Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population

International audienceNile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1 ) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2 ) map the genomic regions associated with these traits and identify candidate genes, 3 ) evaluate the accuracy of breeding value prediction using genomic data, and 4 ) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia ) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; −0.60 and −0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a , ghrh and eif4e3 . The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes

Improving the efficiency of feed utilization in poultry by selection. 1. Genetic parameters of anatomy of the gastro-intestinal tract and digestive efficiency

<p>Abstract</p> <p>Background</p> <p>Feed costs represent about 70% of the costs of raising broilers. The main way to decrease these costs is to improve feed efficiency by modification of diet formulation, but one other possibility would be to use genetic selection. Understanding the genetic architecture of the gastro-intestinal tract (GIT) and the impact of the selection criterion on the GIT would be of particular interest. We therefore studied the genetic parameters of AMEn (Apparent metabolisable energy corrected for zero nitrogen balance), feed efficiency, and GIT traits in chickens.</p> <p>Genetic parameters were estimated for 630 broiler chickens of the eighth generation of a divergent selection experiment on AMEn. Birds were reared until 23 d of age and fed a wheat-based diet. The traits measured were body weight (BW), feed conversion ratio (FCR), AMEn, weights of crop, liver, gizzard and proventriculus, and weight, length and density of the duodenum, jejunum and ileum.</p> <p>Results</p> <p>The heritability estimates of BW, FCR and AMEn were moderate. The heritability estimates were higher for the GIT characteristics except for the weights of the proventriculus and liver. Gizzard weight was negatively correlated with density (weight to length ratio) of duodenum, jejunum and ileum. Proventriculus and gizzard weights were more strongly correlated with AMEn than with FCR, which was not the case for intestine weight and density.</p> <p>Conclusions</p> <p>GIT traits were largely dependent on genetics and that selecting on AMEn or FCR would modify them. Phenotypic observations carried out in the divergent lines selected on AMEn were consistent with estimated genetic correlations between AMEn and GIT traits.</p

Improving the efficiency of feed utilization in poultry by selection. 2. Genetic parameters of excretion traits and correlations with anatomy of the gastro-intestinal tract and digestive efficiency

<p>Abstract</p> <p>Background</p> <p>Poultry production has been widely criticized for its negative environmental impact related to the quantity of manure produced and to its nitrogen and phosphorus content. In this study, we investigated which traits related to excretion could be used to select chickens for lower environmental pollution.</p> <p>The genetic parameters of several excretion traits were estimated on 630 chickens originating from 2 chicken lines divergently selected on apparent metabolisable energy corrected for zero nitrogen (AMEn) at constant body weight. The quantity of excreta relative to feed consumption (CDUDM), the nitrogen and phosphorus excreted, the nitrogen to phosphorus ratio and the water content of excreta were measured, and the consequences of such selection on performance and gastro-intestinal tract (GIT) characteristics estimated. The genetic correlations between excretion, GIT and performance traits were established.</p> <p>Results</p> <p>Heritability estimates were high for CDUDM and the nitrogen excretion rate (0.30 and 0.29, respectively). The other excretion measurements showed low to moderate heritability estimates, ranging from 0.10 for excreta water content to 0.22 for the phosphorus excretion rate. Except for the excreta water content, the CDUDM was highly correlated with the excretion traits, ranging from -0.64 to -1.00. The genetic correlations between AMEn or CDUDM and the GIT characteristics were very similar and showed that a decrease in chicken excretion involves an increase in weight of the upper part of the GIT, and a decrease in the weight of the small intestine.</p> <p>Conclusion</p> <p>In order to limit the environmental impact of chicken production, AMEn and CDUDM seem to be more suitable criteria to include in selection schemes than feed efficiency traits.</p

Species composition in the Molobicus hybrid tilapia strain

The “Molobicus” hybrid breeding programme was initiated to improve tilapia growth performance in brackish water. The base population was created by backcrossing F1 Oreochromis niloticus GIFT strains × feral O. mossambicus to O. mossambicus and selective breeding conducted for performance in brackish water with two lines selected in extensive or intensive rearing conditions. A panel of ten diagnostic SNP markers was applied to estimate the species composition at different stages in the Molobicus programme including parental stocks, F1 and seventh generation fish from the selective lines. The O. aureus-specific markers tested revealed zero or negligible contribution from O. aureus to all the groups analysed. Feral O. mossambicus possessed an estimated 0.98 frequency of O. mossambicus-specific alleles, while GIFT samples had an estimated mean frequency of 0.88 O. niloticus-specific alleles. Hybrid F1 GIFT × feral O. mossambicus samples demonstrated close to 50:50 allele frequencies from O. niloticus and O. mossambicus for seven of the eight SNP loci tested. Analysis of the combined seventh generation Molobicus samples revealed a significant excess of O. niloticus alleles in six out of the eight SNPs tested, with this trend being more pronounced in the line selected in intensive culture conditions and showing increased body weight. PCR-based SNP assays such as these can be used to inform on the individual species contribution of fish stocks and provide tools for the genetic management of the tilapia species and future breeding programmes

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Dans un contexte de développement durable, trouver des moyens de réduire l’impact environnemental de la production avicole est d’une grande importance. L’estimation des paramètres génétiques de nombreux caractères de rejets chez les lignées divergentes D+ et D- nous a permis de définir plusieurs critères pertinents à prendre en compte dans les schémas de sélection pour maîtriser l’excrétion des poulets. Nous avons également montré que l’utilisation de ces critères n’aurait pas de conséquences négatives sur les caractéristiques d’importance économique pour l’industrie avicole. Enfin, nous avons pu montrer que la morphologie du tractus gastro-intestinal était très fortement impliquée dans les variations d’excrétion des poulets. En effet, un important développement du proventricule et du gésier et une réduction du développement de l’intestin grêle sont associés aux animaux produisant moins de rejets et présentant une meilleure efficacité digestive.The reduction of the environmental impact of poultry production is crucial to ensure its sustainability. The estimation of genetic parameters of several excretion characteristics in D+ and D- divergent lines allowed us to define pertinent criteria that could be included in selection schemes in view to reduce chicken excretion. We also showed that using these criteria would not have negative consequences on the traits of economic importance for poultry industry. Finally, we showed that the gastro-intestinal tract morphology is highly implied in the variations of excretion between chickens. Indeed, an important development of the proventriculus and gizzard and a reduction of the small intestine development were associated with birds producing less excreta and showing a higher digestive efficiency