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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.
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ThesisItem Open 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.ThesisItem Open Access GENETIC STUDY OF PARTIAL AND FULL RECORD OF TWO STRAINS OF WHITE LEGHORN CHICKEN(AAU, Anand, 2013) Meshram, Anushree Yuwraj; Joshi, R. S.The present study was undertaken to investigate inheritance and association of various economic traits in IWN and IWP strains of White Leghorn which has completed nine generations of Osborne Index selection for improvement of egg production. A total of 849 and 862 pullets of IWN and IWP strains, were generated by mating of 50 sires and 300 dams of each of the two strains and were maintained under All India Coordinated Research Project on Poultry Breeding at the Department of Poultry Science, College of Veterinary Science and Animal husbandry, Anand Agricultural University Anand. Various traits like body weight (BW) in g at 16, 20, 40, 56, 64 and 72 weeks of age, age at first egg (AFE) in days, total egg number produced up to 40, 56, 64 and 72 weeks of age (TEN), egg weight (EW) in g at 28, 40, 56, 64 and 72 week of age, total egg mass produced up to 40, 56, 64 and 72 weeks (TEM) in kg, feed consumption per dozen of egg (FCDE) produced (kg) and feed consumption per kilo of eggs (FCKE) produced (kg) upto various stages were measured for estimation of Least Squares Means (LSMs), heritability (h2), genetic and phenotypic correlations and genetic gain in the egg production . [The least squares means for body weight (g) at 16, 20, 40, 56, 64 and 72 weeks of age were 978.21 ± 7.00, 1250.47 ± 4.55, 1412.59 ± 7.93, 1462.98 ± 9.41, 1477.26 ± 6.81 and 1526.05 ± 9.60g for IWN strain and 1000.84 ± 5.61, 1280.41 ± 6.14, 1483.76 ± 8.48, 1543.62 ± 9.94, 1534.44 ± 10.97 and 1616.10 ± 12.82g for IWP strain, respectively. The body weight at all stages were significantly (P<0.05) higher in IWP strain as compared to IWN strain. Least squares means for AFE (days) were found to be 134.50 ± 0.78 and 138.13 ± 0.59 days in IWN and IWP strains, respectively. Age at first egg was significantly earlier (P<0.05) in IWN than IWP strain.) The LSMs for total egg number produced up to 40, 56, 64 and 72 weeks of age were 119.26 ± 1.03, 210.51 ± 1.03, 251.75 ± 1.56 and 286.39 ± 1.42 eggs in IWN and 115.55 ± 0.79, 205.69 ± 1.33, 243.59 ± 1.35 and 277.70 ± 1.53 eggs in IWP strain, respectively. IWN strain has produced significantly (P<0.05) more eggs number than IWP strain during all stages. The least squares means for egg weight (g) at 28, 40, 56, 64 and 72 weeks of age were 44.84 ± 0.15, 50.36 ± 0.13, 51.68 ± 0.15, 51.62 ± 0.13 and 52.01 ± 0.12g for IWN strain and 46.26 ± 0.12, 52.52 ± 0.12, 53.48 ± 0.15, 53.57 ± 0.15 and 54.51 ± 0.14g for IWP strain, respectively. The mean egg weight recorded at all ages were significantly (P<0.05) higher in IWP strain as compared to IWN strain. The least squares means for egg mass (kg) upto 40, 56, 64 and 72 weeks of age were 6.002 ± 0.048, 10.909 ± 0.062, 12.997 ± 0.082 and 14.893 ± 0.072 kg in IWN strain while 6.061 ± 0.038, 10.986 ± 0.695, 13.040 ± 0.076 and 14.638 ± 0.083 kg in IWP stain, respectively. The LSMs for feed consumed to produce a dozen of eggs (kg) were 1.718 ± 0.016 , 1.782 ± 0.011, 1.804 ± 0.012 and 1.864 ± 0.011 kg in IWN strain whereas 1.735 ± 0.140, 1.784 ± 0.012, 1.842 ± 0.012 and 1.895 ± 0.012 kg in IWP strain during the period of 21- 40, 21-56, 21-64 and 21-72 weeks of age, respectively. The LSMs for feed consumption per kilo of egg up to 40, 56 ,64 and 72 week of age were 2.850 ± 0.026, 2.874 ± 0.221, 2.921 ± 0.020 and 2.995 ± 0.017 kg in IWN and 2.758 ± 0.020, 2.785 ± 0.018, 2.873 ± 0.019 and 3.011 ± 0.019 kg in IWP strain, respectively. No significance difference have been observed between two strains for egg mass and feed consumption either per dozen or kilo of egg produced. Heritability estimates for BW at different ages varies in magnitude from low to high in IWN strain and IWP strain. The estimate of heritability for AFE was high in IWN strain while of moderate magnitude in IWP strain. Heritability estimates were high in IWN strain and lower to moderate magnitude in IWP strains for egg number. Heritability estimates of egg weight at all stages were low to moderate in both the strains. Whereas, the h2 estimates of egg mass shown higher to lower magnitude as the age advanced. Inheritance of feed efficiency trait (FC/DE and FC/KE) has shown erratic trend from higher to lower in IWN strain while it was moderate in IWP strain. Genetic and phenotypic associations of AFE with TEN were found negative and high in magnitude. The genetic correlation of AFE with TEN in IWN strain was beyond parametric range which might be due to sampling error. Association of TEN and BW at various stages were positive and high in magnitude suggesting unfavourable trend in IWN strain while they were negative and varied in magnitude suggesting favourable trend in IWP strain. The genetic association of TEN with EW at various stages was in general negative and moderate to high in magnitude in both the strain. Genetic and phenotypic correlations of TEN with TEM were all positive at each stage and high in magnitude and many were found beyond the parametric range. Correlation between the TEN and FCDE and FCKE were negative which is favourable in direction and high in magnitude at all stages. Genetic correlations between age at first egg and egg weights at different ages were, in general, positive and showed increasing trend from low to high with advancement in age in IWN strain, where as they were positive and high in IWP strain. Genetic association of AFE with BW was negative in both strains indicates low body weight at time of housing increases the age at sexual maturity. Phenotypic correlations shown erratic trend of weakly positive or negative association found in both strain. Genetic association of AFE with other traits such as egg mass, feed consumption per dozen of egg and per kilo of egg in general were negative and high in magnitude Expected genetic gain was highest at 64 weeks age in IWN strain and at 56 weeks age in IWP strain. High relative efficiency to get maximum genetic gain for egg numbers produced was found at 40 weeks of age in both the strain, therefore selection on the basis of 40 weeks egg production seems to be most efficient in improving annual production than direct selection for annual records.ThesisItem Open Access SNP detection in partial exome sequencing of Jaffarabadi buffalo (Bubalus bubalis(Anand Agricultural University, Anand, 2013) MAULIK UPADHYAY; Dr. C. G. JoshiIn recent years, riverine buffalo has occupied a central role in Indian agriculture/Animal Husbandry sector especially due to its high milk production with high fat percentage compared to Indian cattle. Hence, detecting genetic variants such as SNPs in Indian buffalo can provide insight into traits which is adaptable for and in future, it may also pave the way for marker assisted selection in the species. An SNP is a bi-allelic co-dominant genetic variants found in high frequencyThesisItem Open Access STUDY ON GENETIC ASSOCIATIONS OF BODYWEIGHTWITH IMPORTANT ECONOMIC TRAITS IN IWN AND IWP STRAINS OFWHITE LEGHORN CHICKEN(AAU, Anand, 2012) RAJ KUMAR YADAV; Dr. J. V. SolankiThe present study was undertaken to investigate “Inheritance and associations of body weight with important economic traits in IWN and strains of White Leghorn chicken”. Data pertaining to S7 generation of IWN and strains of White Leghorn maintained at Department of Poultry Science, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand were utilized for the present study. Birds were grouped at 16, 40 and 64 weeks of age on the basis of body weight, with the difference of 150 grams in their body weights. At 16 weeks of age 4 groups, at 40 weeks of age, 5 groups and at 64 weeks of age, 7 groups were formed. Birds were also grouped total number of eggs produced upto 64 weeks of age with the difference of 20 eggs. Total 6 groups were formed.ThesisItem Open Access COMPARISON OF VARIOUS METHODS OF SIRE EVALUATION IN MURRAH GRADED BUFFALOES(AAU, Anand, 2013) CHAUDHARI PRAVINKUMAR NAGJIBHAI; Dr. D. N. RANKThe present study was carried out on comparison of various methods of sire evaluation in Murrah graded buffalo. A total of 2329 test day lactation records of daughters of 79 sires distributed in 47 villages under field progeny testing programme in Anand milk shed were subjected to least squares analysis to study the effect of different non genetic factors. The least squares means for age at first calving (AFC), first lactation milk yield (FLY305) and milk fat percent (Fat %) were 1812.90 ± 12.10 days, 1490.53 ± 9.88 liter and 7.008 ± 0.02 per cent, respectivelyThesisItem Open Access Establishment, Characterization and Transcriptome Profiling of Horn Cancer Cell Line(AAU, Anand, 2014) SHARADINDU SHIL; Dr. R.S. JoshiHorn cancer (HC) is a squamous cell carcinoma (SCC) of horn core mucosa with poorly defined genetic landscape, reported only in Bos indicus and causes heavy economic losses as a result of affecting 1% of cattle population and accounting 83.34% of total tumors found (Joshi et al., 2009). Tumor-derived cell lines are widely used as in vitro cancer models. A major obstacle to obtain more detailed insights into the diversity of phenotypic and molecular changes occurring in horn cancer cells was non- availability of low-passage horn cancer cell lines, which would still closely reflect the phenotype of the horn cancer cells in vivo. Considering that pressing requirement here a novel, low passage number horn cancer cell line was characterized. The cells were originated from horn core squamous cancerous tissue (characterized in the clinics & histopathological study).