Piscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming. Current treatments have been ineffective for the control of the disease. Genetic improvement for P. salmonis resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against P. salmonis in a farmed coho salmon population and identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) which were experimentally challenged against P. salmonis were sequenced using ddRAD sequencing. A total of 4,174 SNP markers were identified in the population. These markers were used to perform a GWAS and testing genomic selection models. One SNP related with iron availability was genome-wide significantly associated with resistance to P. salmonis defined as day of death. Genomic selection models showed similar accuracies and predictive abilities than traditional pedigree-based best linear unbiased prediction (PBLUP) method.
The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection and for inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using ddRAD genomic markers.Linkage disequilibrium was estimated between a total of 7,505 SNPs found in 62 individuals (33 dams and 29 sires) from the breeding population. The makers encompass all 30 coho salmon chromosomes and comprise 1,655.19 Mb of the genome. The average density of markers per chromosome ranged from 3.45 to 6.11 per 1 Mbp. The minor allele frequency averaged 0.20 (with a range from 0.08 to 0.50). The overall average linkage disequilibrium among SNPs pairs measured as r2 was 0.054. The Average r2 value decreased with increasing physical distance, with values ranging from 0.37 to 0.054 at distances lower than 1 kb and up to 10 Mb, respectively. An r2 threshold of 0.1 was reached at distance of approximately 1.3 Mb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (> 0.20 at distances lower than 1 Mb). Average r2 values were lower than 0.1 for all chromosomes at distances greater than 4 Mb. Linkage disequilibrium values suggest that whole genome association and selection studies could be performed using about 75,000 SNPs in aquaculture populations (depending on the trait under investigation). From the identified SNPs, an effective population size of 100 was estimated for the population 10 generation ago, and 1,000, for 139 generations ago.Based on the extent of r2 decay, we suggest that at least 75,000 SNPs would be necessary for an association mapping study. Over 100,000 SNPs would be necessary for a high power study, in the current coho salmon population.
Factores genéticos que inciden en la resistencia a enfermedades infecciosas en salmónidos y su aplicación en programas de mejoramiento #Genetic factors involved in resistance to infectious diseases in salmonids and their application in breeding programmes SUMMARYThe control of infectious diseases is essential in the success of salmon aquaculture. Genetic improvement of disease resistance may provide a feasible and sustainable option for the management of these diseases. Marker-assisted selection (MAS) or Gene-assisted selection (GAS), represent a valuable alternative to the conventional schemes for improving disease resistance using pedigree. Nevertheless a previous knowledge of the genetic factors involved in the trait is necessary to implement this methodology. In this review, the most important aspects of genetic resistance to infectious diseases in salmonids and their suitability for breeding programmes are both reviewed and discussed. Firstly, we briefly mention the most important infectious diseases in Chile. Furthermore, we include aspects related with conventional breeding for this quantitative trait, such as selection criteria, genetic variation of resistance and genetic correlations with other traits. We also review three approaches used in molecular identification of genetic factors involved in resistance: candidate genes, with particular emphasis on the major histocompatibility complex (MHC) or MH genes, detection of quantitative trait loci (QTL) and gene expression studies. Finally, we discuss the use of this information in the implementation of breeding schemes that include disease resistance in their breeding goal.Palabras clave: salmón, resistencia a enfermedades, programas de mejoramiento, QTL. Key words: salmon, disease resistance, breeding programmes, QTL. INTRODUCCIÓNEl cultivo de salmónidos es una de las principales actividades relacionadas con la acuicultura a nivel nacional y una de las que genera productos acuícolas con mayor valor económico a nivel mundial (FAO 2006). Al igual que en otros sistemas intensivos de producción animal el éxito de esta actividad depende en gran medida del control de las enfermedades infecciosas. Un ejemplo claro del impacto que pueden ocasionar ciertas patologías en el cultivo del salmón es la crisis que ha afectado durante los últimos años a la industria salmonicultora nacional como consecuencia de los brotes del virus de la anemia infecciosa del salmón (ISA).Los programas de mejoramiento genético han permitido aumentar el retorno económico de las explotaciones agropecuarias. El objetivo de mejoramiento debe ser definido para cada especie y para cada población. En general, todas aquellas características de importancia económica deberían estar incluidas en el objetivo de mejoramiento. Por esto, en salmones se incluyen caracteres relacionados con el crecimiento corporal, color y textura de la carne, así como también la resistencia genética a enfermedades de tipo viral y bacteriano (Gjedrem 2000). Hasta el momento, los programas de mejoramiento genético han inc...
Limited stocking efforts to introduce Atlantic salmon Salmo salar into Chilean rivers and streams were unsuccessful during the 20th century. Following the arrival of the aquaculture industry during the 1980s, escaped Atlantic salmon have presented an ecological risk to native taxa through predation, competition, and transmission of pathogens or parasites. However, whether commercial aquaculture strains represent the likely source of free-living Atlantic salmon in marine and freshwater environments is unclear. We used 272 single nucleotide polymorphisms to characterize free-living Atlantic salmon (n = 80) captured from 12 marine and freshwater locations in southern Chile. These were compared with 8 reference collections, 6 known commercial strains, and 2 wild populations of Atlantic salmon. We evaluated genetic structure among free-living Atlantic salmon and assessed individual ancestry and origin by assigning mixture samples to reference collections. We found evidence for genetic structure (number of clusters, K = 3) among free-living salmon unexplained by geography, environment, or life stage, but consistent with the number of clusters among commercial aquaculture strains. Most free-living Atlantic salmon had a close ancestry with farmed Norwegian strains, the most widely used by the industry, pointing to recent aquaculture escapes as their origin. Yet recent establishment of self-sustaining populations weakly differentiated from aquaculture broodstock cannot be ruled out. We propose increasing monitoring efforts of free-living Atlantic salmon in remote sites as well as in watersheds located in densely stocked aquaculture areas.
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