Kuldeep Lal

Abstract We characterized mitochondrial ATP synthase (ATPase) 6 and 8 genes in Labeo calbasu (Hamilton, 1822) and determined genetic variation in wild populations across the natural distribution in Indian rivers. A total of 206 individuals were sampled from 11 riverine sites belonging to distinct geographical locations covering five major river basins. Sequencing of 842 base pairs of ATPase 6/8 revealed 21 haplotypes with haplotype diversity ranging from 0.1250 (River Satluj) to 0.8846 (River Bhagirathi). Analysis of molecular variance (AMOVA) of mitochondrial DNA (mtDNA) data revealed significant genetic differentiation among sites (FST = 0.192, p < 0.0001) which was indicative of moderate level of genetic structuring in the wild L. calbasu populations. The patterns of genetic divergence and haplotype network of mtDNA revealed distinct clades present in Indian rivers. The analysis of data demonstrated the potential of ATPase 6/8 genes in determining the genetic diversity and indicated considerable sub-structuring in wild calbasu populations present in different rivers.

Abstract Pangasius pangasius, an endangered freshwater fish species, is an important component of capture fishery from Indian rivers. Samples collected through commercial catches from three riverine populations were analyzed with cytb (307 bp) and ATPase6&8 (842 bp) regions for population variation and differentiation. The sequences of the both the mitochondrial regions revealed high haplotype and low nucleotide diversity. Shallow genetic diversity based on ATPase6&8 was observed, however its haplotypes network clearly indicated two distinct mitochondrial lineages. Mismatch distribution suggested population bottlenecks followed by expansion in Mahanadi population. The present study indicated the…

Abstract The complete nucleotide sequence of Channa asiatica mitochondrial (mtDNA) genome was determined in this study. The genome sequence (GenBank accession number KJ930190) was 16,550 base pairs in length, and the gene content and organization on the mitochondrial genome were similar to the other Channa fishes. The overall base composition of C. asiatica mitogenome is 29.4% A, 26.3% T, 15.3% G, 29.0% C, with a high A + T content of 55.7%. The mitochondrial sequence could provide useful genetic information for studying the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

Abstract Silonia silondia is a commercially important food fish. Samples collected through commercial catches from four rivers in India are described by sequence analysis of two molecular markers. Cytochrome b (1140 bp) and ATPase 6/8 (842 bp) genes were analyzed, which represented high level of genetic differentiation within populations of S. silondia. The sequence alignments of cytochrome b and ATPase 6/8 genes revealed 13 and 11 different haplotypes, respectively. The sequences of both the mitochondrial regions revealed high haplotype and low nucleotide diversities. The patterns of genetic diversity and haplotype networks clearly indicated two distinct mitochondrial lineages, however, haplotypes from both the lineages were not specifically assigned to any population. The results confirm the utility of molecular markers generating baseline information, useful for planning effective strategies for conservation, management and sustainability of Silond catfish fishery.

Heat shock proteins (Hsps) are typically associated with stress response and tolerance. The Indian catfish, Clarias batrachus, is a freshwater air-breathing hypoxia tolerant teleost and is potentially important catfish species for aquaculture and for its economic value as food. The present study aimed at determining the transcriptional response of three Hsps, CbHsc71, CbHsp90α and CbHsp10 in hypoxia tolerant Indian catfish, C. batrachus, under experimental and natural hypoxia. The expression profile of above three genes were studied under different periods of hypoxia, through qRT-PCR. Primers were designed from ESTs obtained through SSH libraries constructed from hypoxia treated fishes. The Hsp10 ESTs and deduced protein was in silico characterized for its ORF and for its physical and chemical properties, respectively, using GeneScan, blastp, scanprosite, superfamily and other softwares. A phylogenetic tree was constructed based on deduced amino acid sequences of Hsc71, Hsp90α, Hsp90β of Homo sapiens and other fishes along with CbHsp10 protein in MEGA4. The deduced protein sequences of CbHsp10 was found to have characteristic Hsp10 family signatures, and it is proposed for inclusion of methionine in the consensus sequences of Hsp10 family signature, after the "proline" residue. At transcription level, these genes were found to be differentially regulated under hypoxia stress, in different tissues of C. batrachus. The CbHsc71 and CbHsp90α were up-regulated after short and long-term hypoxia, whereas CbHsp10 was significantly down-regulated after short-term hypoxia. The differential expression of these Hsps may play a role in protection and survival under hypoxia induced oxidative stress in C. batrachus.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium da...

This study is aimed to identify polymorphic microsatellite markers and establish their potential for population genetics studies in three carp (family cyprinidae; subfamily cyprininae) species, Labeo rohita, Catla catla and Cirrhinus mrigala through use of cyprinid primers. These species have high commercial value and knowledge of genetic variation is important for management of farmed and wild populations. We tested 108 microsatellite primers from 11 species belonging to three different cyprinid subfamilies, Cyprininae, Barbinae and Leuciscinae out of which 63 primers (58.33%) successfully amplified orthologous loci in three focal species. Forty-two loci generated from 29 primers were polymorphic in these three carp species. Sequencing of amplified product confirmed the presence of SSRs in these 42 loci and orthologous nature of the loci. To validate potential of these 42 polymorphic loci in determining the genetic variation, we analyzed 486 samples of three focal species collected from Indus, Ganges and Brahmaputra river systems. Results indicated significant genetic variation, with mean number of alleles per locus ranging from 6.80 to 14.40 and observed heterozygosity ranging from 0.50 to 0.74 in the three focal species. Highly significant (P < 0.00001) allelic homogeneity values revealed that the identified loci can be efficiently used in population genetics analysis of these carp species. Further, thirty-two loci from 19 primers were useful for genotyping in more than one species. The data from the present study was compiled with cross-species amplification data from previous results on eight species of subfamily cyprininae to compare cross-transferability of microsatellite loci. It was revealed that out of 226 heterologous loci amplified, 152 loci that originated from 77 loci exhibited polymorphism and 45 primers were of multispecies utility, common for 2-7 species.

The present study examined partial cytochrome b gene sequence of mitochondrial DNA for polymorphism and its suitability to determine the genetic differentiation in wild Labeo rohita. The 146 samples of L. rohita were collected from nine distant rivers; Satluj, Brahmaputra, Son, Chambal Mahanadi, Rapti, Chauka, Bhagirathi and Tons were analyzed. Sequencing of 307 bp of Cyto b gene revealed 35 haplotypes with haplotype diversity 0.751 and nucleotide diversity (π) 0.005. The within population variation accounted for 84.21% of total variation and 15.79% was found to among population. The total Fst value, 0.158 (P < 0.05) was found to be significant. The results concluded that the partial cyto b is polymorphic and can be a potential marker to determining genetic stock structure of L. rohita wild population.

Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained, out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes.

Hearinge valuation of sixtyfour neonates and infants selected randomly from the outpatient departments of E. N. T., Paediatrics and Obstetrics wards was done by behavioral observation audiometry (BOA), tympanometry, acoustic reflex and auditory brainstem evoked response audiometry (ABR) in selected cases. A good correlation was found between BOA and ABR. Tympanometry and acoustic reflex measurements were not found to be useful for evaluating hearing status in infants and neonates. It was finally recommended that BOA should be used for screening hearing in infants and neonates. Cases who fail in BOA should be subjected to ABR for establishing true threshold of hearing.

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 (F IS = 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.

The population structure of Cirrhinus mrigala from different riverine locations in India was investigated using allozyme and microsatellite loci. C. mrigala samples were obtained from ten rivers belonging to Indus, Ganges, Brahmaputra and Mahanadi basins. Seven (29.2%) out of 24 allozyme loci and seven microsatellite loci were polymorphic, including five from our earlier work. Significant deviation (P < 0.05) from the Hardy–Weinberg expectations were evident for two allozyme loci: G6PDH⁎, XDH⁎, and two microsatellite loci: MFW17, R-12F, in different samples. Both markers types demonstrated concordant results and various estimates revealed genetic variability within the subpopulations but surprisingly low level (θ = 0.015 to 0.02) of genetic differentiation among C. mrigala from different river samples. AMOVA analysis also indicated low differentiation among subpopulations. Common ancestry in the prehistoric period and possible exchange of individuals between rivers in different river basins such as Indus and Ganges could have been responsible for the observed low level of genetic differentiation among wild mrigal populations.

Abstract Recent years have witnessed a rise in sensitivity towards protection of natural genetic resources and the environment at the international level. This is evident from the implementation of the conven-tion on biodiversity (CBD). To conserve and optimize utilization of its ...

ABSTRACT Genetic variation was assessed in 367 samples of Labeo calbasu from twelve riverine locations across India using nine polymorphic microsatellite loci. The mean value of the observed heterozygosity (Hobs.) after correction for null allele ranged from 0.50 (loci R3* and Lr38* in Satluj) to 1.00 (Lr29* in Bhagirathi) whereas mean number of alleles per locus ranged from 4.66 (Narmada) to 10.11 (Ghaghra). The genetic data corrected for possible null alleles, analyzed with score test did not reveal significant deviation from HW equilibrium at any locus in any population after probability level was adjusted for Bonferroni corrections. Pair wise Fst and allelic homogeneity tests indicated distinct population structure in wild L. calbasu. Fst for all the samples combined over all loci was found to be 0.035 suggesting that 3.5% of the total variation was due to genetic differentiation. Analysis of Molecular Variance (AMOVA) indicated that most of the genetic variability was within populations from the same geographical locations.

Twenty-seven enzyme systems, six random amplified polymorphic DNA (RAPD) primers, and two microsatellite loci were tested to determine intraspecific divergence in the natural population of the endangered Indian featherback fish, Chitala chitala, for the first time. The 262 samples of C. chitala were collected from six riverine locations in India: the Satluj, Ganga (Ghagra, Bhagirathi, and Brahmaputra), Mahanadi, and Narmada river systems. The analysis revealed population subdivisions, with an F(ST) value from 0.1235 (95% confidence 0.0868-0.1621) for RAPD and a combined F(ST) of 0.0344 (95% confidence 0.0340-0.0350) for microsatellite loci. An analysis of 38 allozyme loci did not reveal any polymorphism in the samples from any of the riverine localities; a possible explanation for this could be that the ancestors of Chitala could have faced a population reduction in prehistoric periods, as low allozyme variation is also reported for other species of Chitala from south Asia.