic salmon smolts were experimentally challenged against P. salmonis by means of intra-peritoneal injection. These smolts were the progeny of 40 sires and 118 dams from a Chilean breeding population. Mortalities were recorded daily and the experiment ended at day 40 post-inoculation. Fish were genotyped using a 50K Affymetrix® Axiom® myDesignTM Single Nucleotide Polymorphism (SNP) Genotyping Array. A Genome Wide Association Analysis was performed on data from the challenged fish. Linear regression and logistic regression models were tested.ResultsGenome Wide Association Analysis indicated that resistance to P. salmonis is a moderately polygenic trait. There were five SNPs in chromosomes Ssa01 and Ssa17 significantly associated with the traits analysed. The proportion of the phenotypic variance explained by each marker is small, ranging from 0.007 to 0.045. Candidate genes including interleukin receptors and fucosyltransferase have been found to be physically linked with these genetic markers and may play an important role in the differential immune response against this pathogen.ConclusionsDue to the small amount of variance explained by each significant marker we conclude that genetic resistance to this pathogen can be more efficiently improved with the implementation of genetic evaluations incorporating genotype information from a dense SNP array.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2038-7) contains supplementary material, which is available to authorized users.

A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.

The objective of this project was to examine the diversity of breast meat composition and quality traits among unique resource populations. Birds from 5 groups (inbred Leghorn, inbred Fayoumi, commercial broilers, F5 broiler-inbred Leghorn cross, and F5 broiler-inbred Fayoumi cross) were utilized. Contemporary stocks (broilers, inbreds, and crosses) were grown in a single house but in separate pens. Birds were harvested at 8 wk of age. Breast muscle weight, moisture, lipid and protein contents, color, pH, and Kramer shear force values were determined on birds from each group. Breasts from broilers contained lower percentages of protein (P < 0.05) and greater percentages of lipid (P < 0.05) compared with all other groups. The 5 genetic stocks did not differ for Hunter L values or pH. The data indicate that the Leghorn inbred line breasts were a more pure and more intense red color than the crossbred contemporary (P < 0.05). Kramer shear force (kg/g sample) was higher (P < 0.05) in breasts from broilers than in breasts from the inbred lines. Our results demonstrate that the 5 genetic groups differed markedly in breast meat composition and quality characteristics. The described outbred by inbred advanced intercross lines will be useful in searches for genes affecting meat quality traits. Definition of the molecular factors that influence these traits will enhance our ability to make improvements in composition and quality of poultry meats.

One cycle of high-intensity selection on BW was conducted to study correlated effects on performance under high ambient temperature (AT). From a large flock of a commercial sire-line, 3 males and 15 females with the highest BW at 35 d of age were mated and produced a group of 120 BW-selected chicks. Three average-BW males and 15 average-BW females from the same flock were mated to produce a control group of 120 chicks. On Day 17, the two groups were equally divided between two temperature-controlled chambers and housed in individual cages. One chamber was set to a normal AT (NAT; constant 22 C) and the second chamber to high AT (HAT; constant 32 C). Under NAT, the relative advantage of the selected broilers over the controls did not change from 17 to 42 d of age, averaging about 15% for BW gain and 9.7% for feed consumption. These differences were halved under HAT from Days 17 to 28 and were reversed from 28 to 42 d of age, when the selected broilers consumed significantly less feed and gained less BW than the controls. Water-to-feed ratio was measured in each AT treatment. From 28 to 42 d of age, averaged over the two groups, birds under HAT consumed 2.5 g water/g of feed compared to only 1.5 g water/g feed under NAT. The diminished superiority of the selected broilers under HAT led to a substantial genotype-by-environment interaction involving high AT and within-stock genetic differences in growth rate. It appears that broilers selected for rapid growth under optimal conditions do not achieve their genetic potential under high AT. Thus, specific indicators of adaptation to heat, possibly water consumption or body temperature, should be added to commercial selection for rapid growth to improve broiler performance in hot climates.