Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita.

In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.

Population structure and genetic diversity of hatchery stocks as revealed by combined mtDNA fragment sequences in Indian major carp, Catla catla.

Catla catla is the second most important Indian major carp due to high growth rate and acceptance to consumers for food value. It is widely cultured in the Indian subcontinent as monoculture or polyculture. In the present study, genetic diversity among hatchery stocks (total 218 samples of catla) collected from different geographical regions of India was examined using mtDNA fragment sequence of Cyt b (306 bp) and D loop (710 bp). High numbers (57) of population specific haplotypes were observed in the present study. The results revealed significant genetic heterogeneity for the sequence data (FST = 0.27546, p < .05). Analysis of molecular variance revealed significant genetic differentiation among different catla populations. The information generated in present study could be useful to develop broad genetic base populations of catla.

Rapid recovery of complete mitogenome of Indian major carp, Catla catla from low depth paired end Illumina sequencing.

Here we report the reconstruction of the catla (Catla catla) complete mitochondrial genome sequence from low depth paired end Illumina sequencing. The genome is of 16,597 bp in size. Similar to other vertebrate mtgenomes, it consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. The present mtgenome is 3 bp longer than the earlier reported catla mtgenome from our laboratory. Majority of the mitochondrial genes are encoded by the H-strand. Phylogenetics analysis revealed that Catla catla is closer to Labeo rohita than other labeo species. Present study demonstrated the power of next generation sequencing towards hassle free and rapid sequencing of mitochondrial genomes of non-model organisms.

Studies on the identification and control of pathogen Saprolegnia in selected Indian major carp fingerlings at mid hill altitude.

The Indian major carp cultured in ponds in the North Eastern hilly states of India frequently suffer from fungal disease during winter months resulting in mass mortality. This study examined the pathogenic fungi isolated from farmed raised Indian major carp fingerlings and identified as Saprolegnia. For treatment, the diseased fish were exposed to 4g salt per litre of water for 2 min followed by dip treatment with 5ppm KMnO4 for 10 min, thrice every week for a period of 6 weeks. The treatment resulted in recovery from the disease after 6 weeks from the beginning of treatment. Soon after recovery, the pond management practices such as removal of pond bottom soil, application of lime and replenishment with freshwater were followed in the infected ponds. Our study concluded that rapid decrease in pond water temperature from 22 to 8 degrees C that remains low for months together coupled with increased water pH (9) and decreas dissolved oxygen (4ppm) causes saprolegniasis to the fingerlings of Indian major carps.

Karyotypic diversity and evolution of seven mahseer species (Cyprinidae) from India.

Mahseer is a group of fish species that are well known as food and game fishes. The taxonomy of the mahseer species is confusing owing to the morphological variations and habitat adaptation. Detailed karyomorphological investigations have been carried out in seven species of mahseer, using karyotyping, Ag-NOR and fluorescent staining techniques. The basic diploid chromosome number (2n), in all mahseer species, was observed to be 100; however, the karyotype formula varied among the species, which were recorded as: 20m + 14sm + 22st + 44t (fundamental arm number, FN = 134) in Tor khudree; 22m + 24sm + 24st + 30t (FN = 146) in Tor mussullah; 12m + 22sm + 14st + 52t (FN = 134) in Tor putitora; 20m + 24sm + 24st + 32t (FN = 144) in Tor tor; 20m + 30sm + 24st + 26t (FN = 150) in Tor chelynoides; 20m + 20sm + 20st + 40t (FN = 140) in Tor progeneius; and 20m + 18sm + 14st + 48t (FN = 138) in Neolissochilus hexagonolepis. Silver staining of the chromosomes revealed the presence of multiple nucleolar organizer regions (NOR) in these mahseer species. The highest number of NORs was observed in T. tor (four pairs of chromosomes), whereas the other six species possessed Ag-NOR signals on only two pairs of chromosomes. Although chromomycin A(3) (CMA(3)) staining induced bright fluorescence signals on same Ag-NORs sites, with CMA(3), one additional signal was observed on the p arm of subtelocentric chromosomes in T. tor, T. chelynoides, T. progeneius and N. hexagonolepis, which may indicate the presence of inactive NOR in these species. The information on cytogenetic profile of these mahseer species is discussed in the light of cytotaxonomic implications and understanding the karyoevolution of these fish species.