1. KAUTIR (Kerala Agricultural University Theses Information and Retrieval)
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Item High temperature stress on grain phytic acid and mineral bioavaility in rice(Department of plant physiology, College of Agriculture,Vellayani, 2025-11-28) Lishli,D; Beena,RThe study entitled “High temperature stress on grain phytic acid and mineral bioavailability in rice (Oryza sativa L.)” was conducted at the Department of Plant Physiology, College of Agriculture, Vellayani, during 2023–2025. The present study examined the influence of high temperature stress (36 ± 2°C) imposed during the reproductive stage on grain phytic acid accumulation, mineral bioavailability, physiological performance, and yield traits in eleven rice genotypes differing in pericarp colour and stress tolerance. The experiment was conducted during the Rabi 2024 season using a Completely Randomized Design (CRD) with two temperature regimes (ambient and high temperature) and three replications. The plants were maintained under normal conditions until panicle initiation and after which they were exposed to high temperature condition in a polyhouse. Morphophysiological, biochemical, and molecular parameters, including the expression of the SPDT (SULTR-like Phosphorus Distribution Transporter) gene, were analysed to elucidate the molecular basis of genotypic variation in phytic acid content. High temperature stress significantly affected physiological, biochemical, and yield parameters, though the extent of response varied among genotypes. Exposure to elevated temperatures resulted in a 7–18 % reduction in plant height, a 21–51 % decrease in leaf area, and a 15–32 % decline in chlorophyll content. Yield related traits were also adversely affected, with spikelet fertility declining by 2–15 % and grain yield decreasing by 18–50 % due to elevated temperature. Pigmented rice genotypes such as Kalabath and Assam Black maintained higher chlorophyll retention, membrane stability, and yield indicating strong thermotolerance. In contrast, white pericarp genotypes such as Khira, White Jasmine, and Jeerakasala exhibited substantial reductions in photosynthetic efficiency and spikelet fertility, resulting in greater yield losses. Jyothi and Urunikaima demonstrated moderate tolerance, with intermediate stability under stress Under heat stress, a significant biochemical response was evident, reflected by a 2–34 % increase in grain phytic acid compared to plants grown under ambient conditions. This increase reflects a temperature-induced shift in phosphorus metabolism that helps stabilize internal phosphorus reserves. However, it was accompanied by a 20–30% reduction in bioavailable iron and zinc, demonstrating a strong negative correlation between phytic acid accumulation and mineral bioavailability. Molecular analysis revealed that the SPDT gene, responsible for phosphorus transport to grains, was upregulated under stress, thereby promoting enhanced phytic acid biosynthesis. Bran colour exerted a strong influence on stress response and nutrient balance. Pigmented genotypes, particularly those with black and red pericarps, exhibited only a 10–15% reduction in antioxidant activity compared with 25–30% in white rice. Their higher levels of phenolics, anthocyanins, and flavonoids likely mitigated oxidative injury, preserving grain integrity and mineral stability. Conversely, white genotypes, lacking such antioxidant protection, experienced a stronger rise in phytic acid and greater yield decline. In conclusion, high temperature stress during the reproductive stage significantly influenced grain phytic acid content, mineral bioavailability, and yield parameters in rice, with the magnitude and nature of these effects varying among genotypes of different bran colours. The results demonstrate that the increase in phytic acid under heat stress is a protective yet nutritionally disadvantageous response associated with altered phosphorus metabolism and reduced mineral availability. The observed inverse relationship between phytic acid accumulation and mineral bioavailability underscores the importance of developing rice genotypes with optimized phosphorus transport and enhanced thermotolerance. The study thus fulfilled its objective by identifying pigmented genotypes such as Kalabath and Assam Black as promising donor lines combining superior antioxidant potential, balanced phytic acid regulation, and stable mineral bioavailability, providing valuable resources for breeding climate-resilient and nutritionally enriched rice cultivars.Item Baseline susceptibility of rice leaf folder Cnaphalocrocis medinalis (Guenee) (Lepidoptera: Crambidae) to selected insecticides(Department of Agricultural Entomology, College of Agriculture, Vellanikkara, 2025-08-29) Seena R Subhagan; Berin PathroseWith the rising food production demands, pesticides remain essential for achieving high yields, particularly in staple crops like rice. Despite the known environmental hazards of chemical pesticides, their repeated use has become common practice, often leading to selection pressure and the development of insecticide resistance. This issue is exacerbated when insect pests like the rice leaffolder, Cnaphalocrocis medinalis, which undergoes several generations a year, are exposed to the same insecticide across consecutive generations. Recent failures in controlling rice leaffolder outbreaks in Kerala have raised concerns, though no formal studies have documented insecticide resistance in these populations. This study aimed to address this gap by assessing the susceptibility of rice leaffolder populations to selected insecticides and investigating potential resistance mechanisms. Field populations from five agroecological units (AEUs) in Kerala were assessed for insecticide resistance through laboratory bioassays, with WYD (AEU 20) as a susceptible reference. The PKD (AEU 23), KUD (AEU 4), and TCR (AEU 6) populations experienced significant selection pressure, leading to moderate to high resistance to the tested insecticides, surpassing the resistance observed in the ONT (AEU 3) population. Resistance to acephate (5.07- to 172.53-fold) was identified for the first time in India. High resistance to quinalphos (133.24- to 611.37-fold) and carbosulfan (25.40- to 347.96-fold) were also noted. The observed carbosulfan resistance, despite no prior use, likely stems from cross-resistance due to previous organophosphate exposure, as both target acetylcholinesterase. Continuous exposure intensified resistance to lambda-cyhalothrin (up to 763.66-fold) and fipronil (up to 154.83-fold). Diamide resistance was significant, with chlorantraniliprole (1089.63 fold) and flubendiamide (1572.64-fold), marking the first reported flubendiamide resistance in C. medinalis in India. Cross-resistance to cartap (14.85- to 23.90-fold) and emamectin benzoate (24.97- to 81.09-fold) suggested resistance mechanisms driven by non-specific detoxification pathways. Further, the study aimed to elucidate the biochemical mechanisms of resistance by assessing the activities of detoxification enzymes. Resistant populations exhibited significantly elevated activities of carboxylesterase (CarE) (1.1–1.6-fold), cytochrome P450-dependent monooxygenase CytP450) (1.5–2.5-fold), and glutathione S transferase (GST) (2.3–3.0-fold). These findings underscore the increased activity of detoxifying enzymes as a contributing factor to the resistance observed in C. medinalis further confirmed through synergism bioassays. Bioassays with synergists revealed diverse resistance mechanisms across populations, driven by variations in detoxification enzyme activity. Metabolic resistance to acephate, quinalphos, carbosulfan, and lambda-cyhalothrin was primarily associated with CarE, CytP450, and GST, either individually or in combination. Multiple enzyme involvement was evident in PKD, KUD, and TCR, while CytP450 had a dominant role in ONT, highlighting enzyme-specific contributions to insecticide resistance. However, metabolic detoxification was not the primary driver of chlorantraniliprole and flubendiamide resistance in most populations, suggesting the involvement of alternative mechanisms. Minor contributions from CarE and CytP450 were detected in PKD, while slight synergistic effects in KUD may be linked to endosymbiont mediated resistance. In the case of fipronil, resistance was mediated by CytP450 in PKD, KUD, and ONT, whereas non-metabolic mechanisms likely contributed to the high fipronil resistance observed in TCR. These findings underscore the complexity of resistance mechanisms and highlight the need for further investigation into alternative pathways for diamide and fipronil resistance. This study investigated target site insensitivity as a potential resistance mechanism to diamides and fipronil in C. medinalis by analyzing mutations in the ryanodine receptor (RyR) and resistance to dieldrin (Rdl) genes. Gene duplication and a novel I4712N mutation in transmembrane (TM) domain 3 of RyR were detected in ONT and KUD populations, while PKD and TCR populations had a nonsynonymous mutation (F4691L) and a nonsense mutation (Y4692*) in the TM2-TM3 linker of the RyR gene, which may impact diamide binding. Additionally, a K4885K synonymous mutation was identified in TCR in the TM4-5 linker. As these mutations are newly reported, functional validation is required to confirm their role in resistance. Molecular analysis of the Rdl gene identified an A282S mutation in TM 2 of all populations, including the susceptible WYD, suggesting a limited role in fipronil resistance. Notably, this study reports a novel V457F mutation in TM 4 of the Rdl gene in the resistant TCR population, which may have contributed to high fipronil resistance (154.83-fold) by altering GABA receptor function. The absence of target-site mutations for isoxazoline and meta-diamides suggests their continued efficacy against C. medinalis. Metagenome analysis identified Pantoea sp. and Wolbachia sp. as potential endosymbiont contributors to microbial detoxification of chlorantraniliprole and flubendiamide resistance in KUD. These findings provide new insights into resistance mechanisms and highlight the need for further functional confirmation. Rice leaffolder populations in Kerala have developed diverse resistance mechanisms in response to sustained insecticide pressure, exhibiting metabolic and target-site adaptations. This study presents the first detailed evaluation of insecticide resistance in C. medinalis from Kerala, uncovering alarming resistance levels to multiple insecticides, including newly documented cases for acephate, carbosulfan, lambda-cyhalothrin, and flubendiamide. Metabolic detoxification, primarily through CarE, CytP450, and GST, played a key role in resistance against organophosphates, carbamates, and synthetic pyrethroids, with multiple detoxification pathways raising concerns about cross-resistance. Mutations in the RyR and Rdl genes suggest target site insensitivity for diamides and fipronil (TCR), while the potential involvement of endosymbionts in microbial detoxification (KUD) adds another layer of complexity. These findings highlight the urgent need for proactive resistance management strategies, integrating insecticide rotation, biological control, and molecular monitoring to sustain effective pest management in Kerala’s rice ecosystems.Item Nano zinc nutrition in rice based cropping systems in high Phosphorus soils(Department of Agronomy, College of Agriculture,Vellayani, 2025-07-04) Boddu Archana; Bindhu, J SThe project entitled “Nano zinc nutrition in rice based cropping systems in high phosphorus soils” was conducted at College of Agriculture, Vellayani, Thiruvananthapuram, Kerala, during 2020-2025. The objectives of the study were to evaluate the response of rice to nano zinc in high P soils, study the residual effect of nano zinc nutrition on growth and yield of succeeding crops, study the P - Zn interactions and to identify the promising crop sequence in terms of system productivity and profitability. The study comprised three parts which were carried out at Integrated Farming System Research Station (IFSRS), Karamana, Thiruvananthapuram, Kerala during 2022-23. The first and second parts of the experiment were laid out in randomized complete block design with three replications using variety Uma (Mo 16) in virippu and mundakan seasons. The treatments comprised T1- [Soil application (SA) of ZnSO4 at 20 kg ha-1 (applied only in virippu season)], T2- [Nutri priming (NP) with nano Zn at 0.05%], T3- [NP with nano Zn at 0.05% + Foliar spray (FS) with nano Zn at 0.05% at maximum tillering (MT) stage], T4- [NP with ZnSO4 at 0.5%], T5- [NP with ZnSO4 at 0.5% + FS with nano Zn at 0.05% at MT stage], T6-[FS with nano Zn at 0.05% at MT and panicle initiation (PI) stages], T7- [FS with ZnSO4 at 0.5% at MT and PI stages], T8- [Control (Recommended Dose of Nutrients (RDN) without application of P and Zn)]. The RDN were 90:45:45 (N:P2O5:K2O) kg ha-1 modified as 64:22:53 kg ha-1 on soil test basis. The growth and yield attributes of rice were significantly influenced by nano zinc nutrition. Taller plants with the highest number of tillers per m2, higher leaf area per hill, leaf area index and dry matter production were recorded in T3 and was on par with T6 during both the seasons. The yield attributes viz., higher numbers of productive tillers per hill, grains per panicle, grain weight per panicle and lower sterility percentage were observed in T3 and was on par with T6 during both the seasons. The pooled mean over the seasons revealed that the grain yield (5161 kg ha-1) and straw yield (6148 kg ha-1) of rice were higher in T3 and was on par with T6. The grain yield increased by 78 and 69 per cent in T3 and T6, respectively over control. The nutrient uptake by plants at panicle initiation and harvest were significantly affected by zinc nutrition. The higher uptake of N, P, K, Ca and Zn by the rice plants at panicle initiation and harvest were observed in T3 which was comparable to T2 and T6 at panicle initiation and comparable to T6 at harvest during both virippu and mundakan. The nutrient use efficiency of P and Zn in terms of agronomic efficiency was the highest in T3 and T6, respectively during virippu and mundakan. The available nutrient status of the soil after each season was significantly influenced by nano zinc nutrition. The available N, P, K and Zn were higher in T3 and T6 during both virippu and mundakan. The dehydrogenase and phosphatase activities were significantly higher in T3 and were on par with T6. The highest net returns (₹ 76622 ha-1 and ₹ 86368 ha-1) and B:C ratio (1.74 and 1.82) were recorded in T3 during virippu and mundakan, respectively. The third part of the experiment was conducted during summer season to study the residual effect of nano zinc nutrition on growth and yield of succeeding crops. The experiment was laid out in strip plot design and was replicated thrice wherein, each individual plots of previous crop were divided to three sub plots and crops viz., grain cowpea (Kanakamony (PTB 1)) and bhindi (Anjitha) were grown in two sub plots and one sub plot was kept as fallow. The main plot treatments were residual nutrients of the previous seasons (N1 to N8) and the sub plot treatments were three crop sequences (C1- rice-rice-grain cowpea, C2- rice-rice-bhindi, C3- rice-rice-fallow). Growth, yield attributes and yield of summer crops viz., grain cowpea and bhindi were higher in N1. Available N, P, K, Zn, and soil enzyme activities were influenced by the residual nutrient status of the soil and crop sequences. Higher available N was observed in N6 and N5, available P, K and dehydrogenase activity were higher in N3, available Zn was the highest in N6, and phosphatase activity was higher in N1. Among the crop sequences, available P, Zn and dehydrogenase activity were the highest in C1. Among the interactions, the highest available Ca, available Zn and phosphatase activity were observed in n8c2, n3c1 and n1c1, respectively. The highest system yield (11504 kg ha-1) and system productivity (32 kg ha-1 day-1) were observed in N3 which was on par with N6. The crop sequence C2 recorded the highest system yield (10592 kg ha-1), while both C2 and C1 sequences showed higher system productivity. Among the interactions, n3c1 and n3c2 recorded the highest system yield (12100 and 12090 kg ha-1, respectively) and system productivity (33 kg ha-1 day-1, respectively). The highest energy efficiency, the lowest specific energy, the highest energy productivity and the highest energy intensity were recorded in N3. Among the crop sequences, C1 recorded the highest energy efficiency (7.42) and energy productivity was higher in C2 (0.62 kg MJ-1). Among the interactions, n3c3 recorded the highest energy efficiency. The data on nutrient balance showed a net gain of nitrogen in all treatments in C1 and C2, except N8. The rice-rice-fallow sequence showed a net gain in N3, and N6. Available phosphorus showed a net loss among all sequences and all treatments except N8. Potassium had a positive balance in the rice-rice-grain cowpea and rice-rice-bhindi in all treatments except N8. In rice-rice-fallow sequence, net gain of K was observed in N3 and N6. Zinc balance was positive in all the crop sequences and all the treatments except N1 and N7 which recorded net loss of Zn. Among the residual nutrients, the highest system net returns (₹ 173627 ha-1) and B:C ratio (1.49) were observed in N3 whereas, among crop sequences, rice-rice-bhindi (C2) showed the highest net returns (₹ 114127 ha-1) and B:C ratio (1.47). Among the treatment combinations, n3c2 recorded the highest net returns (₹ 182091 ha-1) and the highest B:C ratio (1.79) in n3c3. From the study, it can be concluded that nutri priming with nano zinc at 0.05% (50 ml ha-1) followed by foliar spray of nano zinc at 0.05% (250 ml ha-1) at maximum tillering stage along with soil test basis recommended dose of nutrients was effective way in enhancing the productivity and profitability of rice in high phosphorus soils. The growth and yield of grain cowpea and bhindi were the highest in residual nutrient with soil application of ZnSO4 at 20 kg ha-1 [applied only in virippu]. Rice-rice-bhindi was identified as the promising crop sequence in terms of system productivity and system profitability.Item Endophytic and growth promoting activities of the entomopathogenic fungus, Lecanicilliumsaksenae (Kushwaha) Kurihara and Sukarno in rice(Department of Agricultural Entomology, College of Agriculture, Vellayani, 2025-07-11) Shree Naveena, PThe study entitled “Endophytic and growth promoting activities of the entomopathogenic fungus, Lecanicilliumsaksenae (Kushwaha) Kurihara and Sukarno in rice” was carried out during 2020-2024 in the Department of Agricultural Entomology, College of Agriculture, Vellayani, Thiruvananthapuram. The objective of the study was to establish the entomopathogenic, endophytic and growth promoting attributes of L. saksenae in rice. The infection process of L. saksenae in the rice bug, investigated using Scanning Electron Microscopy (SEM), revealed five step infection processes comprising adhesion, germination, penetration, colonisation/invasion, and conidiation/dissemination at 24, 48, 72, 96 and 120 hours post inoculation (HPI), culminating in dissemination of spores facilitating horizontal transmission and complete mycosis evidenced by mummified appearance, by 144 HPI. Biochemical mechanisms involved in pathogenesis were deciphered using metabolomic analyses of the infected rice bug. Gas Chromatography-Mass Spectrometry (GC-MS) and High-Resolution ORBITRAP Liquid Chromatography Mass Spectrometry (HR-LC-MS) revealed an array of 19 insecticidal compounds, three immunosuppressors, three antimicrobial compounds, and 13 other metabolites related to insect metabolism, highlighting the complex biochemical arsenal employed by L. saksenae in insect pathogenesis. In addition to entomopathogenicity, L. saksenae exhibited significant plant growth-promoting traits. Plate assays and spectrophotometric observations, displayed elevated levels of phytohormones, notably gibberellic acid (GA3: 334.68 µg mL-1) and indole acetic acid (IAA: 30.00 µg mL-1). It also exhibited zinc and phosphate solubilization efficiency (1.15 SE and 1.70 SE), which are related to nutrient assimilation. The siderophore (2.23 AU) and ammonia production (15.42 µmol mL-1) levels which help in nutrient uptake were significant and higher than those in other entomopathogenic fungi. The study further examined endophytic association of L. saksenae upon seed inoculation, in rice through re-isolation, microscopy, and PCR. The fungus could be reisolated from roots, stems, and leaves of the inoculated plants up to 90 days after seed inoculation (DAI) demonstrating its systemic translocation within then plant. Maximum colonisation was noted in roots (72.86 per cent), followed by stem (64.29 per cent) and leaves (40.00 per cent) at 30 DAI, which tapered to 32.86, 17.14 and 11.4 per cent at 90 DAI. SEM observations confirmed internal colonisation of L. saksenae in the leaf stem and root tissues of inoculated rice, which was further established by PCR amplification, that unequivocally matched with the original Accession. MN545844 deposited by Rani et al. (2015). Comparative metabolomic analysis between inoculated and uninoculated plants revealed significant biochemical changes due to L. saksenae colonisation. Significant elevation of proteins, sugars, and phenolic compounds in the inoculated plants indicated a metabolic shift that favours enhanced growth and defence. Untargeted GC-MS analysis revealed predominance of carbohydrates at maximum tillering stage which indicates protection at cellular levels and promotion of plant growth. Untargeted ORBITRAP HR LC-MS detected the presence of 10 insecticidal/insectistatic, one nematicidal, and three antimicrobial compounds, suggesting that L. saksenae induced the defence mechanism in inoculated plants. LC-MS/MS revealed profound modulation of growth and defence related hormones at critical plant growth stages due to fungal inoculation. Inoculated plants showed increased growth related hormones such as indole-3-butyric acid (IBA), IAA, GAs, N6-benzylaminopurine (6-BAP), trans-zeatin (tZ), and trans-zeatin riboside (tZR) at the seedling stage, and IAA, IBA, GA3, GA4, GA7, and tZR at the maximum tillering stage. Defence hormones such as abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), cis-jasmone (CJ), methyl jasmonate (MeJA), epibrassinolide (EBL), and 1 aminocyclopropane-1-carboxylic acid (ACC) were significantly higher in the inoculated plants at the seedling stage and SA, JA, CJ, MeJ, and ACC at the tillering stage, which are related to increased resistance to pest infestation. Inoculated seeds exhibited improved germination (6.38 per cent) and the seedlings exhibited increase in shoot and root length (30.30 per cent, 55.58 per cent), number of leaves and roots (35.29 per cent, 26.58 per cent) and the seedling vigor index (51.46 per cent), compared to the control. Pot culture experiments proved enhancedplant height (25.80 per cent), number of tillers (36.99 per cent), panicle count (30.00 per cent), grain number (24.20 per cent), grain yield (30.00 per cent), and straw yield (28.43 per cent) in the inoculated plants. In L. saksenae colonised, rice bug infested plants, there was a significant reduction in the number of eggs laid (29.40 per cent), number of feeding punctures (32.83 per cent) and grain damage (37.45 per cent) compared to control plants. Gene expression analysis revealed the upregulation of defence related genes, phenyl ammonia lyase (PAL) and lipoxygenase (LOX) in both inoculated and control plants, indicating it as a general stress response to herbivory. However, the pathogenicity related genes of the entomopathogens viz. subtilin like protease (PR1) and chitinase II (CHIT II) were not expressed in the colonised plants, as these genes are typically involved in breaching of insect cuticle. Headspace volatile analysis (GC-MS) of L. saksenae inoculated plants before rice bug infestation revealed the presence of 2-heptanone (natural enemy attractant and insect repellent), and 4-methylbenzaldehyde (oviposition deterrent). L. saksenae inoculated, rice bug infested plants, displayed defence related volatiles, such as S linalool (natural enemy attractant and insect repellent), methyl salicylate (natural enemy attractant), 9-octadecenamide (Z) (insecticidal), N-methyl-1-adamantaneacetamide (insecticidal and repellent). Additionally, there was upregulation of defence related enzymes, PAL, catalase (CAT), superoxide dismutase (SOD), polyphenol oxidase (PPO), peroxidase (POD), and ascorbate peroxide (APX) in inoculated plants. Temporal profiling revealed a dynamic activation pattern, where PPO, SOD, and APX peaked early at 48 hours after insect release (HAR), followed by a surge in PAL and POD at 72 HAR, and a delayed peak of CAT at 96 HAR. Importantly, L. saksenae inoculated plants displayed earlier and more intense upregulation of SOD and PAL, indicating a primed defence in plants during herbivore attack. These biochemical changes may underlie the observed reduction in pest performance and feeding efficiency. The above findings established the entomopathogenic, endophytic and growth promoting attributes of the indigenous isolate, L. saksenae in rice. By elucidating the tritrophic interactions involving the fungus, plant and insect, the study positions L. saksenae, as a "two-in-one" eco-friendly solution for plant health management in rice.Item Compatibility of multinutrient mix sampoorna with herbicides for rice(Department of Agronomy, College of Agriculture , Vellanikkara, 2024) Akhila, P; Prameela, PTank mixing of agrochemicals is a common practise among farmers in order to save labour, time and application cost. However, mixing is done without having a scientific knowledge on effect of tank mixing. Tank mixing of agrochemicals may result in synergistic, antagonistic, or neutral effects on efficacies of chemicals involved. Herbicidal weed control is very common in rice as it is the economically viable and easy method. Usually post emergence herbicides are applied at 15-20 days of sowing or transplanting. There is a possibility of tank mixed spraying if the herbicides are compatible with Sampoorna. Hence a research programme entitled “Compatibility of multinutrient mix Sampoorna with herbicides for rice” was conducted during July to November 2022 to evaluate the weed control efficiency and compatibility of few post emergence herbicides with Sampoorna KAU multimix in transplanted wetland rice. Experiment consisted of thirteen treatments which included application of five herbicides at recommended rates (bispyribac sodium @ 0.03 kg/ ha, cyhalofop butyl @ 0.08 kg/ ha, 2,4-D @ 0.8 kg/ ha and premix herbicides AlmixⓇ (premix of metsulfuron methyl and chlorimuron ethyl) @ 0.004 kg/ ha and Vivaya Ⓡ (premix of cyhalofop butyl and penoxsulam) @ 0.15 kg/ ha. Respective tank mixed applications with Sampoorna KAU multimix @ 10 g/L were also included along with hand weeded plots with or without Sampoorna and unweeded check. The design was RBD replicated thrice and the variety was Uma. Spraying was given 50 days after transplanting. Phytotoxicity to crop was observed third and seventh day after spraying. Growth and yield attributes of crop were studied and weed parameters like weed count and weed dry matter production were also recorded. Phytotoxicity to rice was observed with tank mix application of 2,4- D+ Sampoorna. Brown spots on leaves and yellowing were noticed by third day itself. The symptoms reduced by 7 days after spraying as new leaves were free of toxicity. This also led to reduction in chlorophyll content at panicle initiation and heading stages. The chlorophyll content at PI stage in 2,4-D + Sampoorna was 2.94 mg/g fresh weight where s in 2,4-D alone spray it was 3.42 mg/. In all other treatments Sampoorna application resulted in slight increase in chlorophyll content. In the case of AlmixⓇ + Sampoorna though visual phytotoxicity symptoms were not present, reduction in plant height was noticed. Reduction in plant height in 2, 4-D+ Sampoorna was 17 % and 10 % at 30 and 60 days after transplanting respectively, compared to its sole application. While AlmixⓇ+ Sampoorna resulted in 13 % and 6 % reduction at 30 DAT and 60 DAT respectively. Individual application of herbicides resulted in comparable tiller counts with respect to their Sampoorna- tank mixed applications except in the case of 2, 4-D and AlmixⓇ at 60 DAT. Similar trend was noticed in number of productive tillers, grain yield and straw yield where all herbicides except 2, 4-D and AlmixⓇ registered higher values with tank mixed application with Sampoorna. Grain yield in 2,4-D+ Sampoorna was 15 percent lower than 2,4-D alone and corresponding reduction in AlmixⓇ+ Sampoorna was 8 percent. In the case of bispyribac sodium, cyhalofop butyl and premix cyhalofop+ penoxsulam, the sole application and tank mix registered comparable grain and straw yields and the grain yield ranged from 5444 to 5647 kg/ ha. Hand weeded plots registered the lowest weed dry matter at all stages. Sole application as well as tank mixed application of all herbicides were comparable in weed dry matter production and weed control efficiency. The weed dry matter in unweeded plot was 1373 kg/ ha whereas the values ranged from 150 kg/ha to 203 kg/ ha in all other treatments, indicating that tank mixing herbicides with Sampoorna has not adversely affected efficiency of herbicides. With respect to effect of Sampoorna application on grain yield of rice, the effect was not very conspicuous as the soil experimental field was not deficient with respect to micro nutrient status. The grain yields in hand weeded plots as well as well as hand weeded+ Sampoorna were comparable with grain yield of 5686 kg/ ha and 5722 kg/ ha respectively.2,4-D+ Sampoorna followed by AlmixⓇ with Sampoorna registered yield reduction of 21 percent and 14 percent compared to hand weeding+ Sampoorna spray which registered higher yield of 5722 kg/ ha. Among tank mixed combinations of herbicides and Sampoorna, 2, 4-D registered the lowest N and K uptake on tank mixing with Sampoorna followed by tank mix application of AlmixⓇ with Sampoorna. All other treatments registered comparable P uptake values except unweeded control, which was the inferior to others. It can be concluded that few post emergence herbicides for rice weed control ie; bispyribac sodium, cyhalofop butyl and VivayaⓇ (premix of cyhalofop butyl and penoxsulam) can be recommended for tank mix application with KAU Sampoorna as foliar spray at 15-20 days after sowing or transplanting. 2,4-D and AlmixⓇ are not compatible with Sampoorna and hence are not suitable for tank mix application.Item Targeted editing of rice micro RNA osa-miR396b through CRISPR/Cas9 system(Department of Plant Biotechnology, Centre for Plant Biotechnology and Molecular Biology, College of Agriculture , Vellanikkara, 2022-10-15) Sanjay Sathian; Rehna AugustineRice (Oryza sativa L.) is one of the most produced and consumed food crops in the world. There is an urgent need to increase rice production to feed the increasing population. Rice yield is determined by several components like grain size, grain weight, number and architecture of panicles, number of spikelets per panicle and grain filling. The microRNA family osa-miR396 is known to suppress the expression of rice growth regulating factors (OsGRFs) resulting in reduced growth and yield. The miRNA osa-miR396b is reported to be a negative regulator of spikelet number and inflorescence development. CRISPR/Cas9 mediated knockout of osa-miR396b gene can thus possibly result in an enhanced yield in rice. Hence, the current study ‘Targeted editing of rice microRNA, osa-miR396b through CRISPR/Cas9 system’ was conducted during the period from 2019 to 2022 at the Department of Plant Biotechnology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur. Oryza sativa ssp. japonica cultivar Nipponbare was selected for the study due to well established transformation protocols and higher transformation efficiency. Initially, the sequence information of the rice microRNA gene osa-miR396b was retrieved from ‘miRbase’. The stem loop sequence obtained was used to design guide RNAs (gRNAs) using the software CRISPR-P v2.0 and CRISPR-PLANT v2. The gRNAs were selected for further studies mainly based on GC content and number of off-target sites. The target osa-miR396b gene sequence was confirmed by amplifying the genomic region flanking the target using gene specific primers followed by sequencing and the sequence analysis using Clustal Omega and BLASTn showed 100% similarity with reported sequences. The osa-miR396b G1 CRISPR/Cas9 construct was generated by restriction digestion of CRISPR/Cas9 binary vector pRGEB32 using BsaI restriction enzyme followed by ligation with annealed and phosphorylated gRNA. The osa-miR396b G1 construct was cloned to E. coli strain DH5α. The positive clones were confirmed by Sanger sequencing of the plasmid DNA isolated from the colonies and sequence analysis using Clustal Omega. Three (osa-miR396b G1 #2, osa-miR396b G1 #3 and osa-miR396b G1 #4) out of four plasmids sequenced were having gRNA insertion. The osa-miR396b G1 #4 CRISPR/Cas9 construct was mobilized to A. tumefaciens strain EHA105. Positive clones were confirmed by PCR amplification of hygromycin resistance gene (hptII) using specific primers. Colony #1 of A. tumefaciens with osamiR396b G1 CRISPR/Cas9 construct out of the two positive colonies was used for rice transformation. Genetic transformation of rice was achieved through Agrobacterium-mediated transformation. The first step was induction of calli from dehusked and sterilized Nipponbare seeds. Five-day-old calli were infected with Agrobacterium harbouring osa-miR396b G1 CRISPR/Cas9 construct for 1.5-2 min. and co-cultivated for 48 hours. An empty vector was also transformed as control. After washing off excess Agrobacterium growth with sterile distilled water containing Augmentin (300 mgL-1 ) or carbenicillin (250 mgL-1 ), the calli were kept for selection in selection medium supplemented with hygromycin (50 mgL-1 ) and Augmentin (300 mgL-1 ) or carbenicillin (400 mgL-1 ). The calli showing proliferation of microcalli were transferred to regeneration medium supplemented with NAA (0.02 mgL-1 ) and kinetin (2.0 mgL-1 ) for inducing somatic embryogenesis. The somatic embryos were allowed to develop into small plantlets which were transferred to rooting medium for root development. The rooted plantlets were initially maintained in sterile distilled water and then hardened in sterile soil-cocopeat mixture in paper cups and transferred to pots with soilsand-cow dung mixture. A total of 94 putative transformed plants for osa-miR396b G1 CRISPR/Cas9 construct and four vector control plants were obtained. For confirming successful transformation, PCR amplification of hptII gene using hygromycin gene specific primers was done. DNA extracted from 35 plants and two vector control were used as PCR template. A total of 16 out of 35 transformed and two vector control plants were hygromycin positive, indicating successful transformation. The osa-mir396b partial gene sequence was amplified using gene specific primers and sequenced by Sanger sequencing for detecting mutation. Detection of mutation was carried out using ‘Inference of CRISPR Edits (ICE)’ software by Synthego. Analysis using ‘ICE’ detected indel mutations in seven plants. Five plants (71.42%) had deletions and two (28.57%) had insertions around the cut site. Four plants (57.14%) had heterozygous mutations (mutation in one allele) and three (42.86%) had chimeric (more than two) mutations. The mutation efficiency was calculated to be 43.75%. The mutations obtained could lead to a non-functional osa-miR396b gene in these plants. The study successfully demonstrated application of CRISPR/Cas9 system to mutate rice microRNA gene. The knockout of osa-miR396b gene will likely promote the expression of rice GRF genes improving the grain yield. Further studies should be conducted to study inheritance pattern of mutations in the subsequent generations. Genotypic and phenotypic analyses is to be done to study effect of mutated osamiR396b gene on its target genes and on yield and other agronomically important traits.Item CRISPR/Cas9 mediated editing of microRNA osa-miR1432 for enhanced grain filling in rice(Department of Plant Biotechnology, Centre for Plant Biotechnology and molecular Biology, College of Agriculture , Vellanikkara, 2022-09-26) Varsha, K; Rehna AugustineRice (Oryza sativa L.) is the predominant food crop for almost half of the world population. In light of the rising world population, it has become imperative to increase rice grain yield per unit area to meet the global food demand. The CRISPR/Cas9 technology has recently emerged as a powerful tool for genetically modifying crops due to its simplicity, precision and genome editing capabilities like knock-in, knock-out, knock-down and expression activation. Recent research revealed that knock-down of rice microRNA, osa-miR1432 can simultaneously enhance resistance towards blast disease and overall yield in rice. Hence the current study, ‘CRISPR/Cas9 mediated editing of microRNA osa-miR1432 for enhanced grain filling in rice’ was undertaken at the Department of Plant Biotechnology, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur during the period from 2019-2022 with an objective to improve overall yield in rice by enhancing grain filling rate through targeted editing of microRNA osa-miR1432 using CRISPR/Cas9 system. The genomic sequence information of the osa-miR1432 gene was retrieved from rice genome annotation project. The stem-loop sequence of osa-miR1432 available in the microRNA database, miRBase was used for guide RNA (gRNA) designing. The gRNA was designed using the online design tool CRISPR-P v2.0. The best gRNA (osamiR1432 G1) was selected based on its features like location in the genome, on-score value, GC content and no. of off-target sites. Genomic region of osa-miR1432 gene, flanking the gRNA target was amplified using gene specific primers and sequence of the target region was confirmed using BLASTn and Clustal Omega analysis. The CRISPR/Cas9 binary vector pRGEB32 was used to clone the gRNA. The development of CRISPR/Cas9 construct was accomplished by annealing of the gRNA strands followed by ligating them into the digested and purified pRGEB32 vector using high fidelity BsaI restriction enzyme. The pRGEB32 vector containing the gRNA construct was cloned into E. coli strain DH5α by transformation using the heat shock method. Plasmid DNA was isolated from the colonies obtained on the transformed plate and were Sanger sequenced using universal M13 reverse primer. The third colony (osamiR1432 G1 #3) was confirmed to be a positive clone after analysing the sequence data. The CRISPR/Cas9 construct was then mobilized into Agrobacterium tumefaciens strain EHA105 using freeze-thaw method. The positive clones were confirmed by plasmid PCR using hygromycin gene specific primers as well as guide sequence specific primers. The positive colony in EHA105 (pRGEB32: osa-miR1432 G1#1) was then used for rice genetic transformation experiments. The rice cultivar Nipponbare (Oryza sativa ssp. japonica cv. Nipponbare) was chosen for the study. Nipponbare seeds were inoculated on to N6 medium supplemented with 2, 4- D (3.0 mg/L) for callus induction. Five days old calli were co-cultivated with Agrobacterium cultures harboring the desired gRNA construct. After 1.5 to 2 days of co-cultivation, the calli were washed thoroughly using bacteriostatic agents augmentin or carbenicillin to remove the excess Agrobacterium load. The calli were then placed on selection medium containing hygromycin and augmentin or carbenicillin. The hygromycin resistant calli showed proliferation after 14 days of incubation. These proliferating microcalli were then transferred to regeneration medium containing NAA (0.02 mg/L) and Kinetin (2.0 mg/L). The regenerated shoots were placed in rooting medium which developed proper roots after one week. The plantlets developed were properly hardened in containment polyhouse. Rice genetic transformation protocol was optimized to suit our laboratory and culture conditions. A total of 25 putative transformant T0 plants were examined for the presence of hygromycin resistance gene and 17 plants were found to be hygromycin positive. PCR amplification of the partial osa-miR1432 gene, flanking the gRNA target region was performed in the hygromycin positive plants and the PCR products were Sanger sequenced to detect mutation. Sequence data analysis using the software Sequencher 5.4.6 detected mutation in seven plants. The detected mutations were single base insertions of A (85.7%) or T (14.3%) exactly at 3 bp upstream to the PAM sequence. The mutation efficiency was found to be 41.18% and the mutations detected were classified as homozygous (71.43%) or heterozygous (28.57%). In the current study, using the CRISPR/Cas9 technology rice plants with mutation in the osa-miR1432 gene were successfully developed which can lead to enhanced grain filling in riceItem 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 Impact of biofertilizers on iron homeostasis under elevated CO2 condition in rice, Oryza sativa(Department of Plant Physiology, College of Agriculture , Vellayani, 2023-01-25) Musti Sri Phani Bhavya; Manju, R VThe study entitled “Impact of biofertilizers on iron homeostasis under elevated CO2 condition in rice, Oryza sativa” was proposed with an objective of assessing the impact of biofertilizers on iron uptake, translocation and grain iron content in rice variety Uma, under CO2 enriched condition. The experiment was conducted using open top chamber (OTC) facility at the Department of Plant Physiology, College of Agriculture, Vellayani, during the period 2021-2022. In this experiment, growth, yield, quality and iron uptake characteristics of rice variety Uma under elevated CO2 condition as influenced by the application of different biofertilizers were evaluated. The experiment was laid out in CRD with 4 treatments [(KAU-POP (control), POP+Azolla, POP+PGPR and POP+AMF)] under 2 conditions [(Ambient CO2 (aCO2) and Elevated CO2 (eCO2)-500 ppm)] with 3 replications. The experiment results revealed that elevated CO2 had a significant positive influence on growth of the plants which was further enhanced by biofertilizer application. When yield parameters were considered, increased CO2 was found to have an adverse effect. There was 58 per cent and 39.28 per cent reduction in filled grains per panicle and grain yield when plants were grown under eCO2 condition. The increase in temperature associated with CO2 enhancement can affect the pollen viability resulting in increased grain chaffiness and yield reduction. Application of biofertilizers had significantly increased grain yield, among which AMF treatment had shown highest impact under both the CO2 conditions. Among the physiological parameters, total chlorophyll content, total reducing sugars and photosynthetic rate increased in the plants grown inside OTC. However, a reduction was noted in total soluble proteins and transpiration rate under elevated CO2 condition. In all these physiological parameters, the biofertilizers treated plants showed higher response when compared to control plants. Grain carbohydrate content was significantly increased by 10.6 per cent in control plants under eCO2 while protein and amylose contents of grains decreased by 14 per cent and 13 per cent indicating reduced grain quality under eCO2. Even under eCO2 condition, the protein content in PGPR treated plants increased by 7.1 per cent and amylose content in AMF treated plants increased by 4.86 per cent when compared to control plants (aCO2). 115 CO2 enrichment and biofertilizers application were found to influence iron uptake and translocation significantly. The pre-anthesis Fe uptake in control plants was dropped by 11.76 per cent and Fe-accumulation by 4.4 per cent under eCO2 condition. But application of PGPR could bring 57.89 per cent increase in iron uptake under ambient condition and 64.7 per cent increase under eCO2 condition. During post-anthesis stage, Fe-uptake was found to increase compared to pre-anthesis stage. Fe-accumulation in the shoot decreased during post-anthesis stage due to re-mobilization of accumulated Fe into grains. There was a drop in Fe-uptake in control plants under eCO2 by 12.5 per cent at post-anthesis stage. At pre-anthesis and post-anthesis stages, plants treated with PGPR (eCO2) have shown increase in Fe uptake by 47.36 per cent and 40.7 per cent, respectively, than control plants. All the biofertilizers including Azolla, PGPR and AMF had significant impact on grain Fe-content under both the CO2 conditions. The Fe content of grains in control plants was dropped by 21 per cent under eCO2 condition. Application of PGPR was found to be most effective resulting in 80.5per cent and by 72.8 per cent increase in Fe-content under eCO2 and aCO2 conditions, respectively. The Fe content in grains was partitioned more into bran than into the polished rice. Control plants when exposed to eCO2 reduced Fe-content in bran and polished rice by 12 per cent and 23.4 per cent, respectively. PGPR treatment increased the Fe-content by 28.6 per cent and 61.7 per cent in bran and polished rice under elevated CO2 condition and by 22.3 per cent and 46.2 per cent under ambient condition when compared to control plants. Diminishing quality of rice with the increasing concentration of CO2 is a global concern today. Elevated CO2 had a positive impact on growth but negatively influenced grain yield due to eCO2 associated high temperature. By the response of experimental plants to AMF and PGPR treatments, these bio-fertilizers can be recommended in overcoming the impacts of elevated CO2 associated high temperature and thereby improving the plant performance. In the present programme, iron uptake and translocation were found to be modified in an unfavourable manner under eCO2 which reflected in the lower iron content of rice grains. The response of iron homeostasis of the experimental plants to the application of biofertilizers, especially PGPR, under eCO2 strongly suggests the possibility of utilizing them for designing iron management strategies to achieve higher yield and quality in rice.Item Identifying resilient rice based cropping systems involving tuber crops for lowlands(Department of agronomy, college of agriculture ,Vellayani, 2023-10-09) Anju, B Raj.; Jacob JohnThe study entitled “Identifying resilient rice based cropping systems involving tuber crops for lowlands” was conducted at Department of Agronomy, College of Agriculture, Vellayani during the period from 2019-2023. The major objectives of the study were to evaluate the performance, in terms of yield and economics, of different rice based cropping systems involving tuber crops in lowlands under different nutrient levels, to analyse weed dynamics, soil health and carbon dioxide emission, and to assess the residual effect on the succeeding virippu rice crop. It could be concluded that, among different rice based cropping systems involving tuber crops in lowlands, rice-rice-sweet potato (C2) performed better in terms of yield, economics and weed control. Grain yield of succeeding crop of rice, recorded with F2 and F1 were comparable. Thus it was concluded that FYM, N and P could be reduced by 25 per cent in rice based cropping systems. Rice-(cassava+bush cowpea)-daincha (C4) recorded significantly higher available nutrients, carbon fractions with less CO2 emission. Hence, rice-(cassava+bush cowpea)-daincha (C4) could be adjudged as the resilient rice based cropping system involving tuber crops in lowlands.