Domestication and genetic improvement: balancing improved production against increased disease risks from inbreeding.

Successful selective breeding programmes have been under way in aquacultural species for many decades. Gains in growth rate as high as 900% have been reported. Programmes selecting for resistance and/or tolerance of specific pathogens have had similar success. However, no more than 10-20% of global aquaculture production is sourced from well-documented breeding programmes. Direct selection for resistance and/or tolerance in biosecure breeding programmes is difficult when classical breeding methods are used. Genomic selection is widely expected to become the most effective mode of selection against pathogens in fish and shellfish. In this paper, the authors explore the possible negative effects of genetic improvement programmes, especially those that stem from interactions between genetics and other components of the aquaculture production system, particularly disease. The main focus is the interaction between selective breeding and biosecurity. They suggest that a self-amplifying feedback loop can be created when biosecurity regulation causes a progressive reduction in genetic diversity and an increase in inbreeding, especially in smallholder hatcheries and farms in developing countries. The resulting inbreeding depression causes increased susceptibility to disease, which in turn increases the frequency and severity of epizootics. Greater losses due to disease again increase regulatory pressures and the cycle begins once more. This 'biosecurity-agro-economic-genetic' feedback loop is analogous to an 'extinction vortex' in wild populations. The authors believe that the loop can be broken by biosecure, aquacultural, genetic exchange networks, modelled on existing breed associations for terrestrial domestic animals. Such networks would constitute a global aquacultural gene pool, with enhanced environmental resilience, long-term capacity for adaptation and minimal inbreeding depression. However, such networks will also require innovative new pathogen management procedures, documentation and regulations to facilitate the exchange of broodstock and seed while still maintaining effective biosecurity.

Des programmes d'élevage sélectif d'espèces aquacoles sont mis en œuvre avec succès depuis plusieurs décennies. Des gains de croissance atteignant 900 % ont ainsi été enregistrés. Les programmes de sélection pour la résistance et/ou la tolérance vis-à-vis de certains agents pathogènes ont également été couronnés de succès. Néanmoins, la production issue des programmes de sélection connus et documentés ne représente guère plus de 10 à 20 % de la production aquacole mondiale. Il est difficile de procéder à une sélection directe des traits de résistance et/ou de tolérance tout en garantissant un bon niveau de biosécurité dès lors que les méthodes utilisées relèvent de l'élevage classique. La sélection génomique présente un immense potentiel et deviendra sans aucun doute la méthode de sélection la plus efficace contre les agents pathogènes affectant les poissons, les mollusques et les crustacés. Les auteurs analysent les effets négatifs potentiels associés aux programmes d'amélioration génétique, en particulier ceux résultant d'interactions entre les composantes génétiques et d'autres aspects, notamment sanitaires, des systèmes de production aquacole. Leur analyse est principalement axée sur les interactions entre l'élevage sélectif et la biosécurité. Ils évoquent le risque de création d'une boucle de réaction auto-amplificatrice dans les contextes où l'application de la réglementation en matière de biosécurité entraîne un déclin progressif de la diversité génétique et une hausse de la consanguinité, en particulier dans les écloseries et fermes de petite dimension des pays en développement. Le phénomène de dépression de consanguinité qui en résulte entraîne une sensibilité accrue aux maladies, ce qui à son tour accroît la fréquence et la gravité des épizooties. Le regain des pertes dues à ces maladies se traduit par de nouvelles pressions exercées au plan réglementaire, de sorte que le cycle est relancé une nouvelle fois. Cette boucle de réaction biosécurité-agroéconomie-génétique est similaire à la « spirale de l'extinction ¼ qui affecte les populations sauvages. Les auteurs considèrent que cette boucle peut être rompue en mettant en place des réseaux d'échange de ressources génétiques biosécurisées pour l'aquaculture, sur le modèle des associations d'éleveurs opérant dans le domaine des espèces domestiques terrestres. Ces réseaux permettraient de constituer un patrimoine génétique mondial pour l'aquaculture doté d'une résilience environnementale améliorée, d'une capacité d'adaptation sur le long terme et d'un niveau minime de dépression de consanguinité. Néanmoins, de tels réseaux nécessiteront des procédures nouvelles et innovantes de gestion des agents pathogènes, ainsi qu'une documentation et des réglementations spécifiques afin de faciliter les échanges de stocks de géniteurs et de semence tout en garantissant un niveau approprié de biosécurité.

Hace ya muchos decenios que se vienen aplicando con éxito programas de reproducción selectiva de especies acuícolas, con aumentos de las tasas de crecimiento que llegan a veces hasta un 900%. Los programas de selección de rasgos de resistencia y/o de tolerancia a determinados patógenos han cosechado un éxito similar. Sin embargo, no más de un 10% a un 20% de la producción acuícola mundial tiene su origen en programas de reproducción bien documentados. La selección directa de rasgos de resistencia y/o tolerancia mediante programas reproductivos que ofrezcan garantías de seguridad biológica resulta difícil cuando se aplican métodos clásicos de cría. Ahora cunde la expectativa de que la selección genómica llegue a ser el modo de selección más eficaz contra la presencia de patógenos en el pescado y el marisco. Los autores examinan los posibles efectos negativos de los programas de mejora genética, sobre todo los que resultan de la interacción entre la genética y otros componentes del sistema de producción acuícola, en particular las enfermedades, prestando especial atención a la interacción entre cría selectiva y seguridad biológica y postulando que se puede engendrar un ciclo de retroalimentación que se va autoamplificando cuando los reglamentos de seguridad biológica inducen una progresiva reducción de la diversidad genética y un incremento de la consanguinidad (o endogamia), especialmente en los pequeños viveros y granjas de países en desarrollo. La consiguiente depresión endogámica genera una mayor sensibilidad a las enfermedades, lo que a su vez incrementa la frecuencia y gravedad de las epizootias. El aumento de las pérdidas por enfermedades se traduce en una mayor presión reglamentaria, y así da comienzo de nuevo el ciclo. Este ciclo de retroalimentación entre seguridad biológica, agroeconomía y genética es análogo a un «vórtice de extinción¼ en las poblaciones silvestres. Los autores piensan que es posible quebrar esta dinámica recurriendo a redes de intercambio de material genético biológicamente seguro en el ámbito de la acuicultura, a imagen de las asociaciones que existen entre los criadores de animales domésticos terrestres. Estas redes constituirían una reserva mundial de genes de acuicultura que ofrecerían mayor resiliencia a las condiciones ambientales y una duradera capacidad de adaptación, así como niveles mínimos de depresión endogámica. Semejantes redes, sin embargo, también exigirán nuevos y novedosos procedimientos de lucha contra patógenos, sistemas de documentación y reglamentos que faciliten el intercambio de genitores y alevines manteniendo a la vez niveles elevados de seguridad biológica.

Morphological and molecular approaches revealed a new species of snapping shrimp genus Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from Lakshadweep Islands, India.

A new species of the alpheid genus Alpheus Fabricius, 1798, Alpheus sulcipalma sp. nov., is described and illustrated based on the specimens collected from the intertidal zone of Agatti Island, Lakshadweep, India at 0.5-1.0 m depth. This species belongs to the A. edwardsii group by absences of tooth in the orbital hoods and presence of compressed major chela with dorsal and ventral notches. Alpheus sulcipalma sp. nov. is morphologically closely related with A. pacificus Dana, 1852, absence of balaeniceps crests in the minor chela and absences of spine in the merus of major pereiopod of both sexes. However, the new species differs from A. pacificus in presence of strong and broad triangular groove on the dorsolateral and dorsomesial surface of the palm of major chela; length ratio and armature of fingers and palm of minor chela, carpus segments of second and third pereiopods and telson length. The results of phylogenetic analyses using partial sequences of mitochondrial COI gene data compared between A. sulcipalma sp. nov. with congener species which strongly support the description of new species with available limited sequences. The interspecific genetic divergences of the COI gene for A. sulcipalma sp. nov. and A. pacificus were observed higher in ranges (11.1-28.9%).

Comparative assessment of genetic variability in the populations of endemic and endangered yellow catfish, Horabagrus brachysoma (Teleostei: Horabagridae), based on allozyme, RAPD, and microsatellite markers.

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.

A new alpheid shrimp, Alpheus mannarensis sp. nov. (Crustacea; Decapoda; Alpheidae) from Gulf of Mannar, Southern India.

A new species of the genus Alpheus Fabricius, 1798, A. mannarensis sp. nov. is described and represented based on the materials collected from the shallow and rocky reefs, Gulf of Mannar (Thoothukudi waters), Southern India. This is the first report of Alpheus species from the Gulf of Mannar region. The new species is assigned to the Alpheus brevirostris group, and is distinguished from other species of this group by the combination of the following features: rostral ridge lower than orbital hood in lateral view and postrostral carina not extended to the middle of the carapace, palm of major chela with a transverse groove near the base of dactylus, the ultimate segment of the third maxilliped slender, fingers of minor chela of male slightly longer than palm, the first carpal segment of second pereiopods shorter than second segment, merus of third pereiopods slender and unarmed, dactylus of third pereiopods slender and subspatulate, and unique colour patterns of longitudinal light lines on the reddish body.

Two new records of hippolytoid shrimps, Lysmata hochi Baeza amp; Anker, 2008 (Decapoda: Lysmatidae) and Lysmata amboinensis (de Man, 1888) from Lakshadweep Islands, India with taxonomic notes.

The present study reports the new records of two species of the hippolytid shrimp genus Lysmata Risso, 1816 in the water off Lakshadweep Islands, India from the Arabian Sea, viz. Lysmata hochi Baeza Anker, 2008 and Lysmata amboinensis (De Man, 1888) with more taxonomic information. Moreover, L. hochi is the first distributional report from the Indian Ocean. It is morphologically similar to L. kuekenthali and differences are discussed. Colour pattern and morphological trait of L. amboinensis are very close to L. grabhami which also differs in the presence of anti-penultimate segment of 3rd maxilliped more than 2.0 times as long as penultimate segment and stylocerite does not reaching the distal end of the cornea. These specimens were obtained at a depth of 0.5-2 m from the intertidal region of Agatti Island. Additionally, we estimated pairwise genetic distances for these two species and congeneric species using cytochrome oxidase subunit I gene sequences where interspecific distances ranged from 11-25.8 %.

Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers.

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.

New record of Thor hainanensis Xu amp; Li, 2014 and taxonomical remarks on Lysmata ternatensis de Man, 1902 (Decapoda: Thoridae amp; Lysmatidae) from the Lakshadweep Islands, India.

The present study reports the new record of Thor hainanensis Xu Li, 2014, on the basis of material from Agatti Islands in the Lakshadweep, India. This species was recently described from Hainan Island, China. Relationship of this species to two closely related species (T. paschalis and T. amboinensis) is discussed in this manuscript. Similarly, the present study also reports the rediscovery of other species, Lysmata ternatensis De Man, 1902 from the Lakshadweep waters with detailed taxonomic description. The present specimens were found to occur in the intertidal region in small crevices and rocks at a depth of 0.5-2.0 m. Genetic analysis using the mitochondrial COI sequences for both the species reveals close agreement for the morphological identification and showed the significant variation from the closely related species.

DNA barcoding Indian freshwater fishes.

DNA barcoding is a promising technique for species identification using a short mitochondrial DNA sequence of cytochrome c oxidase I (COI) gene. In the present study, DNA barcodes were generated from 72 species of freshwater fish covering the Orders Cypriniformes, Siluriformes, Perciformes, Synbranchiformes, and Osteoglossiformes representing 50 genera and 19 families. All the samples were collected from diverse sites except the species endemic to a particular location. Species were represented by multiple specimens in the great majority of the barcoded species. A total of 284 COI sequences were generated. After amplification and sequencing of 700 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two-parameter (K2P) distances within-species, genera, families, and orders were 0.40%, 9.60%, 13.10%, and 17.16%, respectively. DNA barcode discriminated congeneric species without any confusion. The study strongly validated the efficiency of COI as an ideal marker for DNA barcoding of Indian freshwater fishes.

Sulfidation of silver nanoparticle reduces its toxicity in zebrafish.

Chemical transformations of metal nanoparticles can be an important way to mitigate nanoparticle toxicity. Sulfidation of silver nanoparticle (AgNPs) is a natural process shown to occur in environment. Very few studies, employing microbes and embryonic stages of zebrafish, have shown reduction in AgNPs toxicity as a direct result of sulfidation. However the feasibility of reducing nanoparticle toxicity by sulfidation of AgNPs has never been studied in adult vertebrates. In this study, we have used adult zebrafish as a model to study the efficacy of sulfidation of AgNPs in reducing nanoparticle toxicity by employing a battery of biomarkers in liver and brain. While AgNPs enhanced liver oxidative stress, altered detoxification enzymes and affected brain acetylcholinesterase activity, sulfidation of AgNPs resulted in significant alleviation of changes in these parameters. Histopathological analyses of liver and sulphydryl levels also support the significance of sulfidated AgNPs in controlling the toxicity of AgNPs. Our study provides the first biochemical data on the importance of sulfidation of AgNPs in reducing biological toxicity in adult vertebrates.

Role of nitric oxide in motility and fertilizing ability of sperm of Heteropneustes fossilis (Bloch.).

The presence of neuronal nitric oxide synthase (nNOS), inducible NOS (iNOS) and nitric oxide (NO) in the testis of seasonally breeding catfish has previously been demonstrated. The present study was aimed to investigate the presence of NO in fish gametes and its role in sperm physiology and strengthen the previous findings. NO, a biological signalling molecule is synthesized during the conversion of l-arginine to l-citrulline by nitric oxide synthases (NOS) in the presence of NADPH and oxygen. In the present study, a considerable amount of NO content was detected in the fresh sperm suspension of fish. A drastic reduction in NO content of the sperm suspension was observed after cryopreservation. Ovarian fluid collected from freshly stripped eggs also contained a substantial amount of NO. Further, effects of a NO donor, sodium nitroprusside (SNP), and NOS inhibitor, N-(G)-nitro-l-arginine-methyl ester (l-NAME) were evaluated on motility and fertilizing ability of fresh and cryopreserved sperm. The percentage of motile fresh sperm (66.2±3.7%) was enhanced (P<0.05) by SNP at the dose of 10(-3)M, whereas the greater and lesser concentrations of SNP did not influence the percentage of motility as compared to the control. However, a significant reduction in the percentage of motile fresh sperm was observed at the tested doses of 10(-3)M and 10(-4)M of l-NAME. The maximum reduction (23.0±3.4%) was evoked at the greatest concentration (10(-3)M); while at the smallest dose of 10(-5)M, reduction was insignificant. Ovarian fluid also enhanced sperm motility. Altogether, findings of the present study suggest that NO plays an important role in sperm performance of fish.

DNA barcoding Indian marine fishes.

DNA barcoding has been adopted as a global bio-identification system for animals in recent years. A major national programme on DNA barcoding of fish and marine life was initiated in India by the authors during 2006 and 115 species of marine fish covering Carangids, Clupeids, Scombrids, Groupers, Sciaenids, Silverbellies, Mullids, Polynemids and Silurids representing 79 Genera and 37 Families from the Indian Ocean have been barcoded for the first time using cytochrome c oxidase I gene (COI) of the mtDNA. The species were represented by multiple specimens and a total of 397 sequences were generated. After amplification and sequencing of 707 base pair fragment of COI, primers were trimmed which invariably generated a 655 base pair barcode sequence. The average Kimura two parameter (K2P) distances within species, genera, families, orders were 0.30%, 6.60%, 9.91%, 16.00%, respectively. In addition to barcode-based species identification system, phylogenetic relationships among the species have also been attempted. The neighbour-joining tree revealed distinct clusters in concurrence with the taxonomic status of the species.

Population genetic structure of endemic and endangered yellow catfish, Horabagrus brachysoma, using allozyme markers.

The allozyme variation and population genetic structure of Horabagrus brachysoma in three natural populations from the southern part of the Western Ghats region, India, were investigated by polyacrylamide gel electrophoresis. Variations at 14 loci from 14 enzyme systems were analyzed. The allozyme analysis revealed a high level of genetic variation in this species, with an average of observed alleles per locus of 2.357 and observed heterozygosity of 0.178. The positive value of the fixation index (FIS=0.507) implied a significant deficiency of heterozygosity at the population level. The highly significant probability (P<0.0001) for the overall loci suggested that the three sample sets were not part of the same gene pool.

Cortical deafness following head injury -a case report.

Cortical deafness is a rare entity. Only few case reports are available. In this paper, a case of right fronto-temporal contusion following head injury causing bilateral cortical deafness has been reported. Most of the cases reported in the past were because of cerebral infarcts due to arterial occlusion.

Bera in normal neonates and infants: (Some observations on maturation of auditory pathways).

This study includes eight normal, not at-risk for deafness, neonates and infants of age ranging from 2 days to 1 year. BERA was done at 2 kHz. frequency at 80 dB intensity. In the majority of the subjects, only wave I, II, III and V could be definitely identified. It was observed that latencies of waves decreased as age of neonate/infant increased. Decrease of latency was more marked in first 6 months of life (wave V from 7.2 ms to 6. / ms) as compared to next six months (wave V from 6. 1 ms to 5.9 ms). This could be because of rapid myelination in the first six months of life.