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ThesisItem Open Access Evaluation of Second Generation (S1) of Indigenous Chicken Pertaining to two Divisions of Karnataka(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-01-15) Mohan Kumar, T. R.; Narasimha Murathy, H.N.; Jayashankar, M.R.; Nagaraja, C.S.; Shri Krishna IsloorA study was undertaken to evaluate the S1 generation of indigenous chicken pertaining to Bengaluru and Mysore divisions of Karnataka, being maintained at AICRP on Poultry Breeding for Meat, Bengaluru centre and to compare with S0 generation for morphological and production traits as per NBAGR proforma. The morphological features recorded revealed 100% normal feather morphology indicating no structural variations in feather such as frizzle, silky and crested. The most prevalent plumage colour observed was brown followed by mixed and black. The most prevalent primary plumage pattern observed was solid, dull, patchy and mottled. The major secondary plumage pattern observed was self-red and self-black colour. Other secondary plumage patterns recorded were self-white, self-blue, mottled, barred and lacing. All the birds evaluated had red ear lobes. Major eye colour observed was brown and grey. Majority of birds had yellow shank. The predominant egg shell colour recorded was brown followed by light brown and creamy. The average egg weight of indigenous chicken ranged from 45.22 g to 46.53 g. The shape index was between 74 to 75. The average values for albumen weight, albumen index, yolk weight, yolk index, Haugh unit score and shell thickness of the eggs ranged from 23 g to 24 g, 0.061 to 0.068, 14 g to 16 g, 0.42 to 0.44, 65 to 70 and 0.35 mm. The present study indicated no significant difference between the two generations with respect to morphological and performance parameters.ThesisItem Open Access Studies on Genetic Polymorphism of Alpha S1 Casein Gene in Nandidurga Goats(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 12-12-14) Umesha Kavali; Jayashankar, M.R.; Nagaraja, R.; Bhaskaran, R.; Girish Kumar, V.A study was conducted with the objective of analyzing the genetic variation at Alpha S1 Casein gene region in Nandidurga non-descriptive goats of Karnataka by using PCR - RFLP technique. Genomic DNA was isolated from blood samples of 85 animals. The genetic diversity of caprine Alpha S1CSN locus was investigated by PCR - RFLP by amplifying part of intron 8, exon 9 and part of intron 9 of the Alpha S1 CSN gene. Restriction endonuclease enzyme XmnI was used to detect the genetic variation of the experimental unit in Alpha S1 CSN gene. Upon PCR - RFLP analysis, two patterns were observed which allowed the identification of two alleles A and B, and two genotypes, AA and BB. Further PCR - RFLP study in 35 Osmanabadi and 50 Bidri goats prevalent in North Karnataka revealed similar observations. Ironically AB type was not observed in any of these goats. The sequence analysis indicated that there was a high homology between the present result and the published caprine Alpha S1CSN gene sequences. There was query coverage to the extent of 100 per cent. This is one of the first studies in non-descript goats. Presence of predominant 'A' allele among these goats provides other selection criteria in addition to traditional selection methods, for increased milk protein.ThesisItem Open Access Study on Genetic Polymorphism of Dazl Gene in Sheep(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-11-14) Vageesh Pandith, S.; Nagaraja, R.; Jayashankar, M.R.; Nagaraja, C.S.; Krishnaswamy, A.The present study was carried out with objective of identifying and analyzing the genetic polymorphism in Ovine DAZL gene of native sheep (Mandya sheep), using PCRRFLP technique. A total of sixty five (65) Mandya sheep were randomly selected from two different Mandya sheep flock units viz., Livestock Research and Information Centre (Sheep), KVAFSU, Nagamangala and Department of Instructional livestock Farm complex, Veterinary College, KVAFSU, Bengaluru. From each representative animal, about 10 ml of venous blood was collected in vaccutainer tubes containing 0.5 per cent EDTA. The blood samples were immediately transported to the laboratory at 4 °C and genomic DNA was isolated within 24 hrs. A 655 bp fragment of Ovine DAZL gene sequence spanning part of exon 3, intron 3 and part of exon 4 was amplified by following standard PCR procedure. The PCR amplified sequence of Ovine DAZL gene was confirmed through nucleotide sequencing. Upon RFLP analysis using DdeI restriction enzyme, a polymorphic pattern revealed two alleles viz., Allele-A (348 and 307 bp fragments) and Allele-B (348, 153 and 154 bp fragments). In the studied population of Mandya sheep the allelic frequencies for A and B were 0.62 and 0.37, respectively. The frequencies of AA, AB and BB genotypes were 0.43, 0.38 and 0.18, respectively. The sequence analysis revealed two novel SNPs with transitions viz., C→T and T→G in Intron 3 of Ovine DAZL gene. BLASTn sequence analysis revealed high homology (99 per cent) with that of predicted Ovine DAZL gene (NC_019458) sequence of Ovine chromosome one.ThesisItem Open Access Study on Beta Casein Polymorphism in Malnad Gidda and Crossbred Cattle(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 12-08-14) Navyashree, T.C.; Nagaraja, C.S.; Jayashankar, M.R.; Satyanarayan, K.; Shettar, V.B.The exon 7 region of beta casein gene of Malnad Gidda and crossbred cattle was studied with an objective of analyzing its polymorphism. PCR–RFLP analysis of the amplified region revealed monomorphic pattern in Malnad Gidda and polymorphic pattern in crossbred cattle. Only A2A2 genotype was found in Malnad Gidda cattle. A2 allele was predominant in crossbred cattle with an allelic frequency of 0.79 while A1 allelic frequency was 0.21. The frequencies of A1A1, A1A2 and A2A2 genotypes were 0.13, 0.18 and 0.69 respectively, in crossbred cattle. The Malnad Gidda population was in Hardy Weinberg equilibrium indicating absence of selection pressure while crossbred population was not in equilibrium. The sequence analysis confirmed the difference between A1 and A2 allele due to SNP resulting in substitution of ‘C’ to ‘A’ causing replacement of proline by histidine. The present study confirmed the theory that A2 allele of beta casein is predominant in Bos indicus and crossbred cattle possess both A1A2 heterozygotes and A2A2 homozygotes.ThesisItem Open Access Molecular Genetic Studies on Butyrophilin Gene in Malnad Gidda Cattle and its Association with Milk Quality Traits(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-05-14) Vishwanath, B.; Nagaraja, C.S.; Jayashankar, M.R.; Narasimha Murathy; Shri Krishna IsloorThe present work was aimed at studying the Butyrophilin gene polymorphism and its association with milk quality traits in Malnad Gidda cattle. Blood and milk samples were collected from 50 Malnad Gidda cattle from Uttar Kannada district and Chickmagaloor districts of Karnataka. Milk samples were collected at fortnight intervals, for six times from the same animals. Genomic DNA was isolated by Miller’s High Salt method and Fat, SNF and Total Ash were analyzed by Gerber method, Formula method and Gravimetric method respectively. The genetic polymorphism of Butyrophilin gene was investigated by PCR-RFLP technique. An 893bp fragment of exon 8 of Butyrophilin gene was amplified. The amplified products were digested with restriction enzyme HaeIII. The restricted products were subjected to three per cent agarose gel electrophoresis and revealed two alleles A and B and genotypes AA and AB. The genotype BB was absent in the population studied. The highest gene and genotype frequencies were observed for A allele (0.88) and AA genotype (0.76) and lowest gene and genotype frequencies were observed for B allele (0.12) and AB genotype (0.24) respectively. The population studied was in Hardy- Weinberg equilibrium. Sequence analysis indicated 100 % homology to B.taurus and 99 per cent to B.indicus. There was a significant association between milk quality traits like Fat and SNF with genotypes AA and AB where A allele was gene was favorable, whereas total ash was not associated with any genotype. The present study revealed the polymorphism of BTN1A1 gene and its association with milk quality traits.ThesisItem Open Access Genetic Polymorphism of Major histocompatibility Complex Class Ii DRB Genes in Nandidurg Goats(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-06-13) Ayswarya R. Venu; Jayashankar, M.R.; Nagaraja, C.S.; Satyanarayan, K.; Byregowda, S.M.The current study was conducted to analyse the PCR-RFLP polymorphism and the sequences of second exon of Major histocompatibility complex class II DRB genein 82 Nandidurg goats. The amplified fragment with size of 285 bp was digested by the restriction enzyme Pst I. Two restriction patterns, A having fragments of size 226, 44 and15 bp, and B having fragements of size 270 and 15 bp were detected from Pst I RFLP. In case of heterozygotes, four bands of 270, 226, 44 and 15 bp fragments were resolved on the gel indicating the presence of two Pst I recognition site on one chromosome and one recognition site on the homologous pair. The gene frequencies of A and B were 0.51 and 0.49 respectively, and the genotype frequencies were 0.21 (AA), 0.59 (AB) and 0.20 (BB). The studied population of Nandidurg goats was found to be in Hardy Weinberg equilibrium. The sequencing of DRB gene exon two revealed two different DRB alleles which were more similar to Capra hircus (97-100%). The Pst I site was found to be associated with a TAC codon at position 78 and the absence was found to be associated with GTG codon in the sequenced sample. The close association of Pst I restriction sites and amino acid substitution at position 78 suggests that PCR-RFLP could be a useful tool in relating amino acid substitution at critical position with disease resistance.ThesisItem Open Access Studies on Genetic Polymorphism of Beta-Lactoglobulin Gene in Nandidurg Goat(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-09-13) Arshan Shaheed, A.; Nagaraja, C.S.; Jayashankar, M.R.; Girish Kumar, V; Veere Gowda, B.M.A study was conducted with the objective of analyzing the genetic variation at the β-lactoglobulin region of Nandidurg non-descriptive breed of goat by using PCR- RFLP technique. Genomic DNA was isolated from blood samples of 85 animals. The genetic diversity of caprine β-lactoglobulin locus was investigated by PCR- RFLP. A 426 bp fragment of exon 7 to the 3‟ flanking region of the β-lactoglobulin gene was amplified. The size of the amplified product was same in all the animals studied indicating conservation of DNA at this locus. A restriction endonuclease SacII was used to detect the genetic variation of the experimental unit in the β-lactoglobulin gene. β-LG/SacII polymorphism was observed as three patterns which allowed the identification of two alleles viz., A and B. The genotypic frequencies of AA, AB and BB were 0.35, 0.54 and 0.11 respectively. The allelic frequencies for A and B alleles were 0.62 and 0.38 respectively, among them allele A was predominant in studied population. The population studied was in Hardy-Weinberg equilibrium. The sequence analysis indicated that there was a high homology between the present result and the published caprine β-lactoglobulin sequences. There was query coverage to the extent of 100 per cent. The present study revealed the genetic variability at β-lactoglobulin gene locus in Nandidurg goat. Further study is suggested to understand the association of this gene with milk production traits.ThesisItem Open Access Molecular Genetic Studies on Fec B and Insulin like Growth Factor Genes in Different Sheep Breeds of Karnataka(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-06-11) Sudarshan S. Gadad; Jayashankar, M.R.; Nagaraja, C.S.; Satyanarayan, K.; Byregowda, S.M.A study was conducted with the objective of analyzing the genetic variation of the FecB gene and IGFBP-3 gene region of 50 each of Bannur and Tumkur sheep by using PCR-RFLP technique. Genomic DNA was isolated from blood samples of 50 each of Bannur and Tumkur animals. Approximately 140 bp fragment of exon 6 of FecB gene and 654 bp fragment of exon 2, intron 2, exon 3 and a part of intron 3 region of IGFBP-3 gene were amplified. The sizes of the amplified products were uniform with no variation in size within the breeds of animals studied indicating conservation of DNA at this locus. Restriction endonucleases AvaII and Hinf I were used to detect the genetic variation in the FecB gene and IGFBP-3 gene respectively. AvaII restriction enzyme did not detect any polymorphism, revealing the absence of FecB mutation in Bannur and Tumkur sheep suggesting that all the animals were non-carriers for FecB mutation gene. Hinf I restriction enzyme did not detect any polymorphism in animals studied and yielded a single restriction pattern of 315, 133, 109 and 97 bp revealing monomorphic pattern of IGFBP-3 gene in all the Bannur and Tumkur sheep studied. Two SNPs each at FecB locus, and five SNPs each at IGFBP-3 locus, were identified in Bannur and Tumkur sheep, respectively. AppendicesThesisItem Open Access Molecular Studies on Meat Quality Gene in Bandur Sheep(Karnataka Veterinary, Animal and Fisheries Sciences University, Bidar, 15-09-10) Sunil Kumar, M.A.; Nagaraja, C.S.; Jayashankar, M.R.; Nadeem Fairoze; Veere Gowda, B.M.A study was conducted with the objective of analyzing the genetic variation at the CAST region of Bandur breed of sheep by using PCR-RFLP technique. Genomic DNA was isolated from blood samples of 79 Bandur animals. The genetic diversity of ovine CAST locus was investigated by PCR-RFLP. A 622 bp fragment of exon 1C/1D from domain 1 region including the intron was amplified. The size of the amplified product was same in all the animals studied indicating conservation of DNA at this locus. Two restriction endonucleases MspI and NcoI were used to detect the genetic variation of the experimental unit in the CAST gene. CAST/MspI polymorphism was observed as three patterns which allowed the identification of two alleles viz., A and B. The allelic frequencies for A and B alleles were 0.74 and 0.26 respectively. The population studied was in Hardy- Weinberg equilibrium. CAST/NcoI polymorphism also showed three genotypes with two alleles, viz., A and B, the gene frequencies were 0.697 and 0.303 respectively. The NcoI digested the allele B amplicon, but not allele A. The population studied was in Hardy- Weinberg equilibrium. The sequence analysis indicated that there is high homology between the present result and the published ovine CAST sequences. There was query coverage to the extent of 95%. The present study revealed the genetic variability at CAST gene locus in Bandur sheep. Further study is suggested to understand the association of this gene with meat quality traits.