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Joshi, C. G.
- Identification of Single Nucleotide Polymorphism from Indian Bubalus bubalis through Targeted Sequence Capture
Abstract Views :217 |
PDF Views:79
Authors
A. B. Patel
1,
R. B. Subramanian
1,
H. Padh
1,
T. M. Shah
2,
A. Mohapatra
2,
B. Reddy
2,
S. J. Jakhesara
2,
P. G. Koringa
2,
D. Dash
3,
C. G. Joshi
2
Affiliations
1 BRD School of Biosciences, Sardar Patel University, V. V. Nagar 388 120, IN
2 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
3 Roche Diagnostics India Pvt Ltd, Kolkata 700 107, IN
1 BRD School of Biosciences, Sardar Patel University, V. V. Nagar 388 120, IN
2 Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, IN
3 Roche Diagnostics India Pvt Ltd, Kolkata 700 107, IN
Source
Current Science, Vol 112, No 06 (2017), Pagination: 1230-1239Abstract
Bubalus bubalis (water buffalo) is an agro-economically important livestock species due to its multipurpose use in India and other Asian countries. The aim of this study was to identify single nucleotide polymorphisms (SNPs) from buffalo genome. Genomic DNA was isolated from 24 blood samples of three Indian buffalo breeds and subjected to targeted pyrosequencing, followed by variant calling and annotation. Target probes for enrichment were designed from exome and 5' and 3' untranslated regions of cattle genome. By targeted pyro-sequencing and variant calling from 3.92 Gb data, 923,964 high-quality SNPs were identified. Many SNPs were identified in regulatory regions, leading to conformational changes in factor-binding sites, which play a role in gene expression as in the case of LPL gene from low-milkproducing samples. Gene ontology (GO) enrichment and clustering, resulted in the enrichment of GO terms involved in milk production and transport, and fertility-related categories. Around 75% of SNPs were located on cattle quantitative trait loci, supporting trait-wise sample collection approach. Further, PCA analysis from the identified SNPs also supported sample selection strategy based on contrasting trait performance.Keywords
Exome, Gene Ontology, Quantitative Trait Locus, Single Nucleotide Polymorphism.Full Text
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- Transcriptomic Comparison of Primary Bovine Horn Core Carcinoma Culture and Parental Tissue at Early Stage
Abstract Views :157 |
PDF Views:1
Materials and Methods: Whole transcriptome sequencing of horn’s SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified.
Results: Up-regulated genes in SCC of horn’s early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity.
Conclusion: The experiment revealed similar transcriptomic nature of horn’s SCC tissue and its early passage cells.
Authors
Sharadindu Shil
1,
R. S. Joshi
2,
C. G. Joshi
3,
A. K. Patel
4,
Ravi K. Shah
3,
Namrata Patel
3,
Subhash J. Jakhesara
3,
Sumana Kundu
5,
Bhaskar Reddy
3,
P. G. Koringa
3,
D. N. Rank
2
Affiliations
1 Veterinary Officer (WBAH & VS), West Bengal Animal Resources Development Department, Bankura-772152, West Bengal, IN
2 Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, IN
3 Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, IN
4 Hester Biosciences Limited, Ahmedabad, Gujarat, IN
5 Veterinary Officer, MVC Sarenga, Government of West Bengal, Bankura, West Bengal, IN
1 Veterinary Officer (WBAH & VS), West Bengal Animal Resources Development Department, Bankura-772152, West Bengal, IN
2 Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, IN
3 Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, IN
4 Hester Biosciences Limited, Ahmedabad, Gujarat, IN
5 Veterinary Officer, MVC Sarenga, Government of West Bengal, Bankura, West Bengal, IN
Source
Veterinary World, Vol 10, No 1 (2017), Pagination: 38-55Abstract
Aim: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn’s SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study.Materials and Methods: Whole transcriptome sequencing of horn’s SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified.
Results: Up-regulated genes in SCC of horn’s early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity.
Conclusion: The experiment revealed similar transcriptomic nature of horn’s SCC tissue and its early passage cells.
Keywords
Cummerbund, Gene Ontology, Primary Culture, RNA-Sequencing, Squamous Cell Carcinoma of Horn, Transcriptome Profiling.Full Text
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