Fish Karyome: A karyological information network database of Indian Fishes

‘Fish Karyome’, a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes

Growth Characteristics, Yield Components and Yield of Wheat (Triticum aestivum L.) as Affected by Integrated Nutrient Management on under Central Plain Zone of Uttar Pradesh

Field experiments were carried out at Chandra Shekhar Azad University of Agriculture & Technology, Kanpur, to investigate the influence of integrated nutrient management on wheat growth metrics, yield components, and yield during the rabi seasons of 2021-22 and 2022-23.The trial included 11 treatment combinations in a randomised block design with three replications and each treatment combination likely involves different combinations of inorganic fertilizers, organic manure, and biofertilizers. Wheat variety HD-2967 was grown with the using prescribed agronomic practices. According to investigation results the maximum plant height at maturity is 99.85 cm and 102.79 cm, the maximum number of effective tillers is 101.45 cm and 104.83, and the maximum ear length is 11.29 cm and 11.76 cm are associated with the treatment T10 [100 % NPK + S40 + Zn5 + Fe10 + Azotobacter + PSB + 5 tonne FYM] during both years of experimentation. Similarly, among the yield components and productivity parameters maximum values with regard to the number of spikelet ear-1 (22.64 and 22.95), grain ear-1 (43.11 and 46.03), 1000 grain wt. (41.17 and 42.13 gm), grain yield (48.60 and 49.93 q ha-1) and straw yield (63.15 and 67.53 q ha-1) have been observed in the treatment T10 [100 % NPK + S40 + Zn5 + Fe10 + Azotobacter + PSB + 5 tonne FYM] during both the years of the experimentation. The objective of the study to understand how different combinations of inorganic fertilizers, organic manure, and biofertilizers affect the growth and productivity of wheat, specifically the HD-2967 variety, when grown using recommended agronomic practices

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Not AvailableCyprinus carpio is world’s most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (−4,900 to +100) sequences of 31,466 protein coding genes was downloaded from “Gene” and “RefSeq” databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi

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Not AvailableThe connective tissue growth factor gene plays important role in several biological processes and also responsive to hypoxia stress in fishes. The freshwater fish, Labeo rohita, highly cultured in Indian subcontinent for food, is reported as hypoxia sensitive but annotation and sequences of nuclear genes were not available for this species so far in the public domain, except some transcripts. In this study, an attempt was made for isolation and annotation of the CTGF gene in L. rohita using information of zebrafish from the same family. The CTGF gene sequence was obtained by aligning assembled genome of L. rohita, (NCBI BioProject ID: PRJNA437789), with the CTGF protein of zebrafish. Eight overlapping sets of forward and reverse primers from aligned region were designed for amplification of around 600 bp long successive overlapping fragments of CTGF gene in L. rohita. Assembly and annotation of overlapping fragments confirmed a complete 2421 bp long CTGF gene sequence with a full coding region that comprised of five exons between 308 and 1921 positions. This annotated CTGF gene sequence was submitted to GenBank (Acc. No. KY940466). Characterization of CTGF will be an initiative in identification of hypoxia response genes in L. rohita which may further help in understanding the mechanism of hypoxia tolerability in this species.CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi

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Not AvailableSeveral studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.CABin Scheme of ICAR, implemented through ICAR-IASRI, New Delhi

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Authors are thankful to the Director, ICAR-NBFGR, Lucknow, for providing necessary facilities to carry out this work. Authors are also thankful to the CABin Scheme of ICAR and CABin Division, ICAR-IASRI, New Delhi, for financial assistance and guidance. Authors are highly thankful to the project personnel of the research project entitled `Whole genome sequencing and development of allied genomic resources in two commercially important fish-Labeo rohita and Clarias batrachus' funded by Department of Biotechnology, Government of India, New Delhi, for utilizing the assembled genome sequence of the L. rohita. Authors are also thankful to Department of Biotechnology, Government of India, New Delhi. Authors are indebted to Dr. N S Nagpure, Principal Scientist, ICAR-CIFE, Mumbai, for his support, guidance, suggestions etc. Authors are also grateful to Dr. Satarudra Prakash Singh and Dr. Vineet Awasthi, Amity University Uttar Pradesh, Lucknow campus, for their continued suggestions.The HMOX1 gene plays role in several biological processes and is also responsive to hypoxia stress. Freshwater carp fish, Labeo rohita, is reported as hypoxia sensitive, but the information of annotated hypoxia genes in public domain is very scanty for this species. Here, an attempt was made to isolate and characterize HMOX1 gene in L. rohita using information from zebrafish. HMOX1 gene was obtained by mapping HMOX1 protein of zebrafish over assembled genome of L. rohita. Aligned region was used for designing primers for HMOX1 amplification. Eight overlapping sets of primers were designed for amplifying similar to 540 bp long successive overlapping fragments. Splicing of overlapping amplicons generated 3715 bp fragment that was confirmed as HMOX1 gene having full coding region with 6 exons between 184 and 2156 bp positions. HMOX1 characterization is an initiative for L. rohita genes annotation to support the characterization of new genes in the important species.CABin Scheme of ICARCABin Division, ICAR-IASRI, New DelhiDepartment of Biotechnology, Government of India, New DelhiDepartment of Biotechnology (DBT) Indi

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Not AvailableThe HMOX1 gene plays role in several biological processes and is also responsive to hypoxia stress. Freshwater carp fish, Labeo rohita, is reported as hypoxia sensitive, but the information of annotated hypoxia genes in public domain is very scanty for this species. Here, an attempt was made to isolate and characterize HMOX1 gene in L. rohita using information from zebrafish. HMOX1 gene was obtained by mapping HMOX1 protein of zebrafish over assembled genome of L. rohita. Aligned region was used for designing primers for HMOX1 amplification. Eight overlapping sets of primers were designed for amplifying ~540 bp long successive overlapping fragments. Splicing of overlapping amplicons generated 3715 bp fragment that was confirmed as HMOX1 gene having full coding region with 6 exons between 184 and 2156 bp positions. HMOX1 characterization is an initiative for L. rohita genes annotation to support the characterization of new genes in the important species.CABin Scheme of ICAR and CABin Division of ICAR-IASRI, New Delhi

Pattern of reproductive biology of the endangered golden mahseer Tor putitora (Hamilton 1822) with special reference to regional climate change implications on breeding phenology from lesser Himalayan region, India

Mahseer is an important group of endemic game fish found in the Indian subcontinent inhabiting in streams, riverine pools and lakes. Besides commercial fishery, it also forms lucrative sport fishery in the Himalayan rivers. Samples of golden mahseer (Tor putitora) were collected from the river Kosi at Ramnagar area (lesser Himalayan region) of Uttarakhand, India during 2014–2016 to study reproductive biology and trace any changes in breeding phenology from earlier records. The observed breeding season was from July till September. In males (310–565 mm, 355–1750 g) and females (315–580 mm, 260–2500 g), GSI values surged from late June to early July and peaked in August. Absolute and relative fecundity ranged from 4217 to 8365 and from 3667 to 7348 per kg, respectively. The maximum water temperature was usually recorded in May (30.5°C) and minimum (18.4°C) in January. Sex ratio was estimated at 1:1.25 with χ2 value of 3.20 and the difference was non-significant. The breeding phenology of golden mahseer may likely have gone through two distinct steps of transformation viz. shifting-prolongation (1911–1981) and reduction-stabilization (1981–present). Even after a probable reduction in duration of breeding season and shift (delay) in onset of breeding in Golden mahseer population of lesser Himalayan region during 1911–1981, some stabilization in breeding phenology appears to have been attained since 2000s. It is predicted that the species appears to be continuously adapting to changing climate in lesser Himalayas

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Not AvailableMahseer is an important group of endemic game fish found in the Indian subcontinent inhabiting in streams, riverine pools and lakes. Besides commercial fishery, it also forms lucrative sport fishery in the Himalayan rivers. Samples of golden mahseer (Tor putitora) were collected from the river Kosi at Ramnagar area (lesser Himalayan region) of Uttarakhand, India during 2014–2016 to study reproductive biology and trace any changes in breeding phenology from earlier records. The observed breeding season was from July till September. In males (310–565 mm, 355–1750 g) and females (315–580 mm, 260–2500 g), GSI values surged from late June to early July and peaked in August. Absolute and relative fecundity ranged from 4217 to 8365 and from 3667 to 7348 per kg, respectively. The maximum water temperature was usually recorded in May (30.5°C) and minimum (18.4°C) in January. Sex ratio was estimated at 1:1.25 with χ2 value of 3.20 and the difference was non-significant. The breeding phenology of golden mahseer may likely have gone through two distinct steps of transformation viz. shifting-prolongation (1911–1981) and reduction-stabilization (1981–present). Even after a probable reduction in duration of breeding season and shift (delay) in onset of breeding in Golden mahseer population of lesser Himalayan region during 1911–1981, some stabilization in breeding phenology appears to have been attained since 2000s. It is predicted that the species appears to be continuously adapting to changing climate in lesser Himalayas.ICAR NICR

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Not AvailableMahseer is an important group of endemic game fish found in the Indian subcontinent inhabiting in streams, riverine pools and lakes. Besides commercial fishery, it also forms lucrative sport fishery in the Himalayan rivers. Samples of golden mahseer (Tor putitora) were collected from the river Kosi at Ramnagar area (lesser Himalayan region) of Uttarakhand, India during 2014–2016 to study reproductive biology and trace any changes in breeding phenology from earlier records. The observed breeding season was from July till September. In males (310–565 mm, 355–1750 g) and females (315–580 mm, 260–2500 g), GSI values surged from late June to early July and peaked in August. Absolute and relative fecundity ranged from 4217 to 8365 and from 3667 to 7348 per kg, respectively. The maximum water temperature was usually recorded in May (30.5°C) and minimum (18.4°C) in January. Sex ratio was estimated at 1:1.25 with χ2 value of 3.20 and the difference was non-significant. The breeding phenology of golden mahseer may likely have gone through two distinct steps of transformation viz. shifting-prolongation (1911–1981) and reduction-stabilization (1981–present). Even after a probable reduction in duration of breeding season and shift (delay) in onset of breeding in Golden mahseer population of lesser Himalayan region during 1911–1981, some stabilization in breeding phenology appears to have been attained since 2000s. It is predicted that the species appears to be continuously adapting to changing climate in lesser Himalayas.The financial help of ICAR-CRIDA for funding in the project National Innovations in Climate Resilient Agriculture (NICRA) is also gratefully acknowledged