Commercial implementation of genomic selection in Tasmanian Atlantic salmon: Scheme evolution and validation.

Genomic information was included for the first time in the prediction of breeding values for Atlantic salmon within the Australian Salmon Enterprises of Tasmania Pty Ltd selective breeding program in 2016. The process to realize genomic selection in the breeding program begun in 2014 with the scheme finalized and fully implemented for the first time in 2018. The high potential of within family selection to accelerate genetic gain, something not possible using the traditional pedigree-based approach, provided the impetus for implementation. Efficient and effective genotyping platforms are essential for genomic selection. Genotype data from high density arrays revealed extensive persistence of linkage disequilibrium in the Tasmania Atlantic salmon population, resulting in high accuracies of both imputation and genomic breeding values when using imputed data. Consequently, a low-density novel genotype-by-sequence assay was designed and incorporated into the scheme. Through the use of a static high- and dynamic low-density genotyping platforms, an optimized genotyping scheme was devised and implemented such that all individuals in every year class are genotyped efficiently while maximizing the genetic gains and minimizing costs. The increase in the rates of genetic gain attributed to the implementation of genomic selection is significant across both the breeding programs primary and secondary traits. Substantial improvement in the ability to select parents prior to progeny testing is observed across multiple years. The resultant economic impacts for the industry are considerable based on the increases in genetic gain for traits achieved within the breeding program and the use of genomic selection for commercial production.

[Project Report: Evaluation of the Practical Year (PY) at the Charité Medical School, University Medicine Berlin]. / Evaluation des Medizinischen Praktischen Jahres (PJ) an der Charité­Universitätsmedizin Berlin.

BACKGROUND: In Germany, the final year of medical school consists of a series of clinical externships termed "Practical Year" (PY). Logbooks have been introduced to document the clinical experience and the value of the teaching program (First Ordinance amending the Licensing Regulations for Physicians, July 14, 2012). However, little is known about how PY education is experienced by students, what problems they face, what support they seek to manage their problems, and how the logbooks contribute to training. OBJECTIVE: We assessed the PY education at the Charité Medical School (University Medicine Berlin) in terms of the requirement profile, quality of training, logbooks, satisfaction, and general conditions. MATERIAL AND METHODS: We developed a questionnaire to assess PY education by relying on medical students' experiences. This tool was developed in parallel with the introduction of the logbooks. We contacted 6,068 students between May 2014 to September 2017 via e-mail. The students were asked to participate in the evaluation on a voluntary basis and answer 39 questions. The questionnaire was completed using an anonymous online form, taking into account legal data protection regulations. RESULTS: We evaluated 1,957 questionnaires (31.1 %). The students were mostly satisfied (67.6 %) with their supervision. Patient encounters were, for the most part (85.5 %), perceived as informative, and the quality of continuing education as high (91.3 %), and most students (76.1 %) were directly involved in patient care. The students (87.8 %) felt that they had made progress during the PY teaching period, although the logbooks were rarely (14 %) used and apparently not reviewed by the teaching staff. The students judged some rotations harshly when they were dissatisfied with both teaching and supervision. CONCLUSIONS: In general, the PY experience at the Charité was rated positively. Some rotations receiving poor evaluations desperately need to be reviewed. The role of the logbook seems to be imperfectly defined. The survey results suggest that further evaluation of our program is needed with ongoing participation of students and their representatives.

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon.

BACKGROUND: A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts. RESULTS: We report genome wide association studies (GWAS) using fish measured for sexual maturation in freshwater or the marine environment. Genotypic data from a custom 50 K single nucleotide polymorphism (SNP) array was used to identify 13 significantly associated SNP for freshwater maturation with the most strongly associated on chromosomes 10 and 11. A higher number of associations (48) were detected for marine maturation, and the two peak loci were found to be the same for both traits. The number and broad distribution of GWAS hits confirmed a highly polygenetic nature, and GWAS performed separately within males and females revealed sex specific genetic behaviour for loci co-located with positional candidate genes phosphatidylinositol-binding clathrin assembly protein-like (picalm) and membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (magi2). CONCLUSIONS: The results extend earlier work and have implications for future applied breeding strategies to delay maturation in this important aquaculture species.

Evolution of Sex Determination Loci in Atlantic Salmon.

Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male fish carry a single copy of the male specific region, consistent with an XX/XY or male heterogametric sex system. Haplotype analysis revealed deep divergence between the putatively ancestral locus on chromosome 2, compared with loci on chromosomes 3 and 6. Haplotypes in fish carrying either the chromosome 3 or 6 loci were nearly indistinguishable, indicating a founding event that occurred following the speciation event that defined Salmo salar from other salmonids. These findings highlight the evolutionarily fluid state of sex determination systems in salmonids, and resolve to the sequence level differences in animals with divergent sex lineages.

Populations of Pacific oysters Crassostrea gigas respond variably to elevated CO2 and predation by Morula marginalba.

Ocean acidification is anticipated to decrease calcification and increase dissolution of shelled molluscs. Molluscs with thinner and weaker shells may be more susceptible to predation, but not all studies have measured negative responses of molluscs to elevated pCO2. Recent studies measuring the response of molluscs have found greater variability at the population level than first expected. Here we investigate the impact of acidification on the predatory whelk Morula marginalba and genetically distinct subpopulations of the Pacific oyster Crassostrea gigas. Whelks and eight family lines of C. gigas were separately exposed to ambient (385 ppm) and elevated (1000 ppm) pCO2 for 6 weeks. Following this period, individuals of M. marginalba were transferred into tanks with oysters at ambient and elevated pCO2 for 17 days. The increase in shell height of the oysters was on average 63% less at elevated compared to ambient pCO2. There were differences in shell compression strength, thickness, and mass among family lines of C. gigas, with sometimes an interaction between pCO2 and family line. Against expectations, this study found increased shell strength in the prey and reduced shell strength in the predator at elevated compared to ambient pCO2. After 10 days, the whelks consumed significantly more oysters regardless of whether C. gigas had been exposed to ambient or elevated CO2, but this was not dependent on the family line and the effect was not significant after 17 days. Our study found an increase in predation after exposure of the predator to predicted near-future levels of estuarine pCO2.