1. KAUTIR (Kerala Agricultural University Theses Information and Retrieval)
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Item Development of cytoplasmic male sterile line in an identified rice variety of Kerala through marker assisted back crossing(Department of Plant Breeding & Genetics, College of Agriculture, Vellayani, 2019) Tejashree Shivaputra Lachyan; Jayalekshmy, V GItem Breeding cowpea (Vigna unguiculata (L.) Walp.) for resistance to spotted pod borer (Maruca vitrata Fab.)(Department of Plant Breeding and Genetics, Vellanikkara, 2018) Ambavane Ajinkya Rajendra; Jiji JosephItem Characterization and validation of microsatelite markers for resistance to vascular streak dieback disease in cocoa (Theobroma cacao L.)(Centre for Plant Biotechnolgy and Molecular Biology, College of Horticulture, Vellanikkara, 2016) Waghmare Sandesh Tulshiram; Deepu MathewCocoa is the third important plantation crop next to coffee and tea. The global production and consumption of cocoa is 27.00 lakh MT. Among the fungal diseases, Vascular Streak Dieback (VSD) caused by Ceratobasidium theobromae is the main constraint in cocoa growing countries, causing heavy losses in mature trees as well as seedlings. The VSD disease cannot be effectively controlled by chemicals and hence breeding for the development of resistant varieties is the best strategy to tackle the disease. In order to confirm the transfer of a desired gene into the offspring, conventional breeding methods rely on the field screening which will be highly influenced by the environmental factors. Marker assisted selection is an alternate where the tightly linked molecular markers will be employed to confirm the presence of the gene of interest in the selected plants. Five ISSR and one SSR markers linked to VSD resistance were identified at Kerala Agricultural University (Chandrakant, 2014). The present study was undertaken with the objective of validating the identified SSR and ISSR markers and to characterize the ISSR markers to identify the corresponding SSR markers. For validation and characterization, twenty VSD resistant hybrids and four susceptible clones were used. For molecular analyses, good quality genomic DNA was isolated from twenty four genotypes and ISSR markers UBC 811, UBC 815, UBC 826, UBC 857, UBC 866 and SSR marker mTcCIR 42 were screened. ISSR analysis had shown that all the primers are capable to differentiate resistant and susceptible genotypes. The SSR assay has also differentiated the resistant and susceptible genotypes. The distinct markers generated in resistant genotypes using UBC 811, UBC 826 and UBC 857 were eluted, cloned to pGEMT vector and sequenced. The nucleotide sequences were annotated using BLAST, ORF finder and SSR finder. The BLASTn of UBC811A and UBC811D nucleotide sequence have shown that this resistance locus lie in the chromosome V of Theobroma cacao genome. BLASTn of UBC826A, UBC826B and UBC857 has positioned these loci in chromosome III. ORF1 and ORF3 in UBC811D are shown to code for aflatoxin biosynthesis regulatory protein and NAD(P)H dehydrogenase quinine, respectively. ORF1 in UBC826B and ORF5 in UBC857-2 code for potassium transporter 27 (0sHAK-27) and structural polyprotein precursor of VP2, capsid protein VP2, respectively. All these proteins are identified to have definite roles in defence pathways. The frequency and distribution of SSR motifs, dimmers to decamers, in these ISSR markers and the corresponding primers were identified. The reported ISSR and SSR markers were validated and found to be successful in differentiating resistant and susceptible genotypes of cocoa; thereby these markers can be used in marker assisted breeding for VSD resistance.Item Diversity analysis in landraces of rice(oryza sativa L.) in Wayanad through morphological and molecular polymorphism study(Department of Plant Breeding and Genetics,College of Horticulture, Vellanikkara, Thrissur, 2018) Manjunatha, G A; Elsy, C RThe present investigation entitled “Diversity analysis in landraces of rice (Oryza sativa L.) in Wayanad through morphological and molecular polymorphism study” was conducted at the Department of Plant Breeding and Genetics, College of Horticulture, Vellanikkara, Thrissur and Regional Agricultural Research Station, Ambalavayal, Wayanad during the period 2015- 2018. The study aimed to collect and characterize the rice landraces of Wayanad at morphological level and also to characterize the popular aromatic genotypes of the area at molecular level. DUS characterization revealed that, all the landraces under the study exhibited presence of leaf collar, absence of anthocyanin colouration of leaf collar, presence of leaf ligule, split shape of leaf ligule, absence of anthocyanin colouration for plant parts like lemma (keel), area below apex of lemma, stem nodes and presence of secondary branching in panicle. Variability was exhibited for majority of characters namely coleoptile colour, basal leaf sheath colour, intensity of green colour of leaf, anthocyanin colouration of plant parts like leaf, leaf sheath, auricles, ligules, lemma apex, area below apex of lemma, distribution of anthocyanin colouration in leaf, pubescence of leaf blade surface, leaf auricles, culm attitude, density of pubescence of lemma, colour of stigma, attitude of flag leaf blade, curvature of main axis of panicle, lemma and palea colour, presence and colour of awns, distribution of awns in panicle, secondary branching in panicle, attitude of branches in panicle, panicle exsertion, leaf senescence, sterile lemma colour, shape, colour and aroma of decorticated grain, gelatinization temperature and lodging nature.Thavalakannan, Mullan puncha and Sugandhamathi exhibited distinct morphological characters. Among the 60 landraces, Kanni kayama, Ambalavayal-1, Kothandan, Onamottan, Thondi-2, Chenthadi, Kannali and Thondi-1 exhibited significantly high grain yield per plant, which was on par with that of Uma and Aathira (high yielding check varieties), indicating the possibility of commercial cultivation of these cultivars. High PCV value than GCV for all the characters under study, indicated the influences of environmental factors on the characters. High heritability and high genetic gain was exhibited by the characters like length of leaf blade, width of leaf blade, stem thickness, stem length, number of tillers per plant, number of panicles per plant, length of panicle main axis, number of spikelets per panicle, number of grains per panicle, seed setting (per cent), 1000 grain weight, grain length, grain L/B ratio, decorticated grain L/B ratio and grain yield per plant, indicating that these characters could be used in crop improvement programmes. Character association studies including correlation and path-analysis revealed that, five characters viz., width of leaf blade, stem length, number of panicles per plant, weight of 1000 grains and decorticated grain width showed both positive correlation and positive direct effect on grain yield per plant. Cluster analysis based on qualitative characters categorized 60 landraces into 11 clusters at 74 percent similarity level. Based on D2 statistics analysis, the landraces were grouped into seven clusters with variable number of landraces in each cluster, indicating wide genetic diversity in the Wayanad landraces. All the inter-cluster distances were higher than the intra-cluster distance, indicating the wider genetic diversity among landraces of different clusters. Molecular characterization of aromatic rice genotypes of Wayanad by SSR (RM) profiling revealed high level of genetic polymorphism among the genotypes studied. Out of 86 SSR markers used for molecular characterization, 44 markers were polymorphic and remaining 42 were monomorphic. Maximum number of amplicons was exhibited by RM247 with five amplicons, followed by RM85, RM251, RM248 and RM493 with four amplicons each. The highest PIC value was exhibited by RM247 (0.90), followed by RM85, RM251 and RM493 with 0.88 PIC value each. Out of 86 SSR (RM) markers, 21 markers distinguished Basmati from traditional aromatic landraces of Wayanad viz., Gandhakasala and Jeerakasala. Seven SSR markers distinguished Gandhakasala from Jeerakasala, whereas 23 markers distinguished Basmati from Jeerakasala. Twenty-two markers distinguished Basmati from Gandhakasala and 23 markers distinguished aromatic group from non-aromatic group. Cluster analysis for molecular characterization revealed maximum similarity coefficient (1.00) within all the Jeerakasala morphotypes and all the Gandhakasala morphotypes. Cluster analysis effectively differentiated Basmati, Jeerakasala, Gandhakasala, Uma and Aathira from each other. Among the five clusters formed, cluster III was the largest one comprising all the 12 Gandhakasala morphotypes, followed by cluster IV with all Jeerakasala morphotypes. Cluster I, Cluster II and Cluster V exhibited one genotype each namely Aathira, Uma and Basmati, indicating their genetic distinctness.Item Development of near isogenic lines of rice variety 'uma' for blast resistance genes through molecular marker assisted backcross breeding(Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, 2017) Harikrishnan, P J; Jayalekshmy, V GItem Polymorphism of ovine fecundity gene linked microsatellite markers in malabari goats(Department of Animal Breeding and Genetics, College of Veterinary and Animal Sciences, Mannuthy, 2006) Seena, T X; Raghavan, K CThe objective of the present study was to explore the polymorphism of ovine fecundity gene linked microsatellite markers in Malabari goats. Malabari goats are one of the most prolific breeds in India. The microsatellite markers OarAE101, BMS2508 and BM1329 linked to the Booroola gene (FecB) and the microsatellite markers TGLA54 and TGLA68 linked to Inverdale (FecX1) gene in sheep were selected for the study. The DNA samples from 120 Malabari goats which had given birth to singles, twins, triplets and quadruplets in the second and subsequent parities were utilized for the study. DNA was isolated by phenol chloroform extraction procedure with some modifications. The DNA samples were amplified by PCR using the radioactively labeled microsatellite primers. The amplified products were resolved by polyacrylamide gel electrophoresis followed by autoradiography. The genotypes of animals were determined for each microsatellite loci by comparing the sizes of alleles with M13 phage DNA sequencing ladder. The microsatellite markers OarAE101, BMS2508 and TGLA54 were found to be monomorphic in the population under study. The microsatellite markers BM1329 and TGLA68 were found to be highly polymorphic in Malabari goats. A total of 15 alleles with 167-195 bp for the locus BM1329 and 8 alleles with a size range of 98-114 bp were observed for the locus TGLA68. The total number of genotypes observed was 34 for BM1329 locus and 12 for TGLA68 locus. Heterozygosity of 0.8660 for the locus BM1329 and 0.8024 for the locus TGLA68 were observed. The polymorphic information content (PIC) computed was 0.8526 and 0.7823 for the loci BM1329 and TGLA68 respectively. A significant difference in the alleles 181bp and 191 bp (P≤0.01) and the alleles 179 bp and 185 bp (P≤0.05) and the genotype 177/191 (P≤0.01) for the locus BM1329 were found in different types of births. The genotype 175/185 of the microsatellite marker BM1329 was found to be significantly related to a higher litter size when compared to the mean litter size of the population in Malabari goats (P≤0.01). The allele 104 bp of the locus TGLA68 was found to be significantly different in different types of births (P≤0.01). The highest frequency (0.4545) was observed in triplets followed by twins (0.2177) and singles (0.1847). The genotype 104/106 was found to be significantly different in different types of birth with triplets having a frequency of (0.4545), followed by singles (0.1087) and twins (0.0333). The season of birth had no significant effect on the type of birth and number of kidding in Malabari goats. Identification and selection of individuals that carry the alleles and genotypes associated with high prolificacy is possible in Malabari goats based on the above result. So new breeding strategies involving selection for high prolificacy can maximize the net profit of farmers. This study has brought to light important information improving the reproductive performance of Malabari goats by marker assisted selection.Item Genetic divergence in rabbits used for breeding in Kerala(Department of Animal Breeding and Genetics, College of Veterinary and Animal Sciences, Mannuthy, 2007) NIsha Valsan; Bindhu, K AThe genetic divergence among three breeds of rabbit, viz. Newzealand White, Soviet Chinchilla and Grey Giant was studied using microsatellite markers. A set of twelve microsatellite markers were tested, out of which three markers (Sol 03, Sol 33 and Sol 44) were selected based on their polymorphism. The PCR products were separated by denaturing polyacrylamide gel electrophoresis and autoradiographed. The Sol 03 locus was found to be the most polymorphic with fourteen alleles in the pooled population. The values for heterozygosity and PIC in Newzealand White at the Sol 03 locus were recorded as 0.840 and 0.836, in Soviet Chinchilla as 0.766 and 0.764, while in Grey Giant, the heterozygosity and PIC values stood at 0.775 and 0.765, respectively. Eight alleles were detected at the Sol 33 locus. The maximum values for heterozygosity (0.858) and PIC (0.854) were observed in Grey Giant while Newzealand White (0.672 and 0.667, respectively) recorded the lowest. In Soviet Chinchilla, values for heterozygosity and PIC were 0.691 and 0.680 respectively. with mean heterozygosity and PIC values of 0.740 and 0.764. Sol 44 locus revealed four alleles. The highest values for heterozygosity (0.728) and PIC (0.702) at the Sol 44 locus were recorded in Grey Giant, while the lowest (0.567 and 0.477) in Soviet Chinchilla. The heterozygosity and PIC values were 0.586 and 0.502, respectively in Newzealand White. The genetic distance was calculated based on Nei’s formula, and the highest value was noticed between Soviet Chinchilla and Grey Giant (0.6942) while the lowest between Newzealand White and Soviet Chinchilla (0.2022). The dendrogram constructed using POPGENE program grouped Newzealand White and Soviet Chinchilla in one cluster indicating their closer relationship. Grey Giant was found to be the most widely separated breed.Item Genetic and phenotypic variations of geographically different goat populations of Kerala(Department of Animal Breeding and Genetics, College of Veterinary and Animal Sciences, Mannuthy, 2007) Jimcy Joseph; Raghavan, K CGenetic diversity of four geographically different goat populations in Trivandrum, Kottayam, Thrissur and Kozhikode districts in Kerala was analysed based on physical, biometrical traits and microsatellite markers. Based on physical traits, the populations were not very distinct and uniformity was seen with respect to coat colour, horn pattern, presence or absence of tassels or beard and hair pattern. The animals were predominantly horned and short haired with coat colour of white or a combination of white with either black or brown. Majority of animals did not possess tassels or beard. The biometrical traits observed in the present study were body measurements, peak yield and prolificacy. Body weight of adult female goats was predicted using the regression equation based on the power function of chest girth. It was shown that the animals of Trivandrum district had higher values for almost all body measurements and predicted body weight, while the Thrissur population had lowest values for these growth traits. Animals of Kottayam and Kozhikode came in between. Percentage of multiple births was also higher in Trivandrum goat population (68) compared to other populations indicating high prolificacy. Highest peak yield was recorded for Kottayam goat population. Discriminant analysis based on morphometric measurements revealed that the most discriminative variables were head width and body length, followed by shin circumference and rump length. Mahalanobis distance calculated based on morphometric traits indicated that Thrissur and Trivandrum populations were more distant, while least distance was observed between Kottayam and Kozhikode. Discriminant analysis based on body weight, peak yield and prolificacy revealed that only body weight and peak yield variables have significant discriminative capacity. Trivandrum, Kottayam and Kozhikode populations were grouped together in one cluster based on the distance value. Thrissur population was distant from all other populations. Microsatellite analysis revealed that all the five loci were highly polymorphic with five to nineteen alleles in different populations. The total number of alleles, the mean number of alleles per locus, mean heterozygosity and mean polymorphic information content were 51, 10.2, 0.8201 and 0.8104, respectively. The values indicate that the markers can be successfully used to study the variations existing in the populations. Based on Nei’s genetic distance Thrissur and Trivandrum population were grouped together first and then with Kozhikode population, while the Kottayam population formed a unique branch in dendrogram. Unrelated distance values produced by quantitative and molecular measures of variation may be attributed in part to the environmental influences and local selection pressures. Though use of more number of markers may possibly explain the variation encountered in these traits, the present investigation reveals that selection within each population for traits of economic importance like body weight and milk production is the best method to improve the performance of goats of Kerala.