Chitala chitala (Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in C. chitala from seven river basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in C. chitala. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species.

Background: Tor tor (Hamilton 1922), a natural polyploid fish species, is commonly known as the red-fin or deep bodied mahseer and is the type species of the Tor genus. It was assessed as ?Near Threatened? in the IUCN Red List, due to rapidly declining populations in wild and recently reassessed as Data Deficient. To generate the genetic structure information in this species, co-dominant markers face polyploidy specific hitches in genotyping, such as auto/tetrasomy, double reduction and missing dosage information. Objective: In the present study, a total of 25 polymorphic microsatellite loci was developed through long- read single molecule, real time (SMRT) sequencing technology, to genotype 139 T. tor samples from six natural riverine populations of India, to determine intra-specific genetic variation in this species. Results: Upon sequencing 1.5 kb SMRT bell library, the clustering and assembly of high-quality CCS reads resulted into 9746 contigs and 2129 contained repeat sequences. The majority of repeats were dinucleotide (67.8%), followed by trinucleotide (21.4%) and tetranucleotide (10.7%). Out a total of 118 SSR loci primers designed, 25 loci showed polymorphism. The microsatellite genotype analyses with these loci indicated T. tor as an auto-tetraploid, with tetrasomy segregation and occurrence of double reduction. The microsatellite loci identified were highly polymorphic (average PIC 0.6687).. The genetic diversity parameters, observed and expected heterozygosities ranged from 0.1268 to 0.5047 and from 0.4989 to 0.9212, respectively, whereas inbreeding (F-IS) values from 0.2334 to 0.8379. The average rho statistics value of 0.0739 (p = 0.00) indicated the presence of genetic structure in the natural population, and along with pair-wise rho statistics and DAPC analysis pointed to the occurrence of three genetic stocks. Conclusion: The identified microsatellite loci were found to be useful in generating information on genetic diversity and fine scale population structure of tetraploid T. tor, which would be valuable for conservation and management of this threatened species.

Genetic diversity and population structure in Indian featherback fish, Chitala chitala (Hamilton, 1822) was investigated by combined analyses of two full mitochondrial genes, ATPase 6/8 and Cytochrome b. A total of 403 individuals, collected from 14 rivers yielded 61 haplotypes. Hierarchical partitioning analysis identified 19.01% variance ‘among’ and 80.99% variance ‘within groups and populations’. The mean coefficient of genetic differentiation (FST) was observed to be significant 0.26 (p < 0.05). Mantel tests rejected the hypothesis that genetic and geographic distances were correlated. The patterns of genetic differentiation, AMOVA and principal coordinate analyses indicated that natural populations were sub-structured and comprised of four genetic stocks of C. chitala in Indian rivers. The results also supported the higher resolution potential of concatenated gene sequences. The knowledge of genetic variation and divergence, from this study, can be utilized for its scientific conservation and management in the wild.

Tor tor, Tor mahseer, an endangered cyprinid species, is important as a sport fish. Genetic divergence in natural populations of T. tor was investigated using two mitochondrial genes, Cytb (Cytochrome b) and ATPase6/8. Analysis of 140 sequences of Cytb (1121 bp) and ATPase6/8 (842 bp) genes revealed 12 and 7 haplotypes, respectively, whereas 23 haplotypes were found in concatenated sequences (1963 bp). Sequence analysis of mitochondrial regions revealed balancing selection and displayed low nucleotide and moderate haplotype diversities. Mantel tests identified a positive relationship between pairwise geographical and genetic distances for the study region. Results of AMOVA based on genes pointed out that the genetic variations were mainly due to variation in within populations (ATPase6/8: 62.73%, Cytb: 42.13%, concatenated sequences: 48.31%). The total F-st was found to be significant in both genes with a value of 0.5787 (p < 0.05) and 0.3726 (p < 0.05) for Cytb and ATPase6/8genes respectively, whereas 0.51687 (p < 0.05) was found in combined sequences, which revealed sub-structuring in the T. tor natural populations. Population pair-wise Fst ranged from 0.00901- to 0.85631 for Cytb and 0.09910- to 0.64731 for ATPase6/8genes, whereas 0.02039 to 0.85436 in combined sequences. Results indicated the presence of four genetic stocks in the populations studied. The baseline information about stock characterisation in this study would be applicable for planning strategies for conservation, management and sustainable fisheries of this species.

Evolutionarily significant freshwater primitive fish, Chitala chitala (Hamilton-Buchanan, 1822) is an endangered featherback species with wide distribution in Indian subcontinent, Indonesia, Cambodia, Malaysia and Thailand. In this study, the complete mitochondrial genome is reported for the first time. The mitogenome of C. chitala was sequenced (16375 bp) and mapped to identify 13 protein coding genes (PCG), 22 transfer RNA genes, 2 rRNA genes (12S and 16SrRNA) and a control region. The ratio of synonymous and non synonymous substitutions (Ka/Ks) indicated that 10 genes evolved under purifying selection. Phylogenetic trees were constructed on the basis of concatenated 12 PCGs to ascertain its taxonomic relatedness with other seven orders along with osteoglossiformes. C. chitala displayed monophyly with other congeners, while Notopterus notopterus (Thailand) and Notopterus notopterus (India) showed marked distinction.

In present study, single molecule-real time sequencing technology was used to obtain a validated set of microsatellite markers for application in population genetics of the primitive fish, Chitala chitala. Assembly of circular consensus sequencing reads resulted into 1164 sequences which contained 2005 repetitive motifs. A total of 100 sequences were used for primer designing and amplification yielded a set of 28 validated polymorphic markers. These loci were used to genotype n = 72 samples from three distant riverine populations of India, namely Son, Satluj and Brahmaputra, for determining intraspecific genetic variation. The microsatellite loci exhibited high level of polymorphism with PIC values ranging from 0.281 to 0.901. The genetic parameters revealed that mean heterozygosity ranged from 0.6802 to 0.6826 and the populations were found to be genetically diverse (Fst 0.03–0.06). This indicated the potential application of these microsatellite marker set that can used for stock characterization of C. chitala, in the wild. These newly developed loci were assayed for cross transferability in another notopterid fish, Notopterus notopterus.

The species-specific microsatellite markers in the great snakehead, Channa marulia, were mined from the genome, through an enriched genomic library construction. Total 27 microsatellite loci exhibited polymorphism. The repeat containing sequences were annotated to ensure the genetic neutrality of the loci. Nineteen, consistently scorable loci were validated, and used to estimate the genetic indices in n = 67 individuals sampled from three Indian rivers (Godavari, Mahanadi and Teesta). The polymorphism information content (PIC) values ranged from 0.366 to 0.831, while heterozygosities varied from 0.077 to 0.818. Bayesian model-based clustering grouped the samples into three discrete populations with evidences of little genetic admixture. The results confirmed a set of 19 microsatellite markers, as promising molecular tool, for estimating genetic diversity studies in C. marulia. Successful cross-transferability was observed in three congener species viz. C. punctata, C. gachua, and C. striata. The results can be useful in conservation and management of C. marulia.

Systomus sarana sarana, commonly known as olive barb, is an important food and ornamental fish species with wide distribution in South Asia. Here, the complete mitogenome was sequenced on HiSeq 2500. With 16,590 nucleotides, the base composition was 32.9% (A), 26% (C), 15.4% (G) and 25.7% (T), comparable with other carps. The clustering pattern depicted the monophyly of S. sarana sarana with sister cyprinids.

The stock characterization of wild populations of Silonia silondia is important for its scientific management. At present, the information on genetic parameters of S. silondia is very limited. The species-specific microsatellite markers were developed in current study. The validated markers were used to genotype individuals from four distant rivers. To develop de novo microsatellite loci, an enriched genomic library was constructed for S. silondia using affinity-capture approach. The markers were validated for utility in population genetics. A total number of 76 individuals from four natural riverine populations were used to generate data for population analysis. The screening of isolated repeat sequences yielded eleven novel polymorphic microsatellite loci. The microsatellite loci exhibited high level of polymorphism, with 6-24 alleles per locus and the PIC value ranged from 0.604 to 0.927. The observed (Ho) and expected (He) heterozygosities ranged from 0.081 to 0.84 and 0.66 to 0.938, respectively. The AMOVA analysis indicated significant genetic differentiation among riverine populations (overall FST = 0.075; P < 0.0001) with maximum variation (92.5%) within populations. Cross-priming assessment revealed successful amplification (35-38 %) of heterologous loci in four related species viz. Clupisoma garua, C. taakree, Ailia coila and Eutropiichthys vacha. The results demonstrated that these de novo polymorphic microsatellite loci are promising for population genetic variation and diversity studies in S. silondia. Cross-priming results indicated that these primers can help to get polymorphic microsatellite loci in the related catfish species of family Schilbidae.

Lactobacillus acidophilus comes under the genus Lactobacillus which comprises of large group of beneficial bacteria that have similar properties and all produce lactic acid as an end product of the fermentation process. Previous studies shows that L.acidophilus has its own significant importance as it improves gastrointestinal function, boosts immune system, decreases the frequency of vaginal yeast infection and helps in reducing serum cholesterol levels. The present study is directed towards isolation and identification of antagonistic L. acidophilus from different regions of Allahabad. A total of 50 curd samples were collected from different regions of Allahabad. After careful examination of morphological and biochemical characteristics, all 74 isolates of different Lactobacillus species were found to be present in which 7 strains of L. acidophilus were found. Further these 7 strains were subjected to antagonistic test against selected bacterial pathogens and results revealed that all strains of L.acidophilus were found to be good antagonistic activity against selected bacterial pathogens. This study concluded that curds contain strains of L.acidophilus which shows good antagonistic property; thus revealing that it is safe and beneficial for consumption.

Pigeonpea is one of the most important pulse crops in the semi-arid tropical region, which is prone to several climatic uncertainties like unpredictable temperature, frequent drought and inconsistent rainfall. Additionally, during crop cycle pigeonpea also encounters a wide range of other biotic and abiotic constraints, ultimately leading to its fluctuating production and stagnant productivity. However, recently developed CGMS system has shown noteworthy impacts in enhancing pigeonpea productivity through exploitation of hybrid vigour. At present, A(2)-cytoplasm derived CGMS system has been well established in pigeonpea. Nevertheless, the commercial success of CGMS system relies largely on the continuous supply of genetically pure seeds of hybrids and corresponding parental lines. Traditionally, the genetic purity of seeds is guaranteed through conducting grow out test (GoT). In this context, DNA marker assays offer several advantages over conventional GoT especially in terms of time, space and money. Given its locus-specific and co-dominant nature, SSR or microsatellite marker is particularly suited for hybridity testing and purity assessment. Here we report a set of robust SSR markers, which could act as reliable molecular kit for ensuring the genetic purity of the CGMS-hybrid 'IPH 09-5' and its parental lines 'PA 163A' (A-or Male sterile-line) and 'AK 261322' (R- or Restorer-line).

The complete nucleotide sequence of mitogenome of the great snakehead, Channa marulius (Channidae), was determined and found to be 16,569 base pairs in length. The content and arrangement of different genes on the mitogenome was found similar to other typical teleosts. The overall base composition of the L-strand was found to be T (19.1%), C (31.5%), A (34.8%) and G (14.6%). The control region was 915 nt long and without any repetitive region. The mitogenome sequence data would be useful for studying phylogenetic relationship of C. marulius with other perciform species.