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Theses

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2005 - 20072
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Subject: Genetics and Plant Breeding × End date: 2009 × Start date: 2005 ×
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    ThesisItemOpen Access
    Molecular documentation of njavara types of rice (Oryza sativa L.) for cultivar identification
    (Department of Plant Breeding and Genetics, College of Horticulture, Vellanikkara, 2007) Shareesh, N; KAU; Elsy, C R
    Characterisation and evaluation of Njavara types of rice (Oryza sativa L.) was under taken in the Department of Plant Breeding and Genetics and Centre for Plant Biotechnology and Molecular Biology, College of Horticulture, Vellanikkara during 2005 - 2007 with the objective of molecular characterization and gene sequencing in Njavara for developing suitable molecular markers for cultivar identification. Njavara genotypes exhibited high variability with respect to lemma and palea colour with two major classes viz., yellow (straw colour) and black types. Detailed characterization revealed that yellow type could be further grouped into gold furrows on straw (N3 & N5) and brown furrows on straw (N4 & N7). Three genotypes viz., N1, N2 and N6 exhibited a lemma and palea colour dominated by black. N1 and N2 exhibited variations in black colour for lemma and palea as pure black, black furrows/black patches on straw background whereas N6 exhibited light shade of black. Variations in seed coat colour as red, light brown and brown were also observed among the genotypes. The method suggested by Dellaporta et al. (1983) with slight modifications was found to be effective in isolating good quality genomic DNA from Njavara. Good amplifications were observed when RAPD analysis was performed with sequences OPA 1, OPA 4, OPA 6, OPA7 , OPA 9, OPN 6, OPN 18, OPP 6, OPP 11 and OPE 6. OPA 1 and OPP 11 were found to be promising in the amplification of rice genomic DNA with maximum amplification. Amplification of Njavara DNA with primer OPE 6 exhibited unique bands (1.375 kb , 1.29 kb and 0.44 kb ) for Njavara genotypes and hence are valuable as DNA markers for the identification of this unique cultivar. The dendrogram with RAPD markers showed distinct clusters for Njavara. Cloning and sequencing of the unique molecular band with M 13 primer gave the sequence data of a gene segment of size 762 bp.The homology search of this sequence with BLASTN showed that it has maximum identity with genes from Oryza sativa (japonica cultivar-group) mitochondrial gene for tRNA-Asn, complete sequence, O. sativa mRNA for chilling-inducible protein, O.sativa rbbi2-5 gene for putative Bowman Birk tryspin inhibitor, O.sativa rbbi2-3 gene for putative Bowman Birk trypsin inhibitor, O.sativa rbbi2-4 gene for putative Bowman Birk trypsin inhibitor and O. sativa (japonica cultivar-group) mRNA for chilling tolerance related protein.The homology of cloned DNA fragments of Njavara (N5) with BBI genes (rbbi 2-3, rbbi 2-4 and rbbi 2-5 ) is a preliminary indication of the medicinal property (anticarcinogenic) of this unique medicinal cultivar of Kerala and also its thermostable nature. Sequence analysis revealed the presence of five ORF’s . The longest open reading frame had 180 bases encoding 59 amino acids in the predicted coding region. Among the amino acids, serine was occurring more frequently than other amino acids. ORF in +3 reading frame was found to be of a residue length of 102 bases, encoding 33 amino acids. Genscan tool determined two internal exons from the clone with a length of 91 and 129 residues. Sequence analysis of the data with VecScreen showed strong match to vector sequences in the database eventhough the sequences were not matching with pSCA (vector used in the present study) vector. Alignment of sequences through CLUSTAL W programme revealed poor homology with query sequence and vector sequence used for cloning. Homology was shown between the sequences when BLAST 2 SEQUENCES programme was used. These results are to be confirmed through further studies.
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    ThesisItemOpen Access
    Evaluation of microsatellite markers for selection of crossbred cattle
    (Department of Animal Breeding and Genetics, College of Veterinary and Animal Sciences, Mannuthy, 2005) Naicy, Thomas; KAU; Anilkumar, K
    The possibility of using the informations of the allele frequency, genotype frequency, heterozygosity and PIC of five selected microsatellite markers (ILSTS096, HUJII77, BL41, BM1508 and BM4305) and their associations with the economically important traits for the selection of crossbred cattle were studied. Among the economic traits studied milk fat percentage and AFC showed significant difference among the ten sire families and hence their associations with the selected microsatellite markers were worked out. PCR conditions were standardised for each marker separately. The number of alleles, size range and number of genotypes identified were 12, 188-212 bp and 35 respectively for ILSTS096 locus, 13, 193-221 bp and 36 for HUJII77 locus, 14, 232-266 bp and 36 for BL41 locus, 7, 103-115 bp and 17 at BM1508 locus and 12, 146-168 bp and 37 for BM4305 locus in the unrelated crossbred dairy cattle population. The highest direct count heterozygosity was obtained for ILSTS096 followed by BL41, BM4305, HUJII77 and BM1508 (0.877-0.683). The highest unbiased heterozygosity was obtained for ILSTS096 followed by BL41, BM4305, HUJII77 and BM1508 (0.880-0.686). All the markers were highly informative as their PIC values (0.865-0.630) were more than 0.5. Three sire families namely, Deva, Bull No.250 and Hakkim showed significantly lower milk fat percentage and three other (Dipesh, Onkar and Gopal), showed significantly higher AFC. All the five microsatellite markers had significant effect on milk fat percentage and three of them (ILSTS096, BL41 and BM4305) showed significant effect on AFC. The allelic averages of fat percentage for the allele 188 and 204 at ILSTS096 locus, 205 at HUJII77 locus and 154 at BM4305 locus were significantly lower and that of 198 at ILSTS096 locus, 240 at BL41 locus, 109 and 113 at BM1508 locus and 166 at BM4305 locus were significantly higher. The allelic averages of AFC for the alleles 196 at ILSTS096 locus, 246 at BL41 locus and 154 at BM4305 locus were significantly lower. All these three alleles were absent in the sires of the three families having higher AFC. The allelic frequencies of 188 and 204 of the marker ILSTS096 were low in the population and that of 198 was high. So selection against the alleles 188 and 204 and selection for the allele 198 can be done, but the impact of selection will be meagre. At the BL41 locus, frequency of the allele 240 was comparatively low and the frequency of the allele 242 is very high in the population. So the selection for the allele 240 and selection against the allele 242 will have good impact on milk fat percentage of the selected animals. Frequency of allele 246 in the population is comparatively low. Hence selection for this allele will be favourable to reduce the AFC. The frequency of the allele 109 of BM1508 is low. So selection for this allele will be more beneficial. The animals with the allele 166 at BM4305 locus had the highest average of milk fat percentage and the frequency of this allele in the population is very low, hence selection for this allele will have good impact on higher milk fat percentage.