Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information.

Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

Genomics to accelerate genetic improvement in tilapia.

Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth-, quality- and robustness-related traits. Novel phenotyping technologies (i.e. phenomics), lower-cost whole-genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.

Genetic (co)variation in skin pigmentation patterns and growth in rainbow trout.

From a physiological-behavioral perspective, it has been shown that fish with a higher density of black eumelanin spots are more dominant, less sensitive to stress, have higher feed intake, better feed efficiency and therefore are larger in size. Thus, we hypothesized that genetic (co)variation between skin pigmentation patterns and growth exists and it is advantageous in rainbow trout. The objective of this study was to determine the genetic relationships between skin pigmentation patterns and BW in a breeding population of rainbow trout. We performed a genetic analysis of pigmentation traits including dorsal color (DC), lateral band (LB) intensity, amount of spotting above (SA) and below (SB) the lateral line, and BW at harvest (HW). Variance components were estimated using a multi-trait linear animal model fitted by restricted maximum likelihood. Estimated heritabilities were 0.08±0.02, 0.17±0.03, 0.44±0.04, 0.17±0.04 and 0.23±0.04 for DC, LB, SA, SB and HW, respectively. Genetic correlations between HW and skin color traits were 0.42±0.13, 0.32±0.14 and 0.25±0.11 for LB, SA and SB, respectively. These results indicate positive, but low to moderate genetic relationships between the amount of spotting and BW in rainbow trout. Thus, higher levels of spotting are genetically associated with better growth performance in this population.

Bayesian genome-wide association analysis for body weight in farmed Atlantic salmon (Salmo salar L.).

We performed a genome-wide association study to detect markers associated with growth traits in Atlantic salmon. The analyzed traits included body weight at tagging (BWT) and body weight at 25 months (BW25M). Genotypes of 4662 animals were imputed from the 50K SNP chip to the 200K SNP chip using fimpute software. The markers were simultaneously modeled using Bayes C to identify genomic regions associated with the traits. We identified windows explaining a maximum of 3.71% and 3.61% of the genetic variance for BWT and BW25M respectively. We found potential candidate genes located within the top ten 1-Mb windows for BWT and BW25M. For instance, the vitronectin (VTN) gene, which has been previously reported to be associated with cell growth, was found within one of the top ten 1-Mb windows for BWT. In addition, the WNT1-inducible-signaling pathway protein 3, melanocortin 2 receptor accessory protein 2, myosin light chain kinase, transforming growth factor beta receptor type 3 and myosin light chain 1 genes, which have been reported to be associated with skeletal growth in humans, growth stimulation during the larval stage in zebrafish, body weight in pigs, feed conversion in chickens and growth rate of sheep skeletal muscle respectively, were found within some of the top ten 1-Mb windows for BW25M. These results indicate that growth traits are most likely controlled by many variants with relatively small effects in Atlantic salmon. The genomic regions associated with the traits studied here may provide further insight into the functional regions underlying growth traits in this species.

Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.

A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.

Evidence of recent signatures of selection during domestication in an Atlantic salmon population.

Selective breeding practices in Atlantic salmon aquaculture have been carried out intensively since the 1970s. Along with the phenotypic improvement of fish, we expect to observe genomic regions showing evidence of selection for traits related to growth and age at sexual maturation, as well as traits involved in the domestication process. This is mainly linked to the increase in the frequency of favourable alleles at loci that affect the traits of interest in the breeding population. In this study we searched for signatures of selection in the Cermaq Atlantic salmon broodstock, a Mowi strain, which was derived from wild Norwegian populations, and is now farmed in British Columbia, Canada. A 6.5K SNP array was used to genotype 202 fish from the Cermaq population, and the genotypes were compared with four wild populations from Norway. We used three methods based on FST values to detect signatures of selection. Forty four markers showing divergence in allele frequency were identified as outliers by the three detection methods, suggesting the presence of signatures of selection in the Cermaq population relative to their wild counterparts. Markers identified as outliers are associated with molecular functions that could be related to the selection for economically important traits (e.g., growth) as well as the domestication process (e.g., response to pathogens and environmental stressors). Of particular interest were three outlier markers that had been previously associated with grilsing (i.e., early sexual maturation) an undesirable trait, which has been heavily selected against in Atlantic salmon aquaculture. This study provides clear evidence of the presence of signatures of selection and domestication in a farmed Atlantic salmon population.

Characterization of Mycobacterium salmoniphilum as causal agent of mycobacteriosis in Atlantic salmon, Salmo salar L., from a freshwater recirculation system.

Thirty Atlantic salmon, Salmo salar L., with low corporal condition relative to other fish present in the culture system, were sampled from a freshwater recirculation pisciculture located in Chile. The most characteristic signs and lesions were cachexia and presence of multiple greyish-white granulomas within internal organs. The external and internal lesions, along with the microscopic, histologic and biochemical findings, were consistent with mycobacteriosis. The identification of Mycobacterium salmoniphilum as the causal agent of the lesions was possible through the use of molecular analyses. This study represents the first report of Mycobacterium salmoniphilum in a freshwater recirculation system and the first case of fish mycobacteriosis described in Chile.

Assessing footprints of selection in commercial Atlantic salmon populations using microsatellite data.

Relatively large rates of response to traits of economic importance have been observed in different selection experiments in salmon. Several QTL have been mapped in the salmon genome, explaining unprecedented levels of phenotypic variation. Owing to the relatively large selection intensity, individual loci may be indirectly selected, leaving molecular footprints of selection, together with increased inbreeding, as its likely relatives will share the selected loci. We used population differentiation and levels of linkage disequilibrium in chromosomes known to be harbouring QTL for body weight, infectious pancreatic necrosis resistance and infectious salmon anaemia resistance to assess the recent selection history at the genomic level in Atlantic salmon. The results clearly suggest that the marker SSA0343BSFU on chromosome 3 (body weight QTL) showed strong evidence of directional selection. It is intriguing that this marker is physically mapped to a region near the coding sequence of DVL2 , making it an ideal candidate gene to explain the rapid evolutionary response of this chromosome to selection for growth in Salmo salar. Weak evidence of diversifying selection was observed in the QTL associated with infectious pancreatic necrosis and infectious salmon anaemia resistance. Overall, this study showed that artificial selection has produced important changes in the Atlantic salmon genome, validating QTL in commercial salmon populations used for production purposes according to the recent selection history.

Production of probiotic biomass (Lactobacillus casei) in goat milk whey: comparison of batch, continuous and fed-batch cultures.

This contribution examines the technical feasibility of producing high added value probiotic biomass from deproteinized and non-supplemented milk whey. The kinetics of growth of Lactobacillus casei in deproteinized goat milk whey was analyzed. Experiments in batch, continuous and fed-batch conditions were conducted in a 3 L fully instrumented bioreactor. Final substrate and biomass concentrations, yields and productivities are reported for different culture strategies. A kinetic analysis was conducted to characterize biomass production, product inhibition effects, and substrate consumption rates. Due to the strong product inhibition, fed-batch cultures at high biomass concentration rendered higher productivity (0.45 g L(-1) h(-1)) than batch and continuous cultures (0.11 g L(-1) h(-1)), complete lactose conversions (<1.0 g of lactose/L at the end of each fed-batch cycle), and a product with higher viable cell counts (2 x 10(10) cell/g of freeze-dried product). Based on our result, high-cell density fed-batch strategies are recommended for commercial production of probiotic L. casei biomass.

Effect of co-inoculation with mycorrhiza and rhizobia on the nodule trehalose content of different bean genotypes.

Studies on Rhizobium-legume symbiosis show that trehalose content in nodules under drought stress correlates positively with an increase in plant tolerance to this stress. Fewer reports describe trehalose accumulation in mycorrhiza where, in contrast with rhizobia, there is no flux of carbohydrates from the microsymbiont to the plant. However, the trehalose dynamics in the Mycorrhiza-Rhizobium-Legume tripartite symbiosis is unknown. The present study explores the role of this tripartite symbiosis in the trehalose content of nodules grown under contrasting moisture conditions. Three wild genotypes (P. filiformis, P. acutifolis and P. vulgaris) and two commercial genotypes of Phaseolus vulgaris (Pinto villa and Flor de Mayo) were used. Co-inoculation treatments were conducted with Glomus intraradices and a mixture of seven native rhizobial strains, and trehalose content was determined by GC/MS. The results showed a negative effect of mycorrhizal inoculation on nodule development, as mycorrhized plants showed fewer nodules and lower nodule dry weight compared to plants inoculated only with Rhizobium. Mycorrhizal colonization was also higher in plants inoculated only with Glomus as compared to plants co-inoculated with both microsymbionts. In regard to trehalose, co-inoculation negatively affects its accumulation in the nodules of each genotype tested. However, the correlation analysis showed a significantly positive correlation between mycorrhizal colonization and nodule trehalose content.

Buckeye Rot of Tomato Caused by Phytophthora capsici in Michoacan, Mexico.

The state of Michoacan is one of the main fresh pepper (Capsicum annuum L.) and tomato (Lycopersicon esculentum Mill.) producers in Mexico. During the last 5 years, pepper-producing areas in the state have become unproductive due to root-rotting pathogens, mainly Phytophthora capsici Leonian. Growers trying to overcome losses have increased tomato production in areas previously used for pepper production. Field-grown tomato plants with diseased green tomato fruits were observed in Tacambaro, Michoacan, during August 2002. Initially, brown-to-black lesions developed on fruits in contact with soil, followed by infection of the upper fruits in the raceme. Lesions enlarged and dark zonate "buckeye" bands were formed in the affected area. Diseased fruit turned mushy. Symptoms observed were similar to those described for buckeye rot of tomato (1). Diseased fruit were surface disinfested with 70% ethanol, cut into 0.5-cm slices, and incubated in a moist chamber to induce mycelial colonization. Isolation from mycelial tufts growing through the tomato slice was performed 3 days later, and mycelia was transferred to PARP selective medium (corn meal agar (CMA) plus ampicillin, pimaricin, rifampicin, and pentachloronitrobenzene). P. capsici was consistently isolated from diseased tomato fruits. Oomycete identification was based on sporangial and gametangial characteristics of cultures grown on CMA (1). Sporangia microscopically observed were spherical, broadly ellipsoid or obovoid with one papilla (occasionally two papillae), and deciduous with a long pedicel. Chlamydospores were not present (2). The isolates were heterothallic, and oogonia with amphigynous antheridia were observed in pairings with A1 and A2 isolates of P. capsici. Three isolates were A1 and two isolates were A2. To confirm pathogenicity, two experiments were performed using 20 healthy unwounded green tomatoes. One isolate of each mating type was tested. Isolates were grown for 5 days on CMA, and fruits were inoculated by placing P. capsici in contact with the fruit. Inoculated fruits were kept in a moist chamber at room temperature (17 to 20°C). Initial symptoms in the form of brown-to-black lesions appeared 24 h after inoculation. One week after inoculation, symptoms were similar to those observed in field-grown plants, and P. capsici was recovered from the margins of the diseased tissue. All inoculated fruits rotted. To our knowledge, this is the first report of P. capsici causing buckeye rot on tomato in Michoacan and of the presence of both mating types in the area. Reference: (1) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society. St. Paul MN, 1996. (2) M. Aragaki and J. Y. Uchida. Mycologia 93:137, 2001.

Three new European cases of urofacial (Ochoa) syndrome.

We report on three European cases of urofacial (Ochoa) syndrome. This entity was originally described in Colombian patients and very few cases have been reported from other countries. It is likely that they may be missed because of variability of the urinary problems and failure to recognize the characteristic facial grimacing. Establishing an early diagnosis has important consequences for the management and prognosis of urinary problems in these patients.

Acetylene reduction activity on the root of cactaceous plants

El estado de Nuevo León tiene zonas semidesérticas con variedad de plantas cactáceas, pero con poca información sobre la entrada del nitrógeno al ecosistema, se supone que ocurre por la simboisis de Rhizhobium-leguminosas. Se exploró la actividad de reducción de acetileno (fijación biológica de N2) o ARA por bacterias asociadas a raíces de cactaceas; se determinó la relación bacteriana de la rizósfera: suelo (R:S) y se clasificaron las bacterias involucradas, para lo cual se colectaron cactáceas del municipio de Mina, Nuevo León. Hay bacterias con ARA en las raíces de Echinocereus pectinatus, E. conglomeratus, E. enneacanthus, E. blanckii, Echinocatus horizonthalonius, Coryphantha neglecta, C. macromeris, Ancistrocactus scheeri, Thelocactus bicolor y Opuntia cantabrigiensis. La relación R:S fue de 11:1 y las bacterias encontradas fueron: Enterobacter spp., Citrobacter spp., Erwinia spp; Bacillus spp, y Azospirillum lipoferum, lo que sugiere que las bacterias relacionadas con la entrada de nitrógeno al ecosistema son un grupo diverso

[Kidney injuries in children]. / Traumatismos renales en niños.

From 1972 to 1985 blunt renal injuries were recorded in 58 children up to the age of 14 years. Early evaluation and treatment of these children is essential in order to preserve maximum renal function. The majority responded well to careful conservative, nonoperative management. Some of those requiring surgical intervention, responded well to initial conservative treatment followed by surgical intervention conducted as an delayed procedure. The critical injuries need early operative intervention.

[Vesico-urethral injuries in patients with pelvic fractures]. / Traumatismos vesicouretrales en pacientes con fracturas pélvicas.

Rupture of the bladder and posterior urethra is a serious complication of pelvis fracture. From 1972 to 1984, 61 patients were admitted for genitourinary injuries. We present a review of 5 cases of bladder and urethral posterior injuries associated with pelvic fractures. We assess some current issues in the treatment and diagnosis.

Analisis de la septicemia bacteriana en el neonato en los ultimos cinco anos en el Servicio de Pediatria del Hospital Regional Leonardo Guzman, de Antofagasta. / Analysis of neonatal septicemia in the last five years in the Servicio de Pediatria, Hospital Regional Leonardo Guzman of Antofagasta

Se analizan las historias clinicas de 15 neonatos con Septicemia comprobada bacteriologicamente, hospitalizados entre 1974 y 1978 en el Hospital Dr. Leonardo Guzman,de Antofagasta. En este periodo nacem 19.018 ninos,de los cuales l.883 pesan menos de 2.500 g. En 41 (2,1%o) se plantea la sospecha clinica de informaccion, la cual se comprueba mediante aislamiento del germen en 15 casos (0,8%), de los cuales 7 corresponden a preterminos (3,7%) y 8 a termino (0,47%). Ocho ninos na cen por parto normal y el resto corresponde a algun tipo de distocia. El APGAR al minuto es superior a 6 en 7 casos, inferior en 6 y 2 no existe registro. No existe diferencia de sexo (8 varones y 7 mujeres).Germenes Gram negativos se identifican en 13 casos,correspondiendo a Aerobacter/Klebsiella el 53,3%. Los signos y sintomas encontrados corresponden a lo descrito en la literatura.El hemograma revela desviacion a izquierda en 8 casos y mas de 20% de baciliformes en relacion al numero total de neutrofilos en 7 casos. El antibiotico mas usado fue la Gentamicina asociada a alguna penicilina. La letalidad global fue de 26,7%. Se plantean las medidas tendientes a mejorar el pronostico de esta patologia