![]() ![]() Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. In this study, we used genomic information that was recently made available for turbot ( Scophthalmus maximus ), gilthead seabream ( Sparus aurata ), European seabass ( Dicentrarchus labrax ) and common carp ( Cyprinus carpio ) to obtain accurate estimates of the effective size for commercial populations. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. first time we have studied the extent of effective population size ion order to develop policies regarding secure genetic variation in this species These results highlight the importance of monitoring the genetic diversity of aquaculture species from the start of breeding programs to secure their future genetic variation, particularly in challenging environments such as those expected from climate change.įor the. An assumption-free method for estimating the changes in genetic diversity showed that many aquaculture strains had reduced variability. The Chilean strains in particular have been subject to changes in population sizes attributable to their establishment, reductions due to disease outbreaks, and maintenance of small population sizes in culture. ![]() This paper describes the genetic status of several aquaculture strains of Coho salmon from North America, Chile, and Japan and a wild-type hatchery strain from the Pacific Northwest of North America. ![]() Several populations of Coho salmon have been maintained in aquaculture, but the extent of the genetic diversity in these strains is unknown. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. The rate of false positives when using cross-population data was null. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. ![]() Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (Seriola lalandi). Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. ![]()
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