Thumbnail Image

Anand Agricultural University, Anand

Anand Agricultural University (AAU) was established in 2004 at Anand with the support of the Government of Gujarat, Act No.(Guj 5 of 2004) dated April 29, 2004. Caved out of the erstwhile Gujarat Agricultural University (GAU), the dream institution of Sardar Vallabhbhai Patel and Dr. K. M. Munshi, the AAU was set up to provide support to the farming community in three facets namely education, research and extension activities in Agriculture, Horticulture Engineering, product Processing and Home Science. At present there seven Colleges, seventeen Research Centers and six Extension Education Institute working in nine districts of Gujarat namely Ahmedabad, Anand, Dahod, Kheda, Panchmahal, Vadodara, Mahisagar, Botad and Chhotaudepur AAU's activities have expanded to span newer commodity sectors such as soil health card, bio-diesel, medicinal plants apart from the mandatory ones like rice, maize, tobacco, vegetable crops, fruit crops, forage crops, animal breeding, nutrition and dairy products etc. the core of AAU's operating philosophy however, continues to create the partnership between the rural people and committed academic as the basic for sustainable rural development. In pursuing its various programmes AAU's overall mission is to promote sustainable growth and economic independence in rural society. AAU aims to do this through education, research and extension education. Thus, AAU works towards the empowerment of the farmers.

Browse

20141
Reset filters
Subject: Animal Genetics and Breeding × Author: KORINGA, PRAKASHKUMAR G. × Thesis Type: Ph.D ×
Reset filters

Search Results

Now showing 1 - 1 of 1
  • Thumbnail Image
    ThesisItemOpen Access
    EXPRESSION PROFILING, SNP DETECTION AND VALIDATION IN SQUAMOUS CELL CARCINOMA OF HORN IN KANKREJ CATTLE (Bos indicus) USING NEXT GENERATION SEQUENCING
    (AAU, Anand, 2014) KORINGA, PRAKASHKUMAR G.; Joshi, Chaitanya G.
    Horn cancer is a widely prevalent cancer amongst Kankrej cattle (Bos indicus) seen sporadically, especially in case of working class of castrated male animals i.e. bullocks. A transcriptome envisaged characterization as well as correlation to known genomic changes such as structural and copy number alterations, focused ins/dels and single nucleotide mutations. Here, we employed high throughput RNA-seq using GS-FLX Titanium for characterization and comparison of normal and cancerous horn transcriptome in Bos indicus. A total of 909,362 reads with average read length of 405bp for horn cancer (HC) and 583,491 reads with average read length of 411bp for horn normal (HN) were obtained by sequencing gene transcripts derived from HC and HN tissues. Assembled data were analyzed for identifying novel as well as differentially expressed transcripts using CLC Genome Workbench. RNA-seq analysis using different bioinformatics pipelines and software identified differentially expressed genes i.e. upregulation of KRT6A, KRT6B, KRT6C, KRT14, SFN, KRT84, PI3, CAl, C0L17A1, ANLN, SERPINB5 etc., as well as down-regulation of NR4A1, FOSB, LRIGl, BOLA, SCGBIAI, CXCL17, KRT19, BPIFBl, NR4A1 and TFF3 etc., in HC tissues. The signaling pathway investigation in this study revealed many of the cancer related pathways which mainly include cell cycle regulation pathways, p53 tumor suppressor pathways, NFKB and MAPKs pathways, LPS signaling pathway and PI3K-Akt pathways. The resuh of transcriptome expression profiling was validated using RT-qPCR in nine randomly selected genes. It revealed concordance of gene expression profile with RNA-seq analysis. We also used transcriptome data to elucidate complexity of the alternative splicing in HC transcriptome. We identified potential candidate splice variants that might be helpful in development of relevant biomarkers for early diagnosis of HC. The fiiture studies targeted at in depth characterization of these potential candidate splice variants might change the currently used clinical approaches. Herein we characterized global landscape of alternative splicing events exhibited by pair of HC and HN tissue and confirmed selected alternative splicing events with significant association to HC by RT-qPCR. Ine analysis of the same RNA-seq data using SeqMan Pro Version 10.0.0 resulted in to a 9532 and 7065 SNPs as well as 1171 and 1172 Indels in HC and HN, respectively. Out of total, 7889 SNPs and 1736 Indels uniquely present in HC, 5886 SNPs and 1146 Indels uniquely present in HN are novel and reported first time in Bos indicus, whereas rest are already reported in Bos taurus dbSNP database at NCBI. The gene-associated SNPs and Indels were high in upregulated genes of HC as compared to HN tissues. SNPs identified in RNA-seq analysis were validated in fiirther studies in two groups consisting of 50 animals each of HC and HN bullocks. DNA from HC tissue and blood of HN individual was extracted and 96 pairs of primers were used to generate amplicons of an average 300bp to get sequenced using Ion Torrent PGM. The resulting reads were assembled using SeqMan N Gen of DNASTAR and data were analyzed using Arraystarll. Case control analysis was carried out to find SNP significantly associated with HC. SNP at position 63251805 (dBSNP ID rsl36870681) identified in BPIFAl can serve as a potential candidate genetic marker in HC. The SNPs and Indels identified in this study will be useful resource for future studies to understand genetic basis for phenotypic variation between Bos taurus and Bos indicus as well as cancers in animals. A very large number of SNPs are essential for the designing and construction of arrays. SNPs identified in this study will enrich the dbSNP database of NCBI (http://www.ncbi.nlm. nih.gov/projects/SNP/) and will be useful resource for array designing. This study is the first attempt to reveal novel transcripts, differentially expressed genes as well as identification and validation of SNPs using digital expression analysis in Bos indicus and provides novel insights into bovine transcriptome. Our study will serve as a step further in detailed characterization of HC transcriptome and provide firm base to explore and mitigate HC at finer resolution. The present findings would provide basis for further screening of genes and identification of markers for early diagnosis and therapeutic intervention of HC.