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Efforts to maintain rice production in the future face many challenges, including the availability of increasingly narrow land, attacks by plant pest organisms, and declining land fertility due to improper cultivation systems. More than 70% of rice fields are in a disturbed ecological status due to cultivation technology that could be more environmentally friendly, which can interfere with the sustainability of rice self-sufficiency. An environmentally friendly rice cultivation system needs to be developed. This study aims to measure the agronomic and physiological responses of 3 rice genotypes in sustainable cultivation systems. The experiment used a Group Random Design on 3 rice genotypes (black, red, and white) in both conventional and sustainable cultivation systems. The research was carried out in the experimental garden of Polinela Organic Farm, Lampung State Polytechnic, from September 2020 to September 2021. The results showed that the plant, leaf greenery, number of tillers, number of panicles, grain weight per panicle, and biomass weight were not significantly different between conventional and sustainable cultivation. At the same time, the harvest and production indices per hectare were significantly different. The physiological responses to the photosynthesis and transpiration rates differed markedly in conventional and continuous cultivation. In contrast, the conductance of stomata did not differ significantly in both cultivation systems. The red rice genotype is the best, and it has a broader adaptation to conventional and sustainable cultivation systems. [ABSTRACT FROM AUTHOR]

Extended Abstract Introduction and Objective: Grain quality is one of the most important goals of rice breeding. One of the important traits in rice grain quality is its aroma, which is the result of the expression of recessive mutations of the OsBadh2 gene and determines the economic value of rice. In this research, the phenotypic and molecular screening of 50 different genotypes of rice was done based on the markers related to the aroma trait. Materials and Methods: In this research, 50 local and improved genotypes of rice were prepared from the collection of the Rice Research Institute of Iran, and the aroma trait was based on biochemical evaluation related to phenotypic selection based on the intensity of the aroma created in the treatment with 1.7 potassium hydroxide solution percentage and genotypic selection were done based on the band pattern created from the amplified gene sequence by using 3 pairs of specific primers (Badh2, Badex7-5 and Nksbad2) contiguous with the gene locations controlling the scent trait. To analyze the correlation between genes and the observed phenotype, the generalized linear logistic regression model was used. Results: Based on phenotypic evaluation, 31 aromatic cultivars and 19 non-aromatic cultivars were identified, which were in full agreement with the data obtained from genotypic screening, and it was found that Badh2 and Nkshad2 markers are able to predict and distinguish aromatic and non-aromatic cultivars with high confidence and accuracy. Conclusion: Badh2 and Nksbad2 markers can be used as efficient markers in genetic localization of diverging populations for fragrance as a Codominant marker instead of a phenotypic evaluation method.

Introduction and Objective: Grain quality is one of the most important goals of rice breeding. One of the important traits in rice grain quality is its aroma, which is the result of the expression of recessive mutations of the OsBadh2 gene and determines the economic value of rice. In this research, the phenotypic and molecular screening of 50 different genotypes of rice was done based on the markers related to the aroma trait. Materials and Methods: In this research, 50 local and improved genotypes of rice were prepared from the collection of the Rice Research Institute of Iran, and the aroma trait was based on biochemical evaluation related to phenotypic selection based on the intensity of the aroma created in the treatment with 1.7 potassium hydroxide solution percentage and genotypic selection were done based on the band pattern created from the amplified gene sequence by using 3 pairs of specific primers (Badh2, Badex7-5 and Nksbad2) contiguous with the gene locations controlling the scent trait. To analyze the correlation between genes and the observed phenotype, the generalized linear logistic regression model was used. Results: Based on phenotypic evaluation, 31 aromatic cultivars and 19 non-aromatic cultivars were identified, which were in full agreement with the data obtained from genotypic screening, and it was found that Badh2 and Nkshad2 markers are able to predict and distinguish aromatic and non-aromatic cultivars with high confidence and accuracy. Conclusion: Badh2 and Nksbad2 markers can be used as efficient markers in genetic localization of diverging populations for fragrance as a Codominant marker instead of a phenotypic evaluation method. [ABSTRACT FROM AUTHOR]

The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha−1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha−1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha−1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha−1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates. [ABSTRACT FROM AUTHOR]

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To mitigate the impact of extreme weather incidents, rice cultivars Way Seputih (WS) and Way Apo Buru (WAB) were evaluated under simulation of continuous wind and rainfall treatments. The research was conducted from July to October 2017 at Leuwikopo Experimental Farm, Bogor, Indonesia. For 15 days at day time, flowering rice hills were treated with about 100 mm/h water shower (Experiment-1), and with 0, 10-15, 20-25 and 35-40 km/h wind velocity (Experiment-2). Results showed that wind and rainfall treatments reduced rice production; the effect depended on the genotypes and flowering stage. Rain treatment from panicle emergence to 50%-emerged increased the number of unfilled grains by 154.6-182.3% and 55.7-101.9% in WS and WAB cultivars, respectively. Rain treatment at 100%-emerged had no effect on WS, but it increased unfilled grain (163.5%) and decreased grain index (12.9%) in the WAB cultivar. Wind speed at 35-40 km/h promoted a high percentage of grain drop (25.7%) and unfilled grains (77.3%), and low grain index (20.8 g) in WS genotype. WAB was more tolerant of wind stress than the WS. The present experiment showed that genotype had different responses to wind and rain treatments implying different mitigation strategies should be applied through genotype selection.

Understanding the genetic and environmental factors that structure root-associated microbiomes is necessary to inform rice (Oryza sativa L.) breeding and fertilizer. Herein, we comprehensivly explored the microbiomes along four fine-scale root compartments, bulk soil, rhizosphere, rhizoplane and endosphere, between traditional Japonica rice and improved hybrid rice acorss three spatially distant locations. Bacterial diversity decreased monotonically from external bulk soil to internal endosphere. The acquisition of endosphere symbionts is governed conjointly by a two-step selection process and an amplification selection process, which depends on the bacterial functional group. The bacterial communities are primarly affected by root compartment and planting location, followed by relatively samll but signifcant rice genotype effect. The exterior bulk soil, rhizosphere and rhizoplane communities are govrned by variable selection. In contrast, the internal endosphere counterparts are shapped by homogenizing selection, which are undiscernible between the two rice genotypes. After ruling out planting location effect, we screened 12 rice genotype-discriminatory orders that contributed an overall 97.22 % accuracy in diagnosing rice genotype. Hybrid rice is inferior to Japonica rice in carbon and nitrogen fixation, nitrogen and phosphorus biomineralization from organic sources. Collectively, we proposed a conceptual model to infer rice genotype effect on the rhizosphere microbiomes, and the subsequent requirement of external fertilizer for sustaining yield. Our findings deepen our understanding of the complex rice genotype–root microbiomes–fertilizer interactions from the prespective of microbially-mediated nutrient cycles. • Endosphere microbes is acquired by two-step selection and amplification-selection processes. • Homogeneous selection governs interior endosphere bacterial assembly, variable selection shapes exterior compartments. • Rice genotype-discriminatory orders contribute 97.2 % accuracy for diagnosing genotype. • Hybrid rice is inferior to Japonica rice in the acquisition of bioavailable nutrients from organic sources. • A conceptual model among rice genotype, rhizosphere microbiome and yield is proposed. [ABSTRACT FROM AUTHOR]

"Late spring coldness" (T) is a frequent meteorological disaster in the spring in southern China, often causing severe yield losses of direct-seeded early rice. In this study, we investigated the mechanisms underlying the differences in the compensatory growth ability of different rice genotypes by focusing on agronomic traits, physiological indicators, and transcriptome. The results showed that there were significant differences in the compensatory growth recovery ability of different genotypes after a combination of four days of low temperature and weak light stress. Only the strong compensatory growth genotype B116 was able to grow rapidly and reduce soluble protein and H2O2 concentrations rapidly after stress. By analyzing enzyme activity as well as endogenous hormone concentration, we found that the high superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and high levels of abscisic acid (ABA) could reduce the damage of B116 during stress. Meanwhile, higher glutamine synthetase (GS) and nitrate reductase (NR) activity and higher levels of gibberellin A3(GA3), indoleacetic acid (IAA), and zeatin nucleoside (ZR) could enable B116 to grow rapidly after stress. The identified differentially expressed genes (DEGs) indicated that there were large differences in POD-related genes and gibberellin metabolism between B116 and B144 after stress; RT-PCR quantification also showed a trend consistent with RNA-seq, which may be an important reason for the differences in compensatory growth ability. [ABSTRACT FROM AUTHOR]

To mitigate the impact of extreme weather incidents, rice cultivars Way Seputih (WS) and Way Apo Buru (WAB) were evaluated under simulation of continuous wind and rainfall treatments. The research was conducted from July to October 2017 at Leuwikopo Experimental Farm, Bogor, Indonesia. For 15 days at day time, flowering rice hills were treated with about 100 mm/h water shower (Experiment-1), and with 0, 10-15, 20-25 and 35-40 km/h wind velocity (Experiment-2). Results showed that wind and rainfall treatments reduced rice production; the effect depended on the genotypes and flowering stage. Rain treatment from panicle emergence to 50%-emerged increased the number of unfilled grains by 154.6-182.3% and 55.7-101.9% in WS and WAB cultivars, respectively. Rain treatment at 100%-emerged had no effect on WS, but it increased unfilled grain (163.5%) and decreased grain index (12.9%) in the WAB cultivar. Wind speed at 35-40 km/h promoted a high percentage of grain drop (25.7%) and unfilled grains (77.3%), and low grain index (20.8 g) in WS genotype. WAB was more tolerant of wind stress than the WS. The present experiment showed that genotype had different responses to wind and rain treatments implying different mitigation strategies should be applied through genotype selection. [ABSTRACT FROM AUTHOR]

Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus , indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production. [ABSTRACT FROM AUTHOR]

“Late spring coldness” (T) is a frequent meteorological disaster in the spring in southern China, often causing severe yield losses of direct-seeded early rice. In this study, we investigated the mechanisms underlying the differences in the compensatory growth ability of different rice genotypes by focusing on agronomic traits, physiological indicators, and transcriptome. The results showed that there were significant differences in the compensatory growth recovery ability of different genotypes after a combination of four days of low temperature and weak light stress. Only the strong compensatory growth genotype B116 was able to grow rapidly and reduce soluble protein and H2O2 concentrations rapidly after stress. By analyzing enzyme activity as well as endogenous hormone concentration, we found that the high superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and high levels of abscisic acid (ABA) could reduce the damage of B116 during stress. Meanwhile, higher glutamine synthetase (GS) and nitrate reductase (NR) activity and higher levels of gibberellin A3(GA3), indoleacetic acid (IAA), and zeatin nucleoside (ZR) could enable B116 to grow rapidly after stress. The identified differentially expressed genes (DEGs) indicated that there were large differences in POD-related genes and gibberellin metabolism between B116 and B144 after stress; RT-PCR quantification also showed a trend consistent with RNA-seq, which may be an important reason for the differences in compensatory growth ability.

Plant responses to nitrogen (N) and phosphorus (P) deficiencies differ among genotypes. Although the rhizosphere microbiome can serve as an indicator of plant functional traits across different genotypes, whether and how genotypic differences in plant tolerance to N and P deficiencies are associated with the rhizosphere microbiome are unknown. In this study, we carried out a paddy field experiment using five previously screened rice (Oryza sativa L.) varieties and examined crop yield and mineral element concentrations as well as the chemical properties and bacterial community of bulk and rhizosphere soils in response to N and P deficiencies. The three high-yield rice genotypes were found to be tolerant to N and P deficiencies, whereas the two low-yield genotypes were sensitive. Rhizosphere bacterial community compositions under different fertilization treatments were clearly separated into two groups corresponding to tolerant and sensitive rice. Eighteen bacterial keystone taxa were identified across the five rice genotypes under different N and P conditions. Tolerant rice harbored more bacterial keystone taxa in the rhizosphere under N or P deficiency than did sensitive rice. The specific bacterial keystone taxa recruited by tolerant rice were functionally associated with soil N transformation, plant-promoting activity, carbon decomposition, and iron cycling. These results suggest that bacterial community selection in the rhizosphere is dependent on the tolerance of rice genotypes to N and P deficiencies. The findings help explain the intrinsic mechanism that potentially controls the yield gap of rice genotypes through rhizosphere-driven microbial functions under N/P-limited agroecosystem conditions. The identified bacterial keystone taxa, which are potentially useful bio-fertilizer inoculants for agricultural production and possible indicators of rice genotypes for breeding N- and P-efficient rice cultivars, may ultimately contribute to sustainable agricultural development, resulting in high crop yields while minimizing fertilizer input and environmental risks. • Fertilization has a greater effect than rice genotype on the bacterial community. • Bacterial community selection in the rhizosphere is rice-genotype dependent. • Rice tolerance to N/P deficiency drives separation of the bacterial community. • Compared with sensitive rice, tolerant rice harbors more bacterial keystone taxa. • Bacterial keystone taxa are associated with C/N transformation and Fe cycling. [ABSTRACT FROM AUTHOR]

Nitrification and denitrification are important processes in the biogeochemical cycle in agricultural soils and are influenced by plant genotype and nitrogen (N) fertilization. However, few studies have evaluated the effects of genotype on nitrification and denitrification in the rhizosphere of rice cultivated in mudflats and their response to N fertilization. In this study, we determined the net nitrification and denitrification rates, quantified the abundance of functional genes involved in nitrification and denitrification, and characterized bacterial communities in the rhizosphere of two rice varieties (japonica and hybrid rice) cultivated in mudflat soil with three N fertilization levels. Results showed that net nitrification rates were strongly influenced by genotype and was higher in the rhizosphere of hybrid rice than in that of japonica rice, which might be related to the N absorption strategy of rice, while net denitrification rates were mainly affected by N fertilization. Unlike hybrid rice, the net nitrification rate in the rhizosphere of japonica rice was strongly influenced by N fertilization and positively correlated to N fertilization levels. In contrast, the net denitrification rate of hybrid rice was strongly influenced by N fertilization and positively correlated to N fertilization levels, while N fertilization had no significant effect on the net denitrification rate of japonica rice. Ammonia-oxidizing bacteria were the main drivers of nitrification in the rhizosphere, and denitrification in the rhizosphere of hybrid rice was mainly driven by nar G-, nir S-, and nor B-type denitrifiers. Furthermore, differences in the assemblages of bacteria associated with the relative abundance of these functional genes provided insight into genotypic differences in nitrification and denitrification responses to N fertilization. Overall, this study provides insight into the underlying mechanisms of nitrification and denitrification influenced by rice genotypes and N fertilization in the rhizospheres of japonica and hybrid rice. [ABSTRACT FROM AUTHOR]