PhD Thesis
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Item Nitrogen use efficient varieties for enhanced productivity in rice (Oryza sativa L.)(Department of Agronomy, College of Agriculture, Vellayani, 2025-07-29) Merin Jose; Shalini Pillai, PThe research entitled “Nitrogen use efficient varieties for enhanced productivity in rice (Oryza sativa L.)” was conducted at the Department of Agronomy, College of Agriculture, Vellayani, during 2021 to 2025. The objectives of the study were to screen selected rice varieties for nitrogen use efficiency (NUE) based on germination and root characteristics, to evaluate the field performance of selected nitrogen-efficient rice varieties at graded doses of nitrogen (N), and to work out the economics. The study was conducted in three parts. The first part was a lab study wherein, 14 popular rice varieties released from Kerala Agricultural University (KAU) were screened for NUE based on germination characteristics. The experiment was laid out in completely randomized design (CRD) with 14 varieties and 5 media, replicated thrice. The treatments comprised seven short duration varieties (SDVs) viz., v1- Makom (MO 9), v2- Prathyasa (MO 21), v3- KAU Manuratna, v4- Jyothi (PTB 39), v5- Harsha (PTB 55), v6- Varsha (PTB 56) and v7- Kanchana (PTB 50) and seven medium duration varieties (MDVs) viz., v8- Bhadra (MO 4), v9- Uma (MO 16), v10- Sreyas (MO 22), v11- Pournami (MO 23), v12- KAU Manuvarna, v13- Athira (PTB 51) and v14- Aiswarya (PTB 52), and Modified Arnon Hoagland (AH) media [(m1- AH media with urea (7.5 mM), m2 - AH media with ammonium chloride (15 mM), m3- AH media without N source, m4- AH media and m5 - distilled water]. In general, the presence of urea or any other additional source of N tends to inhibit germination. However, this inhibitory effect was not observed in the case of Harsha (v5) and Varsha (v6), as both varieties took 39 h each to reach 50 per cent germination in distilled water and in AH media with urea. In the case of MDVs, the germination of all the varieties were inhibited. The SDVs, viz., Varsha (v6), Harsha (v5) and Prathyasa (v2) had longer shoots (10.25 cm ± 1.27 cm, 7.95 cm ± 0.52 cm and 6.63 cm ± 0.79 cm respectively) in the presence of urea as compared to distilled water. In the case of MDVs, Aiswarya (v14), Athira (v13), Sreyas (v10) and Uma (v9) produced longer shoots (9.20 cm ± 0.36 cm, 8.20 cm ± 0.39 cm, 8.13cm ± 0.85 cm and 6.53 cm ± 0.75 cm respectively) in the presence of urea as compared to distilled water. In the presence of urea, Varsha (v6) and Harsha (v5) recorded longer roots (9.13 cm ± 1.91 cm and 9.03 cm ± 2.78 cm). With respect to MDVs, Sreyas (v10) recorded longer roots (12 cm ± 0.28 cm) and this was on par (11.73 cm) with that under distilled water. Higher seedling dry weight (23.15 mg ± 2.25 mg) was recorded in Varsha (v6) which was on par with Kanchana (v7), Harsha (v5) and Jyothi (v4). In the presence of urea, Uma (v9) recorded higher seedling dry weight (23 mg ± 1.83 mg) which was on par with Aiswarya (v14), Sreyas (v10) and KAU Manuvarna (v12). Urease enzyme activity was found to be the highest (0.59 ± 0.01) mM NH4+ min-1 g-1 in Varsha (v6) followed by Harsha (v5). A similar trend was observed in urea and NH₄Cl, where Varsha (v6) recorded higher urease enzyme activity than Harsha (v5). In case of MDVs, urease enzyme activity was the highest (0.47 ± 0.01) mM NH4+ min-1 g-1 in Aiswarya (v14) followed by Sreyas (v10). Seedling vigour index I (SVI I) was higher in Varsha (v6) followed by Harsha (v5) and higher seedling vigour index II (SVI II) was recorded by Kanchana (v7), followed by Varsha (v6) and Harsha (v5). In case of MDVs, Aiswarya (v14) recorded higher SVI I (885.15), followed by Sreyas(v10) (717.28). Whereas, Sreyas (v10) recorded higher SVI II (2288.25) which was followed by Aiswarya (v14) (2278.50). The second part of the study comprised screening the 14 rice varieties in field, under two contrasting N levels. It was carried out in the wetlands of the Integrated Farming System Research Station (IFSRS), Karamana, during June to October 2023. The experiment was laid out in randomised block design (RBD) with the 14 varieties at two levels of nitrogen (n0- 0 % RDN and n1- 100 % RDN), replicated thrice. Among the SDVs, Harsha (v5) and Varsha (v6) and among MDVs, Sreyas (v10) and Aiswarya (v14) proved superior in terms of growth attributes including plant height, tillers m-2, rooting depth and root volume. The same trend was observed in yield attributes and yield. The lower percentage in yield reduction observed in Harsha (23.89%), Varsha (22.50%), Sreyas (27.89%) and Aiswarya (20.61%) at zero per cent RDN compared to 100 per cent RDN pointed towards their higher NUE. These varieties also exhibited higher root dry weight efficiency index (RDWEI) which is also an indicator of NUE. The Partial factor productivity of N (PFPN) also exhibited a similar trend. Based on the cumulative ranking of germination traits (part I) and RDWEI, yield and PFPN (part II) the varieties Harsha, Varsha, Sreyas and Aiswarya were chosen as promising candidates for further field evaluation aimed at validating their production potential, NUE and profitability. The third part of the study entitled ‘Field evaluation of nitrogen- efficient rice varieties’ was also conducted at IFSRS, Karamana from November 2023 to February 2024 (second crop 2023-’24 referred to as season I) and July to November 2024 (first crop 2024 ’25 referred to as season II). The field performance of the four nitrogen-efficient rice varieties chosen from part I and part II were assessed at graded levels of recommended dose of nitrogen (RDN). The experiment was laid out in split plot design with four main plots (n1- 100 % RDN, n2 - 75 % RDN, n3 - 50 % RDN and n4- absolute control) and four sub plots [v1- Harsha (PTB 55), v2- Varsha (PTB 56), v3- Sreyas (MO 22) and v4- Aiswarya (PTB 52)], replicated four times. The results revealed that during seasons I and II, while Harsha at 100% RDN (n1v1) recorded the highest grain yield (4567 kg ha-1 ± 64 kg ha-1 and 4703 kg ha-1 ± 35 kg ha-1 respectively), the yield of Varsha at 100% RDN (n1v2) (4507 kg ha-1 ± 81 kg ha-1 and 4720 kg ha-1 ± 89 kg ha-1) and 75 per cent RDN (n2v2) (4440 kg ha-1 ± 82 kg ha-1 and 4603 kg ha-1 ± 68 kg ha-1) were statistically comparable. The MDVs, Sreyas and Aiswarya also behaved in a similar manner with comparable yields at 100 per cent RDN and 75 per cent RDN. Chlorophyll content was significantly the highest at 100 % RDN in Harsha, Varsha and Sreyas throughout the growth stages. Whereas in Aiswarya, the chlorophyll content at 100 per cent RDN was statistically comparable to that at 75 per cent RDN. In terms of NUE indices, all the four varieties exhibited significantly higher PFPN and agronomic efficiency of nitrogen (AEN) at 50 per cent RDN. However, during season II AEN of both Varsha and Aiswarya at 50 per cent RDN and 75 per cent RDN were comparable. Harsha recorded the highest BCR (1.41± 0.02 and 1.45± 0.01) at 100% RDN (n1v1), while, Varsha recorded the same (1.42 ± 0.03 and 1.49 ± 0.02) at 75 per cent RDN (n2v2). Among the MDVs, Sreyas and Aiswarya recorded higher BCR at 75 per cent RDN. Screening of 14 popular rice varieties released from KAU based on germination characters, RDWEI and PFPN showed that the short duration varieties viz., Harsha (PTB 55) and Varsha (PTB 56) and the medium duration varieties viz., Sreyas (MO 22) and Aiswarya (PTB 55) could be considered as nitrogen efficient. Field evaluation of the nitrogen efficient varieties showed that while the productivity and profitability of Varsha could be sustained at 75 per cent RDN, the variety Harsha required 100 per cent RDN. The study also revealed that, the recommended dose of N (90 kg ha-1) for the nitrogen efficient MDVs, could be reduced by 25 per cent without compromising yield and profitability.Item Development of breeding lines in rice(Oryza sativa L.) Pyramided with R genese for resistance to brown plant hopper (BPH) by marker assisted selection.(Department of plant breeding and genetics, college of agriculture, Vellayani, 2023-07-21) Arun Chacko; Jayalekshmy, V GThe present study ‘Development of breeding lines in rice (Oryza sativa L.) pyramided with R genes for resistance to Brown Plant Hopper (BPH) by markerassisted selection’ was conducted in the Department of Plant Breeding and Genetics, College of Agriculture, Vellayani and Regional Agricultural Research Station, Pattambi, during the year 2019-2022, with an objective to introgress R genes for resistance to BPH in the background of the elite variety Jyothi using marker-assisted selection. The study comprised of two main experiments. Experiment-I aimed at the BPH bioassay, assessment of morphological and biochemical characters linked to BPH resistance in the donor and recipient parents followed by the validation of the presence of genes for resistance using specific molecular markers. Recipient parent (Jyothi) and probable donors for BPH resistance from the results of a concluded project in the Department of Plant Breeding and Genetics, COA, Vellayani, and other R gene introgressed lines from IRRI were selected for screening. The BPH bioassay was done using the modified seedbox screening test (MSST) developed by Velusamy (1986). BPH-affected seedling survival rate was calculated based on the Standard Evaluation System (SES) scale of 0-9 (IRRI, 2013). Among the twelve rice genotypes screened, PTB-33, PTB-21, and IR7103-121-15-B were classified as highly resistant and the genotypes IR65482-7-216-1-2 and RP2068-18-3-5 were classified as resistant to BPH infestation. The japonica variety Kinandang Patong was moderately resistant to BPH. The recipient parent Jyothi and five other genotypes viz., Manu Ratna, White Ponni, Wayrarem, Vandana, and APO were classified as highly susceptible to BPH infestation. Five genotypes, Jyothi (recipient parent), PTB-33, IR7103-121-15-B, IR65482-7-216-1-2, and RP2068-18-3-5 were forwarded for studying the BPH resistance reaction. The antibiosis and tolerance mechanisms of BPH resistance were explored in terms of nymphal survival rate, honey-dew test, functional plant loss index (FPLI), and tolerance index (TI). The recipient parent, ‘Jyothi’ turned out to be highly susceptible, and ‘PTB-33’ showed high resistance to BPH feeding among the rice genotypes screened. Other genotypes, IR65482-7-216-1-2 RP206818-3-5, and IR7103-121-15-B showed intermediate values compared to PTB-33 and the highly susceptible variety ‘Jyothi’. The morphological characters and biochemical parameters linked with BPH resistance of five genotypes were assessed in a completely randomized design (CRD) with four replications. The results revealed that BPH feeding, survival, functional plant loss index, and disease score were positively correlated with protein content and negatively correlated with phenol and ascorbic acid content. Reducing sugar content in plants did not show much effect on BPH resistance. The genetic parameters, phenotypic and genotypic coefficient of variation were higher in seven characters, and moderate in six characters indicating high variability among the parents. High heritability and genetic advance in the characters except for the number of productive tillers, and culm thickness and grain length respectively indicated the presence of additive gene action. The characters, culm thickness, 1000 grain weight, and protein content showed a significant positive correlation with the functional plant loss index (FPLI). Path analysis of morphological and biochemical characters with FPLI as the dependent variable showed the direct positive effect of the number of productive tillers, panicle length, number of grains per panicle, grain breadth, LB ratio, and phenol content on FPLI. The validation of the presence or absence of genes for BPH resistance in donor and recipient parents was done using SSR markers RM589 for the Bph-3 gene, RM3331 for Bph-18, RM8213 for Bph-20, and RM28561 for Bph-21. Distinguishable polymorphic bands were obtained in SSR markers RM589 (200 bp for resistance and 180 bp for susceptibility) and RM3331 (110 bp for resistance and 130 bp for susceptibility). Based on BPH screening, resistant reaction study, and gene validation, the KAU released variety ‘PTB-33’ and IRRI introgression line IR65482-7-216-1-2 were selected as the donors for Bph-3 and Bph-18 gene respectively in the marker-assisted breeding program. The second experiment was marker-assisted backcrossing to introgress the R genes (Bph-3 and Bph-18) into the background of elite high-yielding but susceptible variety Jyothi. The donors PTB-33 and IR65482-7-216-1-2 were crossed independently with Jyothi to obtain the F1 generation followed by backcrossing with Jyothi to develop the BC1F1 generation. Phenotyping for ten morphological characters and genotyping using gene-specific SSR markers were carried out in all the backcross generations. Genotyping of 63 BC1F1 lines derived from the PTB-33 donor parent with RM589 marker identified 28 plants with the Bph-3 gene in heterozygous condition. Genotyping of 78 BC1F1 lines derived from the IR65482-7-216-1-2 donor parent with RM3331 marker identified 36 plants with Bph-18 gene in heterozygous condition. The goodness of fit test (χ2 test) in BC1F1 lines with genotypic data showed that the genes Bph-3 and Bph-18 followed the ratio of simple dominance. Intercrossing of BC1F1 lines involved two crosses viz., the PTB-33 derived BC1F1 lines with Bph-3 in heterozygous condition as the female parent and IR65482-7-216-1-2 derived BC1F1 lines with Bph-18 in heterozygous condition as male parent denoted as ‘ICAB’ and the reciprocal cross denoted as ‘ICBA’. Among the twenty-two ICAB progenies, three plants showed both genes (Bph-3 and Bph18) in heterozygous condition, and among the eighteen ICBA progenies, five plants were obtained with both genes (Bph-3 and Bph-18) in heterozygous condition. The Euclidean Distance of intercrossed BC1F1 lines from the recipient parent Jyothi using proximity dissimilarity matrix analysis was calculated to select the intercrossed BC1F1 lines more similar to the recipient parent. Eight intercrossed BC1F1 lines with Jyothi-specific characters and both genes in heterozygous condition were backcrossed with Jyothi to develop BC2F1 lines. In the genotypic evaluation of twenty-six BC2F1 lines, five lines showed the presence of both genes (Bph-3 and Bph-18) in heterozygous condition. The five BC2F1 lines with maximum similarity in proximity dissimilarity matrix analysis were selfed and three-hundred and twenty BC2F2 lines were forwarded to BPH bioassay in the seedling stage at RARS, Pattambi, and COA, Vellayani. Eighty-nine BC2F2 lines showed different levels of resistance in the BPH bioassay. Genotyping of these lines showed the presence of both genes (Bph-3 and Bph-18) in homozygous resistant condition in four lines namely, ICAB-1/3/6, ICAB-1/3/7, ICAB-1/6/2, and ICAB-1/6/10. The similarity percentage of these four lines with the recipient parent in proximity dissimilarity matrix analysis was obtained as 84.51 per cent in ICAB-1/3/6, 89.27 per cent in ICAB-1/6/10, 91.15 per cent in ICAB-1/6/2, and 91.6 per cent in ICAB-1/3/7. The developed breeding lines, possessing pyramided R genes for BPH resistance in the background of Jyothi, can be used to develop essentially derived varieties from Jyothi with BPH resistance. This will offer an improved and sustainable solution for combating BPH infestations, reducing reliance on chemical insecticides, and enhancing the stability of rice production.Item Bridging productivity loss in aerobic rice (Oryza sativa L.) through land configuration and intercropping(Department of Agronomy ,College of Agriculture,Vellayani, 2023-03-10) Shahana Begum.; Shalini Pillai, PItem High temperature medicated changes in sugar signaling pathway and identification of associated microsatellite markers in rice (Oryza sativa L.)(Department of Plant Physiology, College of Agriculture, Vellayani, 2022-10-02) Stephen Kukkamudi.; Beena RThe research work entitled ‘High temperature mediated changes in sugar signaling pathway and identification of associated microsatellite markers in rice (Oryza sativa L.)’ was undertaken at the College of Agriculture, Vellayani during 2018-2022. The aim of the study was to understand the effect of high temperature stress on the changes in the sugar signaling pathway and to identify the molecular markers associated with heat tolerance in rice. The investigation was carried out as four experiments, the first being the study of heat stress effects on the sugar signaling pathway, and the remaining three experiments being interconnected. The second experiment was the laying of crossing blocks to produce F1 and F2 generation seeds, after which the third experiment was conducted to phenotypically evaluate the F2 population derived from the second experiment. The fourth experiment was conducted to identify polymorphic micro-satellite markers that were associated with heat tolerance in the F2 population evaluated in the previous experiment. In the first experiment, the genotypes NERICA L-44 (NL-44) and Vandana were evaluated under two different temperature conditions viz. high temperature stress (38-42 ˚C) and ambient (26-34 ˚C) which was taken as control. The expression of four genes viz. OsHXK2, OsSnRK1, OsTOR and OsTPS1 was studied using quantitative real-time polymerase chain reaction (qRT-PCR) at the vegetative phase just before panicle initiation and at the grain filling stage. The results of the experiment showed that under high temperature stress conditions, the performance of the variety NL-44 was superior to the variety Vandana, as measured by parameters such as cell membrane stability index (+10%), pollen viability (+19%), panicle length (+4.8 cm), photosynthetic rate (+4.75 µmol cm-2 s - 1 ), stomatal conductance (+0.027 mol m-2 s -1 ), spikelet fertility (+19.1%), 1000 grain weight (+5.5 g) as well as greater photochemical efficiency (Fv/Fm ratio), maximal quantum yield (ΦPSII), electron transport rate and higher water-use efficiency. The results of the experiment clearly reinforce the tolerance characteristics of NL-44 and establish the susceptibility of Vandana to high temperature stress. The expression of each gene was correlated with multiple traits that explained the tolerance or susceptibility of the genotypes 204 under heat stress. Based on such correlations, the proposed pathway of sugar signaling in tolerant rice genotypes should necessarily cause upregulation of OsHXK2, as it indicates high glucose content; down-regulation of OsSnRK1, as it would prevent the induction of catabolic processes; up-regulation of OsTOR, as it indicates higher nutrient status as well as being involved in inducing stress responses; and down-regulation of OsTPS1 as the low T6P content would signal remobilization of nutrients towards stress response. In the second experiment, the two varieties NL-44 (heat-tolerant) and the high yielding Uma (heat-susceptible) were crossed to produce F1 generation hybrids. The F1 seeds were then selfed to produce F2 generation seeds. The F2 seeds produced had morphological characters that were intermediate to the parents with medium length and medium boldness unlike NL-44 which was long and slender grain whereas Uma has characteristic short and bold grain characteristics. 144 F2 plants along with the parents, NL-44 and Uma were phenotypically evaluated under high temperature stress (36-40 ˚C) in the third experiment. . The mean of the population was closer to NL-44 with regards to the traits of plant height, membrane stability index, photosynthetic rate, stomatal conductance, transpiration rate, pollen viability, spikelet fertility and 1000 grain weight. However, for the traits such as tiller number, days to flowering, time of anthesis, leaf temperature and panicle length, the mean of the population was influenced by the susceptible parent, Uma. Based upon the spikelet fertility percentage, the ten most tolerant and ten most susceptible plants were selected from the F2 plants and Bulked Segregant Analysis (BSA) technique was used to identify polymorphic SSR markers that are linked to high temperature tolerance. The results of the study have identified 18 SSR markers that exhibited polymorphism between the parents out of the 100 SSR markers used. The identified polymorphic markers could distinguish between the tolerant and susceptible bulks as seen in their differential banding pattern. The identified polymorphic markers were also found to segregate between the individual lines and characterize them into tolerant or 205 susceptible lines based on their similarity to the banding pattern of the tolerant parent, NL44 or the susceptible parent, Uma. In the present study, the expression levels of the sugar signaling genes and their association with phenotypic characters has elucidated their role in imparting heat tolerance in rice. The phenotyping of the F2 generation indicated that the tolerance traits in the population were majorly contributed by the tolerant parent i.e. NL-44. The identified polymorphic markers were able to segregate the individual lines of F2 population into tolerant and susceptible genotypes. The elucidation of the sugar signaling mechanism in tolerant genotypes of rice and the association of molecular markers linked to the heat tolerance trait in the segregating second generation filial populations is validated to be beneficial in undertaking crop improvement studies for enhanced sugar metabolism as well as to introgress the tolerance traits into high-yielding regional varieties.