GenoTriplo: A SNP genotype calling method for triploids.

Triploidy is very useful in both aquaculture and some cultivated plants as the induced sterility helps to enhance growth and product quality, as well as acting as a barrier against the contamination of wild populations by escapees. To use genetic information from triploids for academic or breeding purposes, an efficient and robust method to genotype triploids is needed. We developed such a method for genotype calling from SNP arrays, and we implemented it in the R package named GenoTriplo. Our method requires no prior information on cluster positions and remains unaffected by shifted luminescence signals. The method relies on starting the clustering algorithm with an initial higher number of groups than expected from the ploidy level of the samples, followed by merging groups that are too close to each other to be considered as distinct genotypes. Accurate classification of SNPs is achieved through multiple thresholds of quality controls. We compared the performance of GenoTriplo with that of fitPoly, the only published method for triploid SNP genotyping with a free software access. This was assessed by comparing the genotypes generated by both methods for a dataset of 1232 triploid rainbow trout genotyped for 38,033 SNPs. The two methods were consistent for 89% of the genotypes, but for 26% of the SNPs, they exhibited a discrepancy in the number of different genotypes identified. For these SNPs, GenoTriplo had >95% concordance with fitPoly when fitPoly genotyped better. On the contrary, when GenoTriplo genotyped better, fitPoly had less than 50% concordance with GenoTriplo. GenoTriplo was more robust with less genotyping errors. It is also efficient at identifying low-frequency genotypes in the sample set. Finally, we assessed parentage assignment based on GenoTriplo genotyping and observed significant differences in mismatch rates between the best and second-best couples, indicating high confidence in the results. GenoTriplo could also be used to genotype diploids as well as individuals with higher ploidy level by adjusting a few input parameters.

Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system.

In most animals, sex determination occurs at conception, when sex chromosomes are segregated following Mendelian laws. However, in multiple reptiles and fishes, this genetic sex can be overridden by external factors after fertilization or birth. In some species, the genetic sex may also be governed by multiple genes, further limiting our understanding of sex determination in such species. We used the European sea bass (Dicentrarchus labrax) as a model and combined genomic (using a single nucleotide polymorphism chip) and transcriptomic (RNA-Sequencing) approaches to thoroughly depict this polygenic sex determination system and its interaction with temperature. We estimated genetic sex tendency (eGST), defined as the estimated genetic liability to become a given sex under a liability threshold model for sex determination, which accurately predicts the future phenotypic sex. We found evidence that energetic pathways, concerning the regulation of lipids and glucose, are involved in sex determination and could explain why females tend to exhibit higher energy levels and improved growth compared to males. Besides, early exposure to high-temperature up-regulated sox3, followed by sox9a in individuals with intermediate eGST, but not in individuals showing highly female-biased eGST, providing the most parsimonious explanation for temperature-induced masculinization. This gonadal state was maintained likely by DNA methylation and the up-regulation of several genes involved in histone modifications, including jmjd1c Overall, we describe a sex determination system resulting from continuous genetic and environmental influences in an animal. Our results provide significant progress in our understanding of the mechanisms underlying temperature-induced masculinization in fish.

Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass.

BACKGROUND: Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. RESULTS: We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A. CONCLUSIONS: We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.

The genetic correlation between feed conversion ratio and growth rate affects the design of a breeding program for more sustainable fish production.

BACKGROUND: Most fish breeding programs aim at improving growth rate and include feed conversion ratio (FCR) neither in the breeding goal nor in the selection index, although decreasing FCR is known to increase farm profit and decrease environmental impacts. This is because FCR is difficult to measure in fish that live in groups and FCR is assumed to have a favourable (negative) genetic correlation with growth, although the magnitude of this correlation is unknown. We investigated the effect of the genetic correlation between growth and FCR on the economic and environmental responses of a two-trait breeding goal (growth and FCR), compared to a single-trait breeding goal (growth only). Next, we evaluated the weights to assign to growth and FCR in a two-trait breeding goal to maximize sustainability of fish production. METHODS: We used pseudo-best linear unbiased prediction (BLUP) index calculations to simulate a breeding program for sea bass. For the single-trait breeding goal, the trait in the breeding goal and in the index was thermal growth coefficient (TGC) and for the two-trait breeding goal, the traits in the breeding goal were TGC and FCR and the traits in the index were TGC and percentage of fat in the dorsal muscle (an indirect measure of FCR). We simulated responses to selection for genetic and phenotypic correlations between TGC and FCR ranging from 0 to - 0.8. Then, in the two-trait breeding goal, we calculated the economic return and the change in eutrophication when using economic values (EV) or environmental values (ENV). RESULTS: When the genetic correlation between TGC and FCR was lower than - 0.45, we found major differences in economic returns and in eutrophication between single and two-trait breeding programs. At a correlation of - 0.25, the two-trait breeding goal based on EV increased economic return by 25% compared to the single-trait breeding goal, while using ENV decreased eutrophication by 1.34% per ton of fish produced after one generation of selection. CONCLUSIONS: The genetic correlation between TGC and FCR affects the magnitude of economic losses due to omitting FCR in the breeding program. In addition, the genetic correlation affects the importance of choosing EV or ENV to reduce eutrophication and increase profit.

Derivation of economic values for production traits in aquaculture species.

BACKGROUND: In breeding programs for aquaculture species, breeding goal traits are often weighted based on the desired gains but economic gain would be higher if economic values were used instead. The objectives of this study were: (1) to develop a bio-economic model to derive economic values for aquaculture species, (2) to apply the model to determine the economic importance and economic values of traits in a case-study on gilthead seabream, and (3) to validate the model by comparison with a profit equation for a simplified production system. METHODS: A bio-economic model was developed to simulate a grow-out farm for gilthead seabream, and then used to simulate gross margin at the current levels of the traits and after one genetic standard deviation change in each trait with the other traits remaining unchanged. Economic values were derived for the traits included in the breeding goal: thermal growth coefficient (TGC), thermal feed intake coefficient (TFC), mortality rate (M), and standard deviation of harvest weight ([Formula: see text]). For a simplified production system, improvement in TGC was assumed to affect harvest weight instead of growing period. Using the bio-economic model and a profit equation, economic values were derived for harvest weight, cumulative feed intake at harvest, and overall survival. RESULTS: Changes in gross margin showed that the order of economic importance of the traits was: TGC, TFC, M, and [Formula: see text]. Economic values in € (kg production)-1 (trait unit)-1 were: 0.40 for TGC, -0.45 for TFC, -7.7 for M, and -0.0011 to -0.0010 for [Formula: see text]. For the simplified production system, similar economic values were obtained with the bio-economic model and the profit equation. The advantage of the profit equation is its simplicity, while that of the bio-economic model is that it can be applied to any aquaculture species, because it can include any limiting factor and/or environmental condition that affects production. CONCLUSIONS: We confirmed the validity of the bio-economic model. TGC is the most important trait to improve, followed by TFC and M, and the effect of [Formula: see text] on gross margin is small.

APIS: an updated parentage assignment software managing triploids induced from diploid parents.

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximizes the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96-192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1,232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low false discovery rate (<0.01), and excellent specificity (0.96-0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents.

An investigation of links between metabolic rate and feed efficiency in European sea bass Dicentrarchus labrax.

Feed efficiency (FE) is the amount of body weight gain for a given feed intake. Improving FE through selective breeding is key for sustainable finfish aquaculture but its evaluation at individual level is technically challenging. We therefore investigated whether individual routine metabolic rate (RMR) was a predictor of individual FE in the European sea bass Dicentrarchus labrax, a major species in European mariculture. The European sea bass has three genetically distinct populations across its geographical range, namely Atlantic (AT), West Mediterranean (WM), and East Mediterranean (EM). We compared FE and RMR of fish from these three populations at 18 or 24 °C. We held 200 fish (62 AT, 66 WM, and 72 EM) in individual aquaria and fed them from ad libitum down to fasting. FI was assessed for an ad libitum feeding rate and for a fixed restricted ration (1% of metabolic body weight·day-1, with metabolic body weight = body weight0.8). After being refed 12 wk in a common tank, individual RMR was measured over 36 h by intermittent flow respirometry. There was a significant effect of temperature whereby fish at 18 °C had greater mean FE (P < 0.05) and lower RMR (P < 0.001). There was also a significant effect of population, where AT fish had lower FE (P < 0.05) and greater RMR (P < 0.001) than WM and EM, at both temperatures. Despite these differences in temperature and population means, individual FE and RMR were not significantly correlated (P > 0.05). Therefore, although the results provide evidence of an association between metabolic rate and FE, RMR was not a predictor of individual FE, for reasons that require further investigation.

Combining Individual Phenotypes of Feed Intake With Genomic Data to Improve Feed Efficiency in Sea Bass.

Measuring individual feed intake of fish in farms is complex and precludes selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content that were possibly linked to FCR. The 588 fish were derived from a full factorial mating between parental lines divergently selected for high (F+) or low (F-) weight loss at fasting. The pedigree was known back to the great grand-parents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs which allowed to calculate the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable (genomic h2 = 0.47 and 0.76, respectively) and strongly genetically correlated (-0.98) meaning that, under restricted feeding, faster growing fish were more efficient. FCR and growth rate in aquariums were also significantly better for fish with both parents from F- (1.38), worse for fish with two parents F+ (1.51) and intermediate for cross breed fish (F+/F- or F-/F+ at 1.46). Muscle fat content was positively genetically correlated to growth rate in aquarium and during fasting. Thus, selecting for higher growth rate in aquarium, lower weight loss during fasting and fatter fish could improve FCR in aquarium. Improving these traits would also improve FCR of fish in normal group rearing conditions, as we showed experimentally that groups composed of fish with good individual FCR were significantly more efficient. The FCR of groups was also better when the fish composing the groups had, on average, lower estimated breeding values for growth rate during fasting (losing less weight). Thus, improving FCR in aquarium and weight loss during fasting is promising to improve FCR of fish in groups but a selection response experiment needs to be done. Finally, we showed that the reliability of estimated breeding values was higher (from+10% up to +125%) with a genomic-based BLUP model than with a traditional pedigree-based BLUP, showing that genomic data would enhance the accuracy of the prediction of EBV of selection candidates.