Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits.

The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.

Imprint of clay mineralogy, sesquioxides, and crop residue addition for evaluation of soil organic carbon stability and associated microbial activity in dominant soil orders of Indian subcontinent.

The full behaviour of natural clay minerals in soil organic carbon (SOC) stabilization in the presence of oxides and external C inputs is yet unknown. Thus, an incubation experiment was conducted in a sand-clay mixture with different soil clay fractions (SCFs) obtained from Alfisol, Inceptisol, Mollisol, and Vertisol in the presence of wheat residues to compare their C stabilization capacity. The C mineralization rates were higher in 1:1 type dominated SCFs (Alfisol and Inceptisol) compared to 2:1 interstratified mineral dominated SCFs (Vertisol). Wheat residues as C source altered SCFs' abilities to stabilize SOC at only moderate dosages of application (3-12 g kg-1). C mineralization and microbial biomass carbon (MBC) fell by 40% and 30%, respectively, as the amount of clay increased from 7.5 to 40%. However, removing sesquioxides from the SCFs boosted C mineralization and MBC by 22% and 16-32%, respectively, which matched with higher enzymatic activities in the sand-clay mixture. The increased C stabilization capacity of Vertisol-SCF may be attributed to its greater specific surface area (SSA) (506 m2 g-1) and cation exchange capacity (CEC) [meq/100 g]. Regression analysis revealed that SSA, CEC, and enzymatic activity explained approximately 86% of total variations in C mineralization. This study highlighted the critical role of 2:1 expanding clay minerals and sesquioxides in greater stabilization of external C input compared to its 1:1 counterpart. It also implied that the role of mineralogy or texture and sesquioxides levels in different soils (Vertisol, Mollisol, Inceptisol, Alfisol) should be prioritized while adding crop residues to reduce C footprint and enhance sequestration.

Soil quality assessment of lowland rice soil of eastern India: Implications of rice husk biochar application.

The role of biochar in improving the soil properties of problem soils is well known, but its long term impact on lowland rice soil is not well recognized. The soil quality indicators of biochar applied lowland rice soil are not widely reported. We developed soil quality index (SQI) of a biochar applied lowland rice soil based on 17 soil properties (indicators). Field experimentation consisted of six treatments such as 0.5, 1, 2, 4, 8 and 10 t ha-1 of rice husk derived biochar (RHB) along with control. An overall SQI was calculated encompassing the indicators using multivariate statistics (principal component analysis) and non-linear scoring functions after generation of minimum data set (MDS). Sequential application of RHB improved the SQI by 4.85% and 16.02% with application of 0.5 t ha-1 and 10 t ha-1 RHB, respectively, over the recommended dose of fertilizer (control). PCA-screening revealed that total organic carbon (Ctot), zinc (Zn), pH and bulk density (BD) were the main soil quality indicators for MDS with 27.79%, 26.61%, 23.67% and 14.47% contributions, respectively. Apart from Ctot, Zn is one of the major contributors to SQI and RHB application can potentially be an effective agronomic practice to improve Zn status in lowland rice soil. The overall SQI was significantly influenced by RHB application even at 0.5 t ha-1. The present study highlights that application of RHB improves the soil quality even in fertile, well managed, lowland rice soil.

A review on effective soil health bio-indicators for ecosystem restoration and sustainability.

Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.

Alteration in plant spacing improves submergence tolerance in Sub1 and non-Sub1 rice (cv. IR64) by better light interception and effective carbohydrate utilisation under stress.

Besides genetic improvement for developing stress-tolerant cultivars, agronomic management may also add considerable tolerance against different abiotic stresses in crop plants. In the present study, we evaluated the effect of six different spacing treatments (S1: 10 × 10 cm; S2: 15 × 10 cm; S3:15 × 15 cm; S4:20 × 10 cm; S5: 20 × 15 cm; S6: 20 × 20 cm (row-row × plant-plant)) for improving submergence tolerance in rice. A high yielding submergence intolerant rice cultivar IR64 was tested against its SUB1 QTL introgressed counterpart (IR64-Sub1) for 12 days of complete submergence for different spacing treatments in field tanks. Relatively wider spaced plants showed higher individual plant biomass and early seedling vigour, which was particularly helpful for IR64 in increasing plant survival (by 150% in S6 over S1) under 12 days of submergence, whereas the improvement was less in IR64-Sub1 (13%). Underwater radiation inside the plant canopy, particularly beyond 40 cm water depth, was significantly greater in wider spacing treatments. Leaf senescence pattern captured by SPAD chlorophyll meter reading and chlorophyll fluorescence imaging data (Fm, Fv/Fm) taken at different time intervals after stress imposition suggested that there was lesser light penetration inside the canopy of closer spaced plants, and that it might hasten leaf senescence and damage to the photosynthetic system. The initial content of total non-structural carbohydrate (NSC) was higher in wider spaced plants of IR64, and also the rate of depletion of NSC was lesser compared with closer spaced plants. In contrast, there was not much difference in NSC depletion rate under different spacing in IR64-Sub1. Further, higher antioxidant enzyme activities in wider spaced plants (both IR64 and IR64-Sub1) after de-submergence indicated better stress recovery and improved tolerance. Taken together we found that wider spacing (row-row: 20 cm and plant-plant: 15 cm and more) can significantly improve submergence tolerance ability in rice, particularly in submergence intolerant non-Sub1 cultivar like IR64, perhaps due to better underwater light penetration, delayed leaf senescence and slower depletion of NSC reserve.

Clay-polymer nanocomposites: Progress and challenges for use in sustainable water treatment.

Contaminant removal from water involves various technologies among which adsorption is considered to be simple, effective, economical, and sustainable. In recent years, nanocomposites prepared by combining clay minerals and polymers have emerged as a novel technology for cleaning contaminated water. Here, we provide an overview of various types of clay-polymer nanocomposites focusing on their synthesis processes, characteristics, and possible applications in water treatment. By evaluating various mechanisms and factors involved in the decontamination processes, we demonstrate that the nanocomposites can overcome the limitations of individual polymer and clay components such as poor specificity, pH dependence, particle size sensitivity, and low water wettability. We also discuss different regeneration and wastewater treatment options (e.g., membrane, coagulant, and barrier/columns) using clay-polymer nanocomposites. Finally, we provide an economic analysis of the use of these adsorbents and suggest future research directions.

Metal(loid)s (As, Hg, Se, Pb and Cd) in paddy soil: Bioavailability and potential risk to human health.

Rice is one of the principal staple foods, essential for safeguarding the global food and nutritional security, but due to different natural and anthropogenic sources, it also acts as one of the biggest reservoirs of potentially toxic metal(loids) like As, Hg, Se, Pb and Cd. This review summarizes mobilization, translocation and speciation mechanism of these metal(loids) in soil-plant continuum as well as available cost-effective remediation measures and future research needs to eliminate the long-term risk to human health. High concentrations of these elements not only cause toxicity problems in plants, but also in animals that consume them and gradual deposition of these elements leads to the risk of bioaccumulation. The extensive occurrence of contaminated rice grains globally poses substantial public health risk and merits immediate action. People living in hotspots of contamination are exposed to higher health risks, however, rice import/export among different countries make the problem of global concern. Accumulation of As, Hg, Se, Pb and Cd in rice grains can be reduced by reducing their bioavailability, and controlling their uptake by rice plants. The contaminated soils can be reclaimed by phytoremediation, bioremediation, chemical amendments and mechanical measures; however these methods are either too expensive and/or too slow. Integration of innovative agronomic practices like crop establishment methods and improved irrigation and nutrient management practices are important steps to help mitigate the accumulation in soil as well as plant parts. Adoption of transgenic techniques for development of rice cultivars with low accumulation in edible plant parts could be a realistic option that would permit rice cultivation in soils with high bioavailability of these metal(loid)s.

A review on biochar modulated soil condition improvements and nutrient dynamics concerning crop yields: Pathways to climate change mitigation and global food security.

The beneficial role of biochar on improvement of soil quality, C sequestration, and enhancing crop yield is widely reported. As such there is not much consolidated information available linking biochar modulated soil condition improvement and soil nutrient availability on crop yields. The present review paper addresses the above issues by compilation of world literature on biochar and a new dimension is introduced in this review by performing a meta-analysis of published data by using multivariate statistical analysis. Hence this review is a new in its kind and is useful to the broad spectrum of readers. Generally, alkalinity in biochar increases with increase in pyrolysis temperature and majority of the biochar is alkaline in nature except a few which are acidic. The N content in many biochar was reported to be more than 4% as well as less than 0.5%. Poultry litter biochar is a rich source of P (3.12%) and K (7.40%), while paper mill sludge biochar is higher in Ca content (31.1%) and swine solids biochar in Zn (49810 mg kg-1), and Fe (74800 mg kg-1) contents. The effect of biochar on enhancing soil pH was higher in Alfisol, Ferrosol and Acrisol. Soil application of biochar could on an average increase (78%), decrease (16%), or show no effect on crop yields under different soil types. Biochar produced at a lower pyrolysis temperature could deliver greater soil nutrient availabilities than that prepared at higher temperature. Principal component analysis (PCA) of available data shows an inverse relationship between [pyrolysis temperature and soil pH], and [biochar application rate and soil cation exchange capacity]. The PCA also suggests that the original soil properties and application rate strongly control crop yield stimulations via biochar amendments. Finally, biochar application shows net soil C gains while also serving for increased plant biomass production that strongly recommends biochar as a useful soil amendment. Therefore, the application of biochar to soils emerges as a 'win-win strategy' for sustainable waste management, climate change mitigation and food security.

Influence of imazethapyr and quizalofop-p-ethyl application on microbial biomass and enzymatic activity in peanut grown soil.

A field experiment was conducted to examine the degradation and impact of two post-emergence herbicides (imazethapyr and quizalofop-p-ethyl) on soil ecosystems at a half recommended rate (HRE), recommended rate (RE), and double recommended rate (DRE) during kharif peanut cultivation. Herbicides were innocuous to soil microbial activity at HRE, however, showed some significant influences at RE and DRE, and exerted temporary toxic effects on microbial biomass carbon and fluorescein diacetate hydrolyzing activity. Dehydrogenase activity also declined for a shorter period except imazethapyr application at DRE. Acid phosphatase activity was inhibited whereas alkaline phosphatase activity fluctuated between promotion and inhibition, but promotion was predominant suggesting a direct role of alkaline soil environment. Soil NH4+ and NO3- nitrogen were increased by the herbicides at initial (after 7 days) and last phases (after 30 days), respectively. After an early period of inhibition, urease activity returned to the control level after 30 days. Dissipation of imazethapyr residues fitted best to bi-exponential order rate kinetics at DRE and RE, whereas it followed first-order rate kinetics at HRE. The residues of quizalofop-p-ethyl were found only up to 1 day after application suggesting its rapid conversion to active acid metabolites. Both the herbicides had transient harmful effects on most of the soil microbiological parameters.

External potassium (K(+)) application improves salinity tolerance by promoting Na(+)-exclusion, K(+)-accumulation and osmotic adjustment in contrasting peanut cultivars.

Achieving salt-tolerance is highly desirable in today's agricultural context. Apart from developing salt-tolerant cultivars, possibility lies with management options, which can improve crop yield and have significant impact on crop physiology as well. Thus present study was aimed to evaluate the ameliorative role of potassium (K(+)) in salinity tolerance of peanut. A field experiment was conducted using two differentially salt-responsive cultivars and three levels of salinity treatment (control, 2.0 dS m(-1), 4.0 dS m(-1)) along with two levels (with and without) of potassium fertilizer (0 and 30 kg K2O ha(-1)). Salinity treatment incurred significant changes in overall physiology in two peanut cultivars, though the responses varied between the tolerant and the susceptible one. External K(+) application resulted in improved salinity tolerance in terms of plant water status, biomass produced under stress, osmotic adjustment and better ionic balance. Tolerant cv. GG 2 showed better salt tolerance by excluding Na(+) from uptake and lesser accumulation in leaf tissue and relied more on organic osmolyte for osmotic adjustment. On the contrary, susceptible cv. TG 37A allowed more Na(+) to accumulate in the leaf tissue and relied more on inorganic solute for osmotic adjustment under saline condition, hence showed more susceptibility to salinity stress. Application of K(+) resulted in nullifying the negative effect of salinity stress with slightly better response in the susceptible cultivar (TG 37A). The present study identified Na(+)-exclusion as a key strategy for salt-tolerance in tolerant cv. GG 2 and also showed the ameliorating role of K(+) in salt-tolerance with varying degree of response amongst tolerant and susceptible cultivars.

Restoration of carbon and microbial activity in salt-induced soil by application of peanut shell biochar during short-term incubation study.

For the present study, soil samples of four artificially-induced salinity gradients (S0: control, S1: 2.0, S2: 4.0, S3: 6.0 ECiw) was incubated with fine-textured peanut shell biochar at various ratios (B0: control, B1: 2.5%, B2: 5.0%, B3: 10% w/w) for 30 days. At 1, 3, 7, 15, 30 days of incubation, samples were analyzed for soil carbon and selected enzyme activities. Results showed that biochar could increase soil organic carbon on application of highest rate of biochar addition (B3), hence potentially restored the saline soils by less C mineralization, and more sequestration of soil C. However, soil enzyme activities were biochar rate(s), day(s) of incubation and enzyme dependent. The lowest rate of biochar addition (B1) showed highest dehydrogenase (20.5 µg TPF g(-1) soil h(-1)), acid phosphatase (29.1 µg PNP g(-1) soil h(-1)) and alkaline phosphatase (16.1 µg PNP g(-1) soil h(-1)) whereas the higher rate (B2) increased the urease (5.51 µg urea-N g(-1) soil h(-1)) and fluorescein diacetate hydrolyzing activities (3.95 µg fluorescein g(-1) OD soil h(-1)) in soil. All the positive changes persisted at higher levels of salinity (S2, S3) suggesting biochar-amended soil may be potential for better nutrient cycling. Soil enzymes were found to be correlated with soil carbon and with each other while principal component analysis (PCA) extracted the most sensitive parameters as the acid and alkaline phosphatases and urease activities in the present experimental condition. This is the first time report of examining soil microbial environment using peanut shell biochar under a degraded (saline) soil.

Simultaneous analysis of herbicides pendimethalin, oxyfluorfen, imazethapyr and quizalofop-p-ethyl by LC-MS/MS and safety evaluation of their harvest time residues in peanut (Arachis hypogaea L.).

This paper reports a simple and rapid method for simultaneous determination of the residues of selected herbicides viz. pendimethalin, oxyfluorfen, imazethapyr and quizalofop-p-ethyl in peanut by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A modified approach of the QuEChERS methodology was used to extract the herbicides from the peanut kernel without any clean-up. The method showed excellent linearity (r(2) > 0.99) with no significant matrix effect. Accuracy of the method in terms of average recoveries of all the four herbicides ranged between 69.4 -94.4 % at spiking levels of 0.05, 0.10 and 0.25 mg kg(-1) with intra-day and inter-day precision RSD (%) between 2.6-16.6 and 8.0-11.3, respectively. Limit of quantification (LOQs) was 5.0 µg kg(-1) for pendimethalin, imazethapyr and quizalofop-p-ethyl and 10.0 µg kg(-1) for oxyfluorfen. The expanded uncertainties were <11 % for determination of these herbicides in peanut. The proposed method was successfully applied for analysis of these herbicide residues in peanut samples harvested from the experimental field and the residues were below the detection level.

Evaluating soil quality under a long-term integrated tillage-water-nutrient experiment with intensive rice-wheat rotation in a semi-arid Inceptisol, India.

Long-term sustainability and a declining trend in productivity of rice-wheat rotation in the Indo-Gangetic plain, often direct towards the changes in soil quality parameters. Soil quality is decided through few sensitive soil physical, chemical and biological indicators as it cannot be measured directly. The present investigation was carried out to develop a valid soil quality index through some chosen indicators under long-term influences of tillage, water and nutrient-management practices in a rice-wheat cropping system. The experiment consisted of two tillage treatments, three irrigation treatments, and nine nutrient management treatments for both rice and wheat, was continued for 8 years. The index was developed using expert-opinion based conceptual framework model. After harvest of rice, the CFSQI-P (productivity) was higher under puddled situation, whereas CFSQI-EP (environmental protection) was more under non-puddled condition and 3-days of drainage was found promising for all the indices. No-tillage practice always showed higher soil quality index. The treatments either receiving full organics (100% N) or 25% substitution of fertilizer N with organics showed higher soil quality indices. Puddling, irrigation after 3 days of drainage and substitution of 25% recommended fertilizer N dose with FYM in rice could be practiced for maintaining or enhancing soil quality. No-tillage, two irrigations, and domestic sewage sludge in wheat can safely be recommended for achieving higher soil quality.