Genome-wide association study for Streptococcus iniae in Nile tilapia (Oreochromis niloticus) identifies a significant QTL for disease resistance.

Streptococcus iniae is a problematic gram-positive bacterium negatively affecting Nile tilapia (Oreochromis niloticus), one of the main aquacultural species produced worldwide. The aim of this study was to identify the genetic architecture of survival to S. iniae and identify single nucleotide polymorphism (SNPs) linked to quantitative trait loci (QTL) related to survival to S. iniae challenge. With this purpose, Nile tilapia from the Spring Genetics breeding program were sent to a controlled S. iniae challenge test where phenotypes were scored as dead for fish that died during challenge test and survivors for the fish alive at the termination of the test. Additionally, fin-clip samples from all fish in the test were collected for DNA extraction. Out of 1904 fish in the challenge test, tissue samples of 321 fish were sent for genotyping using double digest restriction site associated DNA sequencing (ddRADseq). After quality control and filtering, 9,085 SNPs were used to perform a genome-wide association study (GWAS). A significant signal in LG8 was observed indicating association with survival to S. iniae challenge, with SNPs explaining from 12% to 26% of the genetic variance. To demonstrate the usefulness of marker assisted selection (MAS) to selectively breed fish for survival to S. iniae, offspring of breeding candidates classified as "resistant" and "susceptible" based on haplotypes of the four most significant markers were sent to a controlled S. iniae challenge test. At the end of the test, the differences in mortality between the two groups were strikingly different with a final cumulative percent mortality of less than 1% and 73% for offspring from "resistant" and "susceptible" parents, respectively. These results demonstrate that MAS for improved resistance to S. iniae is feasible.

Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax).

Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes (ITPK1, PLK4, HSPA4L, REEP1, CHMP2, MRPL35, and SCUBE) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20-43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes.

Accuracy of genomic selection for a sib-evaluated trait using identity-by-state and identity-by-descent relationships.

BACKGROUND: GBLUP (genomic best linear unbiased prediction) uses high-density single nucleotide polymorphism (SNP) markers to construct genomic identity-by-state (IBS) relationship matrices. However, identity-by-descent (IBD) relationships can be accurately calculated for extremely sparse markers. Here, we compare the accuracy of prediction of genome-wide breeding values (GW-BV) for a sib-evaluated trait in a typical aquaculture population, assuming either IBS or IBD genomic relationship matrices, and by varying marker density and size of the training dataset. METHODS: A simulation study was performed, assuming a population with strong family structure over three subsequent generations. Traditional and genomic BLUP were used to estimate breeding values, the latter using either IBS or IBD genomic relationship matrices, with marker densities ranging from 10 to ~1200 SNPs/Morgan (M). Heritability ranged from 0.1 to 0.8, and phenotypes were recorded on 25 to 45 sibs per full-sib family (50 full-sib families). Models were compared based on their predictive ability (accuracy) with respect to true breeding values of unphenotyped (albeit genotyped) sibs in the last generation. RESULTS: As expected, genomic prediction had greater accuracy compared to pedigree-based prediction. At the highest marker density, genomic prediction based on IBS information (IBS-GS) was slightly superior to that based on IBD information (IBD-GS), while at lower densities (≤100 SNPs/M), IBD-GS was more accurate. At the lowest densities (10 to 20 SNPs/M), IBS-GS was even outperformed by the pedigree-based model. Accuracy of IBD-GS was stable across marker densities performing well even down to 10 SNPs/M (2.5 to 6.1% reduction in accuracy compared to ~1200 SNPs/M). Loss of accuracy due to reduction in the size of training datasets was moderate and similar for both genomic prediction models. The relative superiority of (high-density) IBS-GS over IBD-GS was more pronounced for traits with a low heritability. CONCLUSIONS: Using dense markers, GBLUP based on either IBD or IBS relationship matrices proved to perform better than a pedigree-based model. However, accuracy of IBS-GS declined rapidly with decreasing marker densities, and was even outperformed by a traditional pedigree-based model at the lowest densities. In contrast, the accuracy of IBD-GS was very stable across marker densities.

Frustrative reward omission increases aggressive behaviour of inferior fighters.

Animals use aggressive behaviour to gain access to resources, and individuals adjust their behaviour relative to resource value and own resource holding potential (RHP). Normally, smaller individuals have inferior fighting abilities compared with larger conspecifics. Affective and cognitive processes can alter contest dynamics, but the interaction between such effects and that of differing RHPs has not been adjudged. We investigated effects of omission of expected reward (OER) on competing individuals with contrasting RHPs. Small and large rainbow trout (Oncorhynchus mykiss) were conditioned to associate a light with reward. Thereafter, the reward was omitted for half of the fish prior to a contest between individuals possessing a 36-40% difference in RHP. Small control individuals displayed submissive behaviour and virtually no aggression. By contrast, small OER individuals were more aggressive, and two out of 11 became socially dominant. Increased aggression in small OER individuals was accompanied by increased serotonin levels in the dorsomedial pallium (proposed amygdala homologue), but no changes in limbic dopamine neurochemistry were observed in OER-exposed individuals. The behavioural and physiological response to OER in fish indicates that frustration is an evolutionarily conserved affective state. Moreover, our results indicate that aggressive motivation to reward unpredictability affects low RHP individuals strongest.

Decline of genetic variability in a captive population of Pacific white shrimp Penaeus (Litopenaeus) vannamei using microsatellite and pedigree information

Background: The objective of this study was to estimate the decline of genetic variability and the changes in effective population size in three shrimp populations. One was a wild population collected at several points in the Mexican Pacific Ocean. The other two populations were different generations (7 and 9) from a captive population selected for growth and survival. Microsatellite markers and pedigree were both used to assess genetic variability and effective population size. Results: Using 26 loci, both captive populations showed a decline in the expected heterozygosity (20%) and allelic diversity indices (48 to 91%) compared to the wild population (P < 0.05). The studied captive populations did not differ significantly from each other regarding their expected heterozygosity or allelic diversity indices (P > 0.05). Effective population size estimates based on microsatellites declined from 48.2 to 64.0% in cultured populations (P < 0.05) compared to the wild population. Conclusions: An important decline of genetic variability in the cultured selected population due to domestication, and evidence of a further smaller decline in effective population size across generations in the selected population were observed when analyzing pedigree (41%) and microsatellite data (37%). Pedigree keeping is required to prevent the decline of effective population size and maintain genetic variability in shrimp breeding programs, while microsatellites are useful to assess effective population size changes at the population level.