Gomez-Uchida, D. | bioRxiv Science

bioRxiv2019

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Nile tilapia (Oreochromis niloticus Linnaeus, 1758) belong to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs in this species began in the late 1980s to enhance some traits of commercial interest. The resulting domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, using two complementary methods based in extended haplotype homozygosity (EHH)._Whole-genome sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia from two countries (Brazil and Costa Rica) was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control pipelines, a total of ~1.3M high-quality SNPs were inferred and used as input for the Integrated Haplotype Score (|iHS|) and standardized log-ratio of integrated EHH between pairs of populations (Rsb) methods. We detected 16, 174 and 96 candidate genes subjected to selection in strain A, B, and C, respectively. These candidate genes represent putative genomic landmarks that could contain functions of biological and commercial interest.

genomics↗

bioRxiv2019

Mixed-stock analyses among migratory, non-native Chinook salmon at-sea and assignment to natal sites in freshwater at their introduced range in South America

Invasive species with migratory behavior and complex life cycle represent a challenge for evaluating natal sites among individuals. Private and government-sponsored initiatives resulted in the successful introduction and naturalization of Chinook salmon (Oncorhynchus tshawytscha) throughout northern and southern Patagonia in South America. These migratory fish breed in freshwater, but spend most of their life at sea feeding, forming abundant populations in several watersheds draining into the southeast Pacific Ocean. We used single nucleotide polymorphisms (SNPs) combined with genetic structure and mixed-stock analyses to evaluate natal sites of Chinook salmon at-sea caught in one estuary and two coastal locations compared to reference populations from breeding sites in freshwater. Firstly, Bayesian individual-assignment analyses revealed no genetic structure among adults caught off the coast of the Tolten River and migrating (maturing) adults caught in Tolten River estuary, suggesting they likely belong to a single population. Secondly, mixed-stock genetic analyses revealed that most at-sea Chinook salmon caught in one estuary and two coastal locations likely originated from spawners from the nearest river (90-95%), with a small contribution from adjacent watersheds (5-10%). This appears consistent with Chinook salmon populations in their native range in which juveniles migrate short distances (100-200 km) from their river of origin to coastal feeding grounds, some of which became donor of propagules for non-native Chinook salmon populations under study. Mixed-stock genetic analyses provide considerable potential to identify the population of origin of Chinook salmon mixtures caught off the coast. They also seem an appropriate proof of concept to help identify potential immigrants from other watersheds as well as migration patterns and invasion pathways in a non-native species.

genetics↗