Meta-analysis and validation of genomic loci governing seedling and reproductive stage salinity tolerance in rice.

Identification of concurrent genomic regions contributing tolerance to salinity at the seedling and reproductive stages were done using 45 quantitative trait loci (QTL) mapping studies reporting 915 individual QTLs. The QTL-data were used to perform a meta-analysis to predict, validate and analyze the Meta-QTLs governing component traits contributing to salinity tolerance. We predicted a total of 65 and 49 Meta-QTLs distributed across the genome governing seedling and reproductive stage salinity tolerance, respectively. Salinity stress (EC ~10.0 dSm-1 ) was evaluated in a set of 32 genotypes grown hydroponically, from these eight extreme (highly tolerant and highly susceptible) genotypes were selected for validation of significant Meta-QTLs. Another set of eight previously known and reported (highly tolerant and highly susceptible) genotypes were evaluated under saline micro plot conditions (EC ~8.0 dSm-1 ) and used for validation of significant Meta-QTLs for reproductive stage salinity tolerance. The microsatellite marker "RM5635" linked to MSQTL4.2 (~295.43 kb) was able to clearly differentiate contrasting genotypes for seedling stage salinity tolerance, whereas at the reproductive stage, none of the markers were able to validate the predicted Meta-QTL for salinity tolerance. Earlier reported, gene expression studies were used for candidate gene analysis of validated MSQTL4.2, which indicated the down regulation of Os04g0423100, a gene encoding Mono-oxygenase-FAD binding domain containing protein. The traits associated with this Meta-QTL were root and shoot sodium and potassium concentration and leaf chlorophyll content. The identified and validated genomic region assumes a great significant role in seedling stage salinity tolerance in rice, and it can be used for marker-assisted backcross breeding programs.

Differential response of Indian mustard (Brassica juncea L., Czern and Coss) under salinity: photosynthetic traits and gene expression.

To explore the effect of salt stress on photosynthetic traits and gene expression in Indian mustard, four genotypes CS 54 (national check for salinity), CS 52-SPS-1-2012 (salt tolerant mutant), CS 614-4-1-4-100-13 (salt sensitive mutant) and Pusa bold (high yielding variety) were evaluated under irrigation water salinity (ECiw 12, and 15 dS m-1). Results suggest genotype CS 52-SPS-1-2012 followed by CS 54 performed better under imposed salt stress due to differential regulation of Na+ accumulation in the roots and main stem, restriction of Na+ influx from root to shoot, maintaining higher net photosynthetic traits under saline stress compared to CS 614-4-1-4-100-13 and Pusa bold. Further, overexpression of antiporters (SOS1, SOS2, SOS3, ENH1 and NHX1) and antioxidant (APX1, APX4, DHAR1 and MDHAR) genes in salt tolerant genotypes CS 52-SPS-1-2012 and CS 54 demonstrated their significant role in imparting salt tolerance in Indian mustard.

Can productivity and profitability be enhanced in intensively managed cereal systems while reducing the environmental footprint of production? Assessing sustainable intensification options in the breadbasket of India.

In the most productive area of the Indo-Gangetic Plains in Northwest India where high yields of rice and wheat are commonplace, a medium-term cropping system trial was conducted in Haryana State. The goal of the study was to identify integrated management options for further improving productivity and profitability while rationalizing resource use and reducing environmental externalities (i.e., "sustainable intensification", SI) by drawing on the principles of diversification, precision management, and conservation agriculture. Four scenarios were evaluated: Scenario 1 - "business-as-usual" [conventional puddled transplanted rice (PTR) followed by (fb) conventional-till wheat]; Scenario 2 - reduced tillage with opportunistic diversification and precision resource management [PTR fb zero-till (ZT) wheat fb ZT mungbean]; Scenario 3 - ZT for all crops with opportunistic diversification and precision resource management [ZT direct-seeded rice (ZT-DSR) fb ZT wheat fb ZT mungbean]; and Scenario 4 - ZT for all crops with strategic diversification and precision resource management [ZT maize fb ZT wheat fb ZT mungbean]. Results of this five-year study strongly suggest that, compared with business-as-usual practices, SI strategies that incorporate multi-objective yield, economic, and environmental criteria can be more productive when used in these production environments. For Scenarios 2, 3, and 4, system-level increases in productivity (10-17%) and profitability (24-50%) were observed while using less irrigation water (15-71% reduction) and energy (17-47% reduction), leading to 15-30% lower global warming potential (GWP), with the ranges reflecting the implications of specific innovations. Scenario 3, where early wheat sowing was combined with ZT along with no puddling during the rice phase, resulted in a 13% gain in wheat yield compared with Scenario 2. A similar gain in wheat yield was observed in Scenario 4 vis-à-vis Scenario 2. Compared to Scenario 1, wheat yields in Scenarios 3 and 4 were 15-17% higher, whereas, in Scenario 2, yield was either similar in normal years or higher in warmer years. During the rainy (kharif) season, ZT-DSR provided yields similar to or higher than those of PTR in the first three years and lower (11-30%) in Years 4 and 5, a result that provides a note of caution for interpreting technology performance through short-term trials or simply averaging results over several years. The resource use and economic and environmental advantages of DSR were more stable through time, including reductions in irrigation water (22-40%), production cost (11-17%), energy inputs (13-34%), and total GWP (14-32%). The integration of "best practices" in PTR in Scenario 2 resulted in reductions of 24% in irrigation water and 21% in GWP, with a positive impact on yield (0.9 t/ha) and profitability compared to conventional PTR, demonstrating the power of simple management changes to generate improved SI outcomes. When ZT maize was used as a diversification option instead of rice in Scenario 4, reductions in resource use jumped to 82-89% for irrigation water and 49-66% for energy inputs, with 13-40% lower GWP, similar or higher rice equivalent yield, and higher profitability (27-73%) in comparison to the rice-based scenarios. Despite these advantages, maize value chains are not robust in this part of India and public procurement is absent. Results do demonstrate that transformative opportunities exist to break the cycle of stagnating yields and inefficient resource use in the most productive cereal-based cropping systems of South Asia. However, these SI entry points need to be placed in the context of the major drivers of change in the region, including market conditions, risks, and declining labor availability, and matching with the needs and interests of different types of farmers.

Agronomic improvements can make future cereal systems in South Asia far more productive and result in a lower environmental footprint.

South Asian countries will have to double their food production by 2050 while using resources more efficiently and minimizing environmental problems. Transformative management approaches and technology solutions will be required in the major grain-producing areas that provide the basis for future food and nutrition security. This study was conducted in four locations representing major food production systems of densely populated regions of South Asia. Novel production-scale research platforms were established to assess and optimize three futuristic cropping systems and management scenarios (S2, S3, S4) in comparison with current management (S1). With best agronomic management practices (BMPs), including conservation agriculture (CA) and cropping system diversification, the productivity of rice- and wheat-based cropping systems of South Asia increased substantially, whereas the global warming potential intensity (GWPi) decreased. Positive economic returns and less use of water, labor, nitrogen, and fossil fuel energy per unit food produced were achieved. In comparison with S1, S4, in which BMPs, CA and crop diversification were implemented in the most integrated manner, achieved 54% higher grain energy yield with a 104% increase in economic returns, 35% lower total water input, and a 43% lower GWPi. Conservation agriculture practices were most suitable for intensifying as well as diversifying wheat-rice rotations, but less so for rice-rice systems. This finding also highlights the need for characterizing areas suitable for CA and subsequent technology targeting. A comprehensive baseline dataset generated in this study will allow the prediction of extending benefits to a larger scale.

Assessing the performance of the photo-acoustic infrared gas monitor for measuring CO(2), N(2)O, and CH(4) fluxes in two major cereal rotations.

Rapid, precise, and globally comparable methods for monitoring greenhouse gas (GHG) fluxes are required for accurate GHG inventories from different cropping systems and management practices. Manual gas sampling followed by gas chromatography (GC) is widely used for measuring GHG fluxes in agricultural fields, but is laborious and time-consuming. The photo-acoustic infrared gas monitoring system (PAS) with on-line gas sampling is an attractive option, although it has not been evaluated for measuring GHG fluxes in cereals in general and rice in particular. We compared N2 O, CO2 , and CH4 fluxes measured by GC and PAS from agricultural fields under the rice-wheat and maize-wheat systems during the wheat (winter), and maize/rice (monsoon) seasons in Haryana, India. All the PAS readings were corrected for baseline drifts over time and PAS-CH4 (PCH4 ) readings in flooded rice were corrected for water vapor interferences. The PCH4 readings in ambient air increased by 2.3 ppm for every 1000 mg cm(-3) increase in water vapor. The daily CO2 , N2 O, and CH4 fluxes measured by GC and PAS from the same chamber were not different in 93-98% of all the measurements made but the PAS exhibited greater precision for estimates of CO2 and N2 O fluxes in wheat and maize, and lower precision for CH4 flux in rice, than GC. The seasonal GC- and PAS-N2 O (PN2 O) fluxes in wheat and maize were not different but the PAS-CO2 (PCO2 ) flux in wheat was 14-39% higher than that of GC. In flooded rice, the seasonal PCH4 and PN2 O fluxes across N levels were higher than those of GC-CH4 and GC-N2 O fluxes by about 2- and 4fold, respectively. The PAS (i) proved to be a suitable alternative to GC for N2 O and CO2 flux measurements in wheat, and (ii) showed potential for obtaining accurate measurements of CH4 fluxes in flooded rice after making correction for changes in humidity.

Further evidence that a terminal drought tolerance QTL of pearl millet is associated with reduced salt uptake.

Earlier, we established that a major drought tolerance QTL on linkage group 2 of pearl millet is also associated with reduced salt uptake and enhanced growth under salt stress. Present study was undertaken to re-assess the performance of drought tolerant (PRLT 2/89-33) and drought sensitive (H 77/833-2) parents along with two QTL-NILs (ICMR 01029 and ICMR 01040), under salinity stress specifically imposed during post-flowering growth stages when plants had developed their ion sinks in full. Time course changes in ionic accumulation and their compartmentalization in different plant parts was studied, specifically to monitor and capture changes conferred by the two alleles at this QTL, at small intervals. Amongst different plant parts, higher accumulation of toxic ion Na+ was recorded in roots. Further, the Na+ concentration in roots of the testcross hybrid of the drought-sensitive parent (H 77/833-2) reached its maximum at ECiw 15 dS m-1 within 24 h after salinity imposition, whereas it continued to increase with time in the testcross hybrids of the drought tolerant parent PRLT 2/89-33 as well as those of its QTL-NILs (ICMR 01029 and ICMR 01004) and reached at its maximum at 120 h stage. Comparison of differential distribution of toxic ions in individual leaves revealed that Na+ ions were not uniformly distributed in the leaves of the drought-tolerant parent and drought-tolerant QTL-NILs; but accumulated preferentially in the older leaves, whereas the hybrid of the drought-sensitive parent showed significantly higher Na+ concentration in all main stem leaves irrespective of their age. Dynamics of chlorophyll and proline concentration variation studied under salt stress at late flowering stages revealed a greater reduction, almost twice, in both leaf chlorophyll and proline concentrations in younger leaves in the hybrids of the sensitive parent as compared to the tolerant parent and QTL NILs. Imposition of salinity stress even at flowering stage affected the yield performance in pearl millet, wherein higher yield was recorded in drought tolerant parent and the two QTL-NILs compared to drought sensitive parent.

Climate-smart agricultural practices influence the fungal communities and soil properties under major agri-food systems.

Fungal communities in agricultural soils are assumed to be affected by climate, weather, and anthropogenic activities, and magnitude of their effect depends on the agricultural activities. Therefore, a study was conducted to investigate the impact of the portfolio of management practices on fungal communities and soil physical-chemical properties. The study comprised different climate-smart agriculture (CSA)-based management scenarios (Sc) established on the principles of conservation agriculture (CA), namely, ScI is conventional tillage-based rice-wheat rotation, ScII is partial CA-based rice-wheat-mungbean, ScIII is partial CSA-based rice-wheat-mungbean, ScIV is partial CSA-based maize-wheat-mungbean, and ScV and ScVI are CSA-based scenarios and similar to ScIII and ScIV, respectively, except for fertigation method. All the scenarios were flood irrigated except the ScV and ScVI where water and nitrogen were given through subsurface drip irrigation. Soils of these scenarios were collected from 0 to 15 cm depth and analyzed by Illumina paired-end sequencing of Internal Transcribed Spacer regions (ITS1 and ITS2) for the study of fungal community composition. Analysis of 5 million processed sequences showed a higher Shannon diversity index of 1.47 times and a Simpson index of 1.12 times in maize-based CSA scenarios (ScIV and ScVI) compared with rice-based CSA scenarios (ScIII and ScV). Seven phyla were present in all the scenarios, where Ascomycota was the most abundant phyla and it was followed by Basidiomycota and Zygomycota. Ascomycota was found more abundant in rice-based CSA scenarios as compared to maize-based CSA scenarios. Soil organic carbon and nitrogen were found to be 1.62 and 1.25 times higher in CSA scenarios compared with other scenarios. Bulk density was found highest in farmers' practice (Sc1); however, mean weight diameter and water-stable aggregates were found lowest in ScI. Soil physical, chemical, and biological properties were found better under CSA-based practices, which also increased the wheat grain yield by 12.5% and system yield by 18.8%. These results indicate that bundling/layering of smart agricultural practices over farmers' practices has tremendous effects on soil properties, and hence play an important role in sustaining soil quality/health.

Climate-smart agriculture practices influence weed density and diversity in cereal-based agri-food systems of western Indo-Gangetic plains.

Climate-smart agriculture (CSA)-based management practices are getting popular across South-Asia as an alternative to the conventional system for particular weed suppression, resources conservation and environmental quality. An 8-year study (2012-2013 to 2019-2020) was conducted to understand the shift in weed density and diversity under different CSA-based management practices called scenarios (Sc). These Sc involved: Sc1, conventional tillage (CT)-based rice-wheat system with flood irrigation (farmers' practice); Sc2, CT-rice, zero tillage (ZT)-wheat-mungbean with flood irrigation (partial CA-based); Sc3, ZT rice-wheat-mungbean with flood irrigation (partial CSA-based rice); Sc4, ZT maize-wheat-mungbean with flood irrigation (partial CSA-based maize); Sc5, ZT rice-wheat-mungbean with subsurface drip irrigation (full CSA-based rice); and Sc6, ZT maize-wheat-mungbean with subsurface drip irrigation (full CSA-based maize). The most abundant weed species were P. minor > A. arvensis > M. indicus > C. album and were favored by farmers' practice. However, CSA-based management practices suppressed these species and favored S. nigrum and R. dentatus and the effect of CSAPs was more evident in the long-term. Maximum total weed density was observed for Sc1, while minimum value was recorded under full CSA-based maize systems, where seven weed-species vanished, and P. minor density declined to 0.33 instead of 25.93 plant m-2 after 8-years of continuous cultivation. Full CSA-based maize-wheat system could be a promising alternative for the conveniently managed rice-wheat system in weed suppression in north-west India.

Topsoil Bacterial Community Changes and Nutrient Dynamics Under Cereal Based Climate-Smart Agri-Food Systems.

Soil microorganisms play a critical role in soil biogeochemical processes, nutrient cycling, and resilience of agri-food systems and are immensely influenced by agronomic management practices. Understanding soil bacterial community and nutrient dynamics under contrasting management practices is of utmost importance for building climate-smart agri-food systems. Soil samples were collected at 0-15 cm soil depth from six management scenarios in long-term conservation agriculture (CA) and climate-smart agriculture (CSA) practices. These scenarios (Sc) involved; ScI-conventional tillage based rice-wheat rotation, ScII- partial CA based rice-wheat-mungbean, ScIII- partial CSA based rice-wheat-mungbean, ScIV is partial CSA based maize-wheat-mungbean, ScV and ScVI are CSA based scenarios, were similar to ScIII and ScIV respectively, layered with precision water & nutrient management. The sequencing of soil DNA results revealed that across the six scenarios, a total of forty bacterial phyla were observed, with Proteobacteria as dominant in all scenarios, followed by Acidobacteria and Actinobacteria. The relative abundance of Proteobacteria was 29% higher in rice-based CSA scenarios (ScIII and ScV) and 16% higher in maize-based CSA scenarios (ScIV and ScVI) compared to conventional-till practice (ScI). The relative abundance of Acidobacteria and Actinobacteria was respectively 29% and 91% higher in CT than CSA based rice and 27% and 110% higher than maize-based scenarios. Some taxa are present relatively in very low abundance or exclusively in some scenarios, but these might play important roles there. Three phyla are exclusively present in ScI and ScII i.e., Spirochaetes, Thermi, and Euryarchaeota. Shannon diversity index was 11% higher in CT compared to CSA scenarios. Maize based CSA scenarios recorded higher diversity indices than rice-based CSA scenarios. Similar to changes in soil bacterial community, the nutrient dynamics among the different scenarios also varied significantly. After nine years of continuous cropping, the soil organic carbon was improved by 111% and 31% in CSA and CA scenarios over the CT scenario. Similarly, the available nitrogen, phosphorus, and potassium were improved by, respectively, 38, 70, and 59% in CSA scenarios compared to the CT scenario. These results indicate that CSA based management has a positive influence on soil resilience in terms of relative abundances of bacterial groups, soil organic carbon & available plant nutrients and hence may play a critical role in the sustainability of the intensive cereal based agri-food systems.

Designing profitable, resource use efficient and environmentally sound cereal based systems for the Western Indo-Gangetic plains.

In the western Indo-Gangetic plains, issues of deterioration in soil, water, and environment quality coupled with low profitability jeopardize the sustainability of the dominant rice-wheat (RW) system. To address these issues, crop diversification and conservation agriculture (CA)-based management hold considerable promise but the adoption of both approaches has been low, and additional evidence generation from a multi-criteria productivity and sustainability perspective is likely required to help drive the change. Compared to prevailing farmers' practice (FP), results suggest that CA-based rice management increased profitability by 13% and energy use efficiency (EUE) by 21% while reducing irrigation by 19% and global warming potential (GWP) by 28%. By substituting CA-based maize for rice, similar mean profitability gains were realized (16%) but transformative improvements in irrigation (- 84%), EUE (+ 231%), and GWP (- 95%) were observed compared to FP. Inclusion of mungbean in the rotation (i.e. maize-wheat-mungbean) with CA-based management increased the system productivity, profitability, and EUE by 11, 25 and 103%, respectively while decreasing irrigation water use by 64% and GWP by 106% compared to FP. Despite considerable benefits from the CA-based maize-wheat system, adoption of maize is not widespread due to uneven market demand and assured price guarantees for rice.

Fe-exchanged nano-bentonite outperforms Fe3O4 nanoparticles in removing nitrate and bicarbonate from wastewater.

Nitrate (NO3-) and bicarbonate (HCO3-) are harmful for the water quality and can potentially create negative impacts to aquatic organisms, crops and humans. This study deals with the removal of NO3- and HCO3- from contaminated wastewater using Fe-exchanged nano-bentonite and Fe3O4 nanoparticles. X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, surface area measurement and particle size analysis revealed that the adsorbents fall under the nano-scale size range with high specific surface area, and Fe was successfully exchanged in the nano-bentonite clay. The kinetics of adsorption was well defined by pseudo-first order and pseudo-second order kinetic models for both NO3- and HCO3-. The Fe-exchanged nano-bentonite was a better performing adsorbent of the oxyanions than Fe3O4 nanoparticles. According to the Sips isothermal model, the Fe-exchanged nano-bentonite exhibited the highest NO3- and HCO3- adsorption potential of 64.76 mg g-1 and 9.73 meq g-1, respectively, while the respective values for Fe3O4 nanoparticles were 49.90 mg g-1 and 3.07 meq g-1. Thus, inexpensiveness and easy preparation process of Fe-exchanged nano-bentonite make it attractive for NO3- and HCO3- removal from contaminated wastewater with significant environmental and economic benefits.

Soil bacterial diversity under conservation agriculture-based cereal systems in Indo-Gangetic Plains.

In Indo-Gangetic plains (IGP) of India, natural resources (soil, water, and environment) are degrading under the conventional-till (CT)-based management practices in rice-wheat cropping system. A long-term field experiment was conducted to understand the soil bacterial diversity and abundance under different sets of management scenarios (Sc). The study comprised of four scenarios, namely, -Sc.I CT-based rice-wheat system (farmers' practice); Sc.II, partial conservation agriculture (CA) based in which rice is under CT-wheat and mungbean under zero-tillage (ZT); Sc.III, full CA-based in which rice-wheat-mungbean are under ZT and Sc.IV, where maize-wheat-mungbean are under ZT. These scenarios varied in cropping system, tillage, and crop residue management practices. Using Illumina MiSeq sequencing technology, the variable regions V3-V4 of 16S rRNA were sequenced and the obtained reads were analyzed to study the diversity patterns in the scenarios. Results showed the presence of 53 bacterial phyla across scenarios. The predominant phyla in all scenarios were Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes which accounted for more than 70% of the identified phyla. However, the rice-based systems (Sc.I, Sc.II, and Sc.III) were dominated by phylum Proteobacteria; however, maize-based system (Sc.IV) was dominated by Acidobacteria. The class DA052 and Acidobacteriia of Acidobacteria and Bacteroidetes of Bacteroidia were exceptionally higher in Sc.IV. Shannon diversity index was 8.8% higher in Sc.I, 7.5% in Sc.II, and 2.7% in Sc.III compared to Sc.IV. The findings revealed that soil bacterial diversity and abundance are influenced by agricultural management practices as bacterial diversity under full CA-based management systems (Sc.III and Sc.IV) was lower when compared to farmer's practice (Sc.I) and partial CA (Sc.II) scenarios.

Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.

A pearl millet inbred germplasm association panel (PMiGAP) comprising 250 inbred lines, representative of cultivated germplasm from Africa and Asia, elite improved open-pollinated cultivars, hybrid parental inbreds and inbred mapping population parents, was recently established. This study presents the first report of genetic diversity in PMiGAP and its exploitation for association mapping of drought tolerance traits. For diversity and genetic structure analysis, PMiGAP was genotyped with 37 SSR and CISP markers representing all seven linkage groups. For association analysis, it was phenotyped for yield and yield components and morpho-physiological traits under both well-watered and drought conditions, and genotyped with SNPs and InDels from seventeen genes underlying a major validated drought tolerance (DT) QTL. The average gene diversity in PMiGAP was 0.54. The STRUCTURE analysis revealed six subpopulations within PMiGAP. Significant associations were obtained for 22 SNPs and 3 InDels from 13 genes under different treatments. Seven SNPs associations from 5 genes were common under irrigated and one of the drought stress treatments. Most significantly, an important SNP in putative acetyl CoA carboxylase gene showed constitutive association with grain yield, grain harvest index and panicle yield under all treatments. An InDel in putative chlorophyll a/b binding protein gene was significantly associated with both stay-green and grain yield traits under drought stress. This can be used as a functional marker for selecting high yielding genotypes with 'stay green' phenotype under drought stress. The present study identified useful marker-trait associations of important agronomics traits under irrigated and drought stress conditions with genes underlying a major validated DT-QTL in pearl millet. Results suggest that PMiGAP is a useful panel for association mapping. Expression patterns of genes also shed light on some physiological mechanisms underlying pearl millet drought tolerance.