1. KAUTIR (Kerala Agricultural University Theses Information and Retrieval)
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Item Genetic structure and diversity analysis of traditional rice (Oryza sativa L.) varieties of north Kerala(Department of Genetics and Plant Breeding, College of Agriculture, Padannakkad, 2023) Nisha Suresh Kantamneni; Vaijayanthi, P VThe study entitled “Genetic structure and diversity analysis of traditional rice (Oryza sativa L.) varieties of North Kerala” was carried out at the department of Genetics and Plant Breeding, College of Agriculture, Padannakkad. The main objective of the study was to assess genetic diversity and population genetic structure of traditional rice varieties (TRVs) of North Kerala based on Distinctiveness, Uniformity and Stability (DUS) characterization and SSR marker-based molecular analysis. The material for the study comprised of 50 TRVs collected from different districts of North Kerala. The experiment was laid out in augmented design at IF-II, Karuvacheri (12°14′45′′N; 75° 8′6′′E). Morpho-metric characterization of TRVs for 24 vegetative, 22 reproductive and three seed traits were carried out during September-February 2021 following the DUS descriptor of rice. Quantitative traits (QTs) recorded included five DUS traits and four additional traits (plant height, number of tillers plant-1, number of productive tillers plant-1 and number of spikelets panicle-1). Among 49 DUS traits, seven were monomorphic, 10 were dimorphic and 32 were polymorphic. As per analysis of variance (ANOVA) for QTs, TRVs showed highly significant mean squares for four quantitative traits such as plant height, number of spikelets panicle-1, 1000 grain weight and grain length. Variation due to ‘checks’ were also significant for the said traits. Hence, actual trait mean values were adjusted by calculating the block effect. TRVs showed a mean height of 112.87 cm, 5.61 tillers plant- 1, 5.24 productive tillers-1 and 113.64 spikelets panicle-1 and 23.54 g weight for 1000 grains. Among nine QTs, higher variance was observed for spikelets panicle-1 and plant height. The Phenotypic Coefficient of variation (PCV) and Genotypic Coefficient of Variation (GCV) was higher for number of tillers plant-1, number of productive tillers plant-1, number of panicles plant-1, number of spikelets panicle-1 and 1000 grain weight. High broad-sense heritability coupled with high genetic advance was observed for plant height, number of tillers plant-1, number of spikelets panicle-1, 1000 grain weight and grain length indicating additive gene effects and efficiency of selection-based breeding methods. K-means clustering analysis grouped 50 TRVs into two clusters. The total variability among 50 TRVs were extracted through principal component (PC) analysis 153 and three significant PCs (accounting 72.57% of total variability) were obtained. Further, total variability was visualized in the form of PC1 vs PC2 biplot. In order to decipher molecular diversity among TRVs, laboratory experiment was carried out at NAHEP-CAAST lab, College of Agriculture, Padannakkad. Genomic DNA was isolated from 21 days old seedlings following modified CTAB method. The 50 TRVs were genotyped with 30 SSR markers (shortlisted by IRRI based on genome-wide coverage and higher PIC value) following standard PCR, electrophoresis and visualization techniques. Among SSRs, 18 were monomorphic and 12 were polymorphic. Among polymorphic SSRs, RM 413 and OSR 13 detected 3 alleles/locus and showed highest PIC value (0.559 and 0.594, respectively) and Nei’s genetic diversity (0.55 and 0.59, respectively). STRUCTURE analysis revealed three sub-populations and admixture among 50 TRVs. Population admixture and preferential gene flow among TRVs were further confirmed by Analysis of molecular variance (AMOVA) as estimate of ‘among population’ variance was lower. Among three sub-populations, maximum diversity was observed among TRVs of first sub-population as indicated by higher estimates of the Shannon index and unbiased expected heterozygosity. In conclusion, 50 TRVs were diverse with respect to 32 DUS traits and highly variable for 4 QTs. Polymorphic descriptors like leaf colouration, lemma pubescence, panicle exertion etc. are of special significance as they have the potential to act as morphological markers for TRV conservation and registration. The TRVs namely, ‘Chuvannachitteni’ and ‘Mundom’ were most diverse as per biplot analysis and K means clustering. However, SSR- based diversity analysis revealed low level of polymorphism and population structure among TRVs. Genetic diversity as a whole includes both exon and intron variability, conservation and registration of TRVs will be optimized by complementing DUS characterization with more functional markers.Item Development of fusarium wilt resistant breeding lines of yardlong bean(Vigna unguiculata subsp.sesquipedalis (L.) Verdcourt) variety githika(Department of Genetics and Plant Breeding, College of Agriculture , Vellayani, 2025-02-17) Sreeja, R.; Nivedhitha, M SThe present study entitled “Development of fusarium wilt resistant breeding lines from yard long bean (Vigna unguiculata subsp.sesquipedalis (L.)Verdcourt) variety Githika was conducted in the Department of Genetics and Plant Breeding, College of Agriculture, Vellayani during 2023-24, with an objective of evaluation of back cross progenies from Githika for fusarium wilt resistance and yield related traits. The research program consisted of 4 main experiments. First experiment involved evaluation of 35 BC2F1 lines resistant to fusarium wilt developed in the concluded Ph.D project Shahiba, (2023) for yield and related traits of the recurrent parent Githika and 10 lines with maximum morphological similarity with Githika was selfed to produce BC2F2 seeds.This experiment was done in a completely randomized design (CRD) with 2 replications. Evaluation of biometric as well as quality parameters in the 35 BC2F1 lines showed significant variations. High heritability along with high genetic advance was observed for all the characters studied except days to 50% flowering. In experiment 2, a total of 74 BC2F2 seedlings from the 10 selected BC2F1 lines were artificially screened for fusarium wilt resistance during the seedling stage. The pathogen associated with fusarium wilt in yard long bean was subcultured from the already isolated and cultured fungal culture plates developed in the concluded Ph.D project Shahiba, (2023). The isolate obtained were mass multiplied in the sand:maize (9:1) medium at 28°C. Soil inoculation method with 10% inoculum of the pathogen multiplied in the sand:maize (9:1) medium was used to produce disease symptoms on artificial inoculation. The scoring for disease incidence was done using the 0-4 scale reported by Senthilkumar (2003). Out of this 74 BC2F2 lines screened, seventy-one were resistant, two were moderately resistant and one was highly susceptible. In experiment 3, the resistant BC2F2 segregants which were in close proximity to the recurrent parent and with a disease score of ‘0’ were backcrossed to produce BC3F1 lines. Out of 217 pollinations, 22 set into pods and about 248 seed set was observed and pod set percentage was found to be 10.13%. In experiment 4, the 11 BC3F1 lines having maximum morphological similarity with the recurrent parent was morphologically evaluated for the 7 biometric characters. This experiment was done in a completely randomized design (CRD) with 3 replications. Analysis of variance revealed a significant variation among the lines for 7 biometric characters. High phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) was observed for pod yield per plant and moderate PCV and GCV were observed for number of pods per plant, pod weight and number of seeds per pod. High heritability along with high genetic advance was observed in pod weight and pod yield per plant, thereby indicating that these traits are predominant in additive gene action. Moderate heritability along with high Genetic advance was recorded for traits such as number of pods per plant and number of seeds per pod, while high heritability combined with moderate Genetic advance was observed for the trait pod length. The pod yield per plant was positively correlated with number of primary branches per plant, number of pods per plant, pod weight, pod length, number of seeds per pod and was negatively correlated with days to 50% flowering. Path analysis of biometric characters revealed that the pod weight had the highest direct positive effect on pod yield per plant, followed by number of pods per plant. A high positive indirect effect on pod yield per plant was shown by pod weight through number of seeds per pod. From the study, 11 resistant BC3F1 lines BG3 1-4-1, BG3 6-3-4, BG313-6-2, BG3 50-2-3, BG350-2-5, BG3 50-2-6, BG3123-1-1, BG3 123-5-2, BG3 123-5-7, BG3123-5-8 and BG3130-2-4 which were in close proximity to the recurrent parent, Githika was obtained and could be carried forward for further evaluation. The BC3F2 seeds of 11 lines found resistant to fusarium wilt could be used as breeding lines for developing varieties resistant to fusarium wilt along with the traits of Githika through a backcross program.Item Induction and regulation of flowering in rice bean [Vigna umbellata (Thunb.)](Department of Genetics and Plant Breeding, College of Agriculture,Vellayani, 2025-01-23) Aiswarya Chandrahasan.The present study entitled ―Induction and regulation of flowering in rice bean [Vigna umbellata (Thunb.)]‖ was carried out in the Department of Genetics and Plant Breeding, College of Agriculture, Vellayani during 2022-24. This study aimed to regulate flowering in rice bean through hormonal application and analyze the upregulation of flowering-related genes. The research programme comprised of two experiments. The first experiment was hormonal application to regulate flowering and second experiment included flowering gene expression analysis. The experiment was laid out in randomized block design with ten treatments and three replications. The plot size of 3m2 was followed in the field experiment. The experimental materials for the present study were fodder rice bean varietes Surabhi from KAU and Bidhan-2 from BCKV, Kalyani. The treatments comprised of control, seed inoculation with Piriformospora indica and different doses of foliar sprays (Salicylic acid at 100 and 150 ppm, Gibberellic acid at 200 and 300 ppm, Paclobutrazol at 10 and 20 ppm and KNO3 at 1 and 1.5%) at 30 days after sowing (DAS). The observations on quantitative characters and qualitative characters showed significant differences among treatments, except for field emergence in variety Surabhi. Early flowering was observed in Surabhi treated with SA at 100 ppm (65.36 DAS), followed by GA₃ at 300 ppm (67.72 DAS), SA at 150 ppm (67.81 DAS), and Paclobutrazol at 10 ppm (69.87 DAS), while control flowered last (80.96 DAS). No flowering was observed in Bidhan-2. Seed inoculation with P.indica improved fodder qualities like LAI, number of branches, plant height, number of pods per plant and green fodder yield per plot in rice bean variety Surabhi. The highest seed yield was also recorded in plants treated with P.indica (81.88 g) and lowest in plants treated with Salicylic acid at 150 ppm (47.88 g). A significant positive correlation was exhibited by days to first flowering with days to 50% flowering (0.992) and days to maturity (0.979), whereas number of branches 95 (-0.537) and number of seeds per plant (-0.41) exhibited significant negative correlation. A significant positive correlation was recorded by green fodder yield per plot with LAI (0.997), dry fodder yield per plot (0.962), plant height (0.949), number of branches (0.746) and field emergence (0.335). Path analysis revealed that days to maturity exhibited highest direct effect on days to first flowering (0.912). Rest of the characters showed a negligible direct effect on days to first flowering. The highest positive indirect effect on days to first flowering was observed by days to maturity through days to 50% flowering (0.905). Principal component analysis showed 85.88% contribution of first 4 PC groups towards the total variance and the squared cosine diagram showed that days to first flowering exhibited maximum value in PC1 which accounted for 34.22% of total variance. The RNA isolated from the flower buds of control and the treatment of which showed earliest flowering (SA at 100 ppm) were converted to complementary DNA (cDNA). The expression levels of genes ELF3 and FT in the selected treatments were studied using the quantitative real time PCR. The relative expression of control and treated plants demonstrated the varying degree of flowering gene expression. The relative expression profile using ELF3 gene showed 1.42 fold increase in treated plants (SA at 100 ppm) as compared to control indicating the upregulation of flowering gene ELF3 in treated plants. In conclusion, foliar application of Salicylic acid at 100 ppm was found to be the best treatment in rice bean variety Surabhi for inducing early flowering. Treated plants flowered 15 days before control. Plants treated with GA3 at 300 ppm, Paclobutrazol at 10 ppm and KNO3 at 1% flowered 13, 11 and 3 days respectively before control. Seed inoculation with P.indica resulted in flowering 7.5 days before control in Surabhi. Seed inoculation with P.indica resulted in improvement of fodder qualities like LAI, number of branches, plant height, number of pods per plant and green fodder yield per plot in both the rice bean varieties (Surabhi and Bidhan-2). Seed yield was also highest (Surabhi) in plants treated with P.indica. No flowering was observed in variety Bidhan-2. The 96 differential expression analysis using RT-qPCR revealed an upregulation of ELF3 genes in treated plants which correlated with an accelerated flowering response. Future studies could explore the different range of hormonal concentrations to determine the optimal dose for inducing early flowering in rice bean, as well as any potential toxic effects at higher doses.Item Molecular characterization of brinjal (Solanum melongena L.) genotypes and their performance assessment in summer(Department of Genetics and Plant Breeding, College of Agriculture, Padanakkad, 2023-05-31) Chakravaram, Alekhya; Namboodiri Raji VasudevanItem Genetics of shattering resistance in rice (Oryza sativa L.)(Department of Plant Breeding and Genetics, College of Horticulture, Vellanikkara, 2020) Akhil, K P; Biju, SItem Development of stabilised population of cowpea segregants(Vigna unguiculata (L.) walp.) with high protein content and grain yield(Department of Plant Breeding and Genetics, College of Horticulture, Vellanikkara, 2019) Ashni Varghese; Jiji JosephCowpea (Vigna unguiculata (L.) Walp.) is an important pulse crop providing good source of protein and often referred to as poor man’s meat. It is a versatile crop, of which seeds are utilised as pulse, green pods as vegetable, leaves as forage and helps in restoring soil fertility. Many reports have indicated protein content of more than 30 per cent in certain cowpea genotypes, but at the cost of yield. Hence, the present study was proposed to develop cultures with high grain yield and protein content. The present study was conducted at Department of Plant Breeding and Genetics, College of Horticulture during 2017-2019. Twenty three lines with high yield and protein content in the F3 generation of two cowpea crosses H10 (Anaswara X PKB 3) and H11 (Anaswara X PKB 4) identified in previous studies formed the working material. These lines were evaluated in F4, F5 and F6 generations and pedigree selection was performed to select superior plants. Observations were recorded on 12 characters viz. plant height, number of branches, days to first flowering, days to first harvest, days to last harvest, number of pods per plant, length of pod, pod weight, number of seeds per pod, hundred seed weight, grain yield per plant and protein content. The F4 generation of both the crosses exhibited lower mean value for most of the characters than the parent Anaswara, but recorded moderate to high variance and range. Higher mean value was observed for days to first flowering, first harvest, last harvest, number of branches and protein content. Genetic parameters indicated that GCV was moderate for length of pod, number of seeds per pod, and hundred seed weight and high for grain yield per plant. High heritability coupled with moderate to high genetic advance was recorded for number of pods per plant, number of seeds per pod, hundred seed weight, and grain yield. Correlation studies in F4 generation revealed that grain yield was positively correlated with plant height, number of branches per plant, number of pods per plant, length of pod, pod weight, number of seeds per pod and test weight. There was non-significant correlation between grain yield and seed protein content. Further path analysis confirmed that high positive direct effect on grain yield was given by pods per plant, number of seeds per pod and hundred seed weight. Based on these observations, characters like number of pods per plant, hundred seed weight and number of seeds per pod were simultaneously included along with grain yield for setting selection criteria to select superior individual plants. Based on these set criteria, 13 individual plants from cross H10 and 10 plants from cross H11 were selected and forwarded to F5 generation. In F5 generation, mean values for number of branches, number of pods per plant, number of seeds per pod and protein content were higher than that of Anaswara with sufficient variance and range. GCV was moderate for number of branches, length of pod, pod weight, hundred seed weight and grain yield per plant. High heritability with moderate to high genetic advance was recorded for number of pods per plant, length of pod, pod weight, number of seeds per pod, hundred seed weight and grain yield. Based on the segregation pattern observed, the plants were grouped into two different categories - one with medium long pods and small seeds closely packed within the pod and the other type with long fleshy pods and bold seeds. Hence, separate selection criteria was developed for both the types comprising of characters like number of pods, number of seeds per pod, pod length, hundred seed weight, grain yield and protein content. Based on these set criteria, five individual plants from cross H10 (one type 1 and four type 2) and 17 plants from cross H11 (five type 1 and twelve type 2) were selected and forwarded to F6 generation. In F6 generation, mean value was higher than Anaswara for number of pods per plant but lower for plant height, days to first flowering, days to first harvest, days to last harvest, pod length and hundred seed weight. For other characters, mean value was comparable to Anaswara. Moderate GCV value was recorded for length of pod, pod weight and hundred seed weight. High heritability with high genetic advance was recorded for length of pod, pod weight and hundred seed weight. Separate selection criteria was developed for the two categories of plants and total five individual plants were selected, one from cross H10 and four from cross H11. The selected plants from F6 generation were subjected to organoleptic evaluation to find its suitability to be used for vegetable purpose. Three plants of type 2 and one plant from type 1 were found promising. The identified lines, H11-3.9-1-7-13-7, H11-3.9-1-1-18-13, H11-49.7-1-8-10-15, H10-71-16-1-9-15-12, and H11-2-20-3-14-16-12 can be evaluated in replicated yield trials and tested for stability over locations and seasonsItem Pyramiding bacterial leaf blight resistance genes into popular rice varieties of Kerala through marker assisted selection(Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, 2017) Ramaling Hundekar; Jayalekshmy, V GItem Identification of molecular markers linked to iron toxicity tolerance through bulk segregant analysis (BSA) in rice (Oryza sativa L.)(Department of Plant Breeding and Genetics, College of Horticulture, Vellanikkara, 2016) Amaranatha Reddy, M; Rose Mary FranciesGlobally rice is the most important food crop, serving as staple food for more than half of the world’s population. As in other parts of the country, rice is the major food crop grown in Kerala too. The total annual production of rice is however insufficient to meet the total demand in the state. Iron toxicity prevalent in the rice growing tracts of the state, further compounds the problem of low rice production. Although, several attempts to ameliorate the iron toxic soil conditions are being made, the best way to combat this stress and increase rice production in the affected soils is to develop varieties tolerant to iron toxicity. The present investigation on 'Identification of molecular markers linked to iron toxicity tolerance through bulk segregant analysis (BSA) in rice (Oryza sativa L.)’ was conducted at College of Horticulture, Kerala Agricultural University (KAU), Vellanikkara, Thrissur during 2013 to 2015 year. The study involved screening of thirty rice genotypes for response to iron at toxic levels, hybridization between the most tolerant and susceptible genotype, production of F2 generation of this cross, parental polymorphism study using molecular markers and Bulk Segregant Analysis (BSA). The thirty rice genotypes were selected on the basis of their response to iron stress under KSCSTE project: ‘Donor identification for tolerance to iron toxicity in rice (Oryza sativa L.)’. Further screening of the thirty genotypes (Confirmation test 1 and 2) as per the method advocated by Shimizu et al. (2005) to confirm their tolerance or susceptibility to iron toxicity revealed existence of high significant differences among the genotypes with respect to leaf bronzing and biomass produced under varying concentrations of iron (0 ppm, 600ppm and 800ppm of Fe). Considering that at higher concentrations of Fe, a lower leaf bronzing and reduction in biomass, is a valid criterion for identifying genotypes tolerant to Fe stress, twelve genotypes viz., Cul-8709, Cul-210-29, AM-10-7, Cul-90-03, PM-709, ASD-16, ASD-18, Abhaya, IR-1552, T(N)-1, IR-36 and Cul-3 213 were found to be highly susceptible to iron stress while genotypes Cul-8723, Tulasi, Cul-18716, Kargi and IVT-33 were identified as the most tolerant ones. Selfing of F1s obtained on hybridizing the genotype (Tulasi) and genotype (CUL-8709) which were found respectively to be most tolerant and most susceptible to iron stress was done, to produce F2 population for the conduct of bulk sergegant analysis (BSA). Phenotyping of F2 plants under iron at toxic levels indicated presence of wide variability for shoot length, root length, total number of roots, number of fresh roots, shoot weight, root weight and visual scoring for iron-toxicity symptoms. The measures of skewness and kurtosis for various traits revealed a large quantitative variability. All the above traits except iron content in root of F2 lines exhibited a positive platykurtic distribution pointing to presence of gene interaction in trait expression. Measures of skewness and kurtosis also indicated occurrence of transgressive segregation in the F2 population. Leaf bronzing the typical symptom of Fe toxicity, showed a strong negative correlation with shoot length, root length, total number of roots, number of fresh roots, shoot weight and root weight. The results indicated that leaf bronzing is associated with growth reduction due to Fe2+ toxicity in this F2 population. Parental polymorphism (Tulasi and CUL-8709) survey using 338 Rice Microsatellites (RM) markers revealed 37 RM markers polymorphic between the two. These 37 polymorphic rice microsatellites markers (SSR markers) were found to be distributed over all 12 linkage groups of rice varying between one in case on Chromosome 7 to five each on Chromosome 2, 9 and 10. Bulk segregant analysis indicated that out of the 37 microsatellite markers that were polymorphic between parents seven viz., RM 263, RM 107, RM 12292, RM 24616, RM 24664, RM 13619 showed clear co-segregation with the susceptible parent and susceptible bulk, and resistant parent and resistant bulk. Probability of all seven putative markers was highly significant (P < 0.001) indicating strong association of these markers to the genomic region governing Leaf Bronzing Index which is a valid indicator of tolerance to iron toxicity. Through single marker analysis, three probable quantitative trait loci (QTL’s) of Leaf Bronzing Index were identified, each on 214 chromosome 1, 2 and 9. The QTL on chromosome 1 was located between 42.8 Mb and 43.2 Mb and associated with markers RM 12255 and RM 12292. The QTL for LBI was found to be associated with RM 13619 and RM 263 markers and placed between 24.9 Mb and 25.9 Mb on chromosome 2 while on chromosome 9, it was a located between 19.3 Mb and 20.1 Mb and linked to marker RM 107, RM 24616 and RM 24664.Item Genome analysis of traditional rice varieties of Kerala using ISSR and RAPD markers(Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, 2006) Reshmi Manohar; Jayalekshmy, V GThe research project “Genome analysis of traditional rice varieties of Kerala using ISSR and RAPD markers” was carried out in the Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Thiruvananthapuram during 2004-2006. The major objectives of the study were to characterize indigenous rice collection of Kerala on the basis of two molecular markers viz. ISSR and RAPD and to assess the genetic diversity using molecular marker technique. The study using RAPD markers produced 222 amplicons of which 182 were polymorphic thus giving a polymorphism of 81.98 per cent. Twenty primers were used for the study. Of these the primer OPF-04 gave maximum number of polymorphic products and also produced two unique positive products in the accession Cheruvirippu (size between 1.0 kb and 1.5 kb) and in the accession Njavara yellow (size of less than 0.5 kb). The amplification products had size ranging from 2.0 kb to less than 0.5 kb. The analysis produced nine unique positive products and seven unique negative products. Clustering based on Jaccard’s similarity coefficient revealed the highest similarity between the accessions Chettivirippu and Pokkali 3 (0.825). The least similarity index of 0.451 was between the accessions Cheeravithu and Vellakkoli. The Njavara group of accessions, Njavara yellow and Njavara black, clustered at a similarity value of 0.707. The primer OPB-05 and OPF-01 could distinguish the Njavara accessions from others. OPB-05 produced unique product with a size of less than 1.0 kb and OPF-01 produced product at size of less than 0.5 kb. ISSR analysis was carried out using two primers. The amplification using the two primers produced 19 amplicons of which 16 were polymorphic giving 84.21 per cent polymorphism. The amplification products had size ranging from 0.2 kb to more than 1.0 kb. A unique negative marker was amplified by the primer (GA) 8T in the accession Karuthacheera with a size of nearly 0.6 kb. The UPGMA clustering was done using Jaccard’s similarity coefficient values. The highest similarity of 1.00 was shown by the accessions, Athikiramundakan and Veluthakattamodan and by Vellamundakan and Chettivirippu. The least similarity was between the accessions Karuthacheera and Pandivella (0.230). The accession Karuthacheera was unique and formed a single cluster at similarity value of 0.420. The pattern of clustering for the individual marker systems did not show any congruence with each other. However the cluster analysis of combination of the two marker systems produced a better picture of the genetic relationship. The present study using the two dominant DNA markers, RAPD and ISSR, showed that both the DNA markers are effective and promising for detecting genetic variation. It has been observed that ISSR is superior to RAPD in terms of polymorphism detected.Item Genetic analysis of yield and fusarium wilt resistance in line x tester progeny of yard long bean (vigna unguiculata subsp. sesquipedalis (L) verdcourt)(Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, 2006) Renjana G Nair; Radhadevi, D S