Genetic improvement of canine hip dysplasia through sire selection across countries
Wang, S. ; Strandberg, E. ; Viklund, ; Windig, J.J. ; Malm, S. ; Lewis, T. ; Laloë, D. ; Leroy, G. - \ 2019
The Veterinary Journal 248 (2019). - ISSN 1090-0233 - p. 18 - 24.
Canine - Estimated breeding value - Hip dysplasia - International breeding programme - Stochastic simulation
Breeding against canine hip dysplasia (HD) may benefit from the importation of foreign sires. When foreign sires are evaluated on a different HD scale, this may diminish the efficacy. Using stochastic simulations, we evaluated genetic change and inbreeding levels for different scenarios of importing sires with high genetic merit for HD. Population size and genetic parameters (e.g. heritability, accuracy of selection, genetic correlation) were based on actual data for HD in Golden retrievers and Labrador retrievers in the UK and Sweden. For countries with different HD scales and an estimated breeding value (EBV) evaluation in place, the importation was useful if imported sires had EBV rankings in the top 50% and if genetic correlations between EBV systems were above 0.85. When importing sires with EBV rankings in the top 10%, moderate accuracies of EBVs (>0.40) and moderately strong genetic correlations (>0.70) were needed. Selection against HD without the importation of sires may increase inbreeding levels, while the importation of sires can decrease inbreeding levels. For national genetic evaluation and selection programmes, importing sires with high genetic merit can be an effective breeding strategy, but care is needed to estimate reliable EBVs.
Optimism for mitigation of climate warming impacts for sea turtles through nest shading and relocation
Esteban, N. ; Laloe, J.O. ; Kiggen, F.S.P.L. ; Ubels, S.M. ; Becking, L.E. ; Meesters, Erik ; Berkel, J. ; Hays, G.C. ; Christianen, M.J.A. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
Increasing incubation temperatures may threaten the viability of sea turtle populations. We explored opportunities for decreasing incubation temperatures at a Caribbean rookery with extreme female-biased hatchling production. To investigate the effect of artificial shading, temperatures were measured under simple materials (white sheet, white sand, palm leaves). To test natural drivers of incubation temperature, temperatures were measured at average nest depths with shading on two beaches. Results from a pilot experiment suggest the most effective material was palm leaves. Shading decreased temperatures by a mean of 0.60 °C (SE = 0.10 °C, N = 20). Variation between beaches averaged 1.88 °C (SE = 0.13 °C, N = 20). We used long-term rookery data combined with experimental data to estimate the effect on sex ratio: relocation and shading could shift ratios from current ranges (97–100% female) to 60–90% female. A conservation mitigation matrix summarises our evidence that artificial shading and nest relocation are effective, low-cost, low-technology conservation strategies to mitigate impacts of climate warming for sea turtles.
Which individuals to choose to update the reference population? Minimizing the loss of genetic diversity in animal genomic selection programs
Eynard, Sonia E. ; Croiseau, Pascal ; Laloë, Denis ; Fritz, Sebastien ; Calus, Mario P.L. ; Restoux, Gwendal - \ 2018
G3 : Genes Genomes Genetics 8 (2018)1. - ISSN 2160-1836 - p. 113 - 121.
Genetic diversity - Genomic selection - GenPred - Optimal contribution - Reference population - Shared data resources
Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.
|Updating reference population in genomic selection for genetic diversity conservation. What can we learn from real data and simulations?
Eynard, S.E. ; Croiseau, P. ; Laloë, Denis ; Calus, M.P.L. ; Fritz, S. ; Restoux, G. - \ 2017
Implications of location accuracy and data volume for home range estimation and fine-scale movement analysis : comparing Argos and Fastloc-GPS tracking data
Thomson, J.A. ; Börger, L. ; Christianen, M.J.A. ; Esteban, N. ; Laloë, J.O. ; Hays, G.C. - \ 2017
Marine Biology 164 (2017)10. - ISSN 0025-3162
The advent of Fastloc-GPS is helping to transform marine animal tracking by allowing the collection of high-quality location data for species that surface only briefly. We show how the improved location accuracy of Fastloc-GPS compared to Argos tracking is expected to lead to far more accurate home range estimates, particularly for animals moving over the scale of a few km. We reach this conclusion using simulated data and home range estimates derived from empirical tracking data for green sea turtles (Chelonia mydas) equipped with Argos linked Fastloc-GPS tags at three different foraging areas (western Indian Ocean, Western Australia, and Caribbean). Poor-quality Argos locations (e.g., location classes A, B) produced home range estimates ranging from 10 to 100 times larger than those derived from Fastloc-GPS data, whereas high-quality Argos locations (location classes 1–3) produced home range estimates that were generally comparable to those derived from Fastloc-GPS data. However, the limited number of Argos class 1–3 locations obtained for all three turtles—an average of 14.6 times more Fastloc-GPS locations were obtained compared to Argos class 1–3 locations—resulted in blurred patterns of space use. In contrast, the high volume of Fastloc-GPS locations revealed fine-scale movements in striking detail (i.e., use of discrete patches separated by just a few 100 m). We recommend careful consideration of the effects of location accuracy and data volume when developing sampling regimes for marine tracking studies and make recommendations regarding how sampling can be standardized to facilitate meaningful spatial and temporal comparisons of space use.
|Which individuals to phenotape? Optimal design of reference population for genomic selection while maintaining genetic diversity
Eynard, S.E. ; Laloe, D. ; Croiseau, P. ; Calus, M.P.L. ; Fritz, S. ; Restoix, G. - \ 2016
A mixed-model QTL analysis for salt tolerance in seedlings of crop-wild hybrids of lettuce
Wei, Z. ; Julkowska, M.M. ; Laloe, J.O. ; Hartman, Y. ; Boer, G.J. ; Michelmore, R.W. ; Tienderen, P.H. van; Testerink, C. ; Schranz, M.E. - \ 2014
Molecular Breeding 34 (2014)3. - ISSN 1380-3743 - p. 1389 - 1400.
quantitative trait loci - root-system architecture - salinity tolerance - high-density - plant-root - nonhost resistance - lactuca-saligna - downy mildew - linkage maps - bread wheat
Cultivated lettuce is more sensitive to salinity stress than its wild progenitor species potentially due to differences in root architecture and/or differential uptake and accumulation of sodium. We have identified quantitative trait locis (QTLs) associated with salt-induced changes in root system architecture (RSA) and ion accumulation using a recombinant inbred line population derived from a cross between cultivated lettuce (Lactuca sativa ‘Salinas’) and wild lettuce (L. serriola). Components of RSA were quantified by replicated measurements of seedling growth on vertical agar plates containing different concentrations of NaCl in a controlled growth chamber environment. Accumulation of sodium and potassium ions was measured in replicates of greenhouse-grown plants watered with 100 mM NaCl water. A total of 14 QTLs were identified using multi-trait linkage analysis, including three major QTLs associated with general root development, root growth in salt stress condition, and ion accumulation. The three major QTLs, qRC9.1, qRS2.1, and qLS7.2, were linked with markers E35/M59-F-425, LE9050, and LE1053, respectively. This study provides regions of lettuce genome contributing to salt-induced changes in RSA and ion accumulation. Future fine-mapping of major QTLs will identify candidate genes underlying salt stress tolerance in cultivated lettuce.