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Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop‐weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide‐resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping‐by‐sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy‐related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS‐inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus‐indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus‐like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments. [ABSTRACT FROM AUTHOR]

The aim of this study was to find out how neem leaf extract affected the immune systems of Tilapia (O. niloticus) that had A. hydrophila in their bodies. This included looking at its phytochemistry, antibacterial properties, bioactive compounds, and ability to make the immune system stronger. The extraction uses methanol. The phytochemical test of neem leaf extract includes flavonoids, alkaloids, tannins, saponins, and triterpenoids. We obtained the isolate A. hydrophila from the Jepara Brackish Water Aquaculture. Before use, we store these bacteria in Trypticase Soy Agar (TSA) media at 4 oC and Trypticase Soy Broth (TSB) subcultures. re use. Test antibacterial using published We confirmed flavonoids, tannins, saponins, and triterpenoids through phytochemical tests. firmed. The test against A. hydrophila bacteria found that 100% of the extract was the most effective concentration at stopping the growth of A. hydrophila bacteria. After feeding A. hydrophilla bacteria to Tilapia (O. niloticus), the extract of neem leaf (A. indica) significantly boosted the immune system. bserved. [ABSTRACT FROM AUTHOR]

The aim of this study was to find out how neem leaf extract affected the immune systems of Tilapia (O. niloticus) that had A. hydrophila in their bodies. This included looking at its phytochemistry, antibacterial properties, bioactive compounds, and ability to make the immune system stronger. The extraction uses methanol. The phytochemical test of neem leaf extract includes flavonoids, alkaloids, tannins, saponins, and triterpenoids. We obtained the isolate A. hydrophila from the Jepara Brackish Water Aquaculture. Before use, we store these bacteria in Trypticase Soy Agar (TSA) media at 4 oC and Trypticase Soy Broth (TSB) subcultures. re use. Test antibacterial using published We confirmed flavonoids, tannins, saponins, and triterpenoids through phytochemical tests. firmed. The test against A. hydrophila bacteria found that 100% of the extract was the most effective concentration at stopping the growth of A. hydrophila bacteria. After feeding A. hydrophilla bacteria to Tilapia (O. niloticus), the extract of neem leaf (A. indica) significantly boosted the immune system. bserved.

Introduction: The panicle fertilization strategy for japonica and indica rice under wheat straw return (SR) has not been updated, especially on the elaboration of their impacts on spikelet differentiation and degeneration. This study aimed to verify the hypothesis that SR increases spikelet number by reducing spikelet degeneration and to explore the possibility of simplifying panicle fertilization. Methods: In three consecutive years, four varieties of japonica and indica rice were field-grown in Yangzhou, Jiangsu Province, China. Six panicle fertilization rates and split treatments were applied to SR and no straw return (NR) conditions. Results: The results showed that SR promoted rice yield significantly by 3.77%, and the highest yields were obtained under the T2 (split panicle fertilization at the panicle initiation (PI) and spikelet primordium differentiation (SPD) stages) and T1 (panicle fertilization only at the PI stage) treatments, for indica and japonica rice, respectively. Correlation and path analysis revealed that the number of spikelets per panicle was the most attributable to yield variation. SR significantly increased the concentration of alkali hydrolyzable N in the soil 40 days after rice transplantation, significantly increased the nitrogen accumulation per stem (NA) during the SPD-pollen mother cell meiosis (PMC) stage, and increased the brassinosteroids level in the young panicles at the PMC stage. SR also reduced the degeneration rate of spikelets (DRS) and increased the number of surviving spikelets (NSS). The dry matter accumulation per stem was more important to increasing the NA in japonica rice at the PMC stage, whereas NA was more affected by the N content than the dry matter accumulation in indica rice. In japonica rice, panicle N application once only at the PI stage combined with the N released from SR was enough to improve the plant N content, reduce the DRS, and increase the NSS. For indica rice, split application of N panicle fertilization at both the PI and SPD stages was still necessary to achieve a maximum NSS. Discussion: In conclusion, under wheat SR practice, panicle fertilization could be simplified to once in japonica rice with a significant yield increase, whereas equal splits might still be optimal for indica rice. [ABSTRACT FROM AUTHOR]

Background: The microspores of five tropical japonica and five indica rice genotypes were subjected to androgenic studies. The effect of growth regulators on callus induction were studied to improve the anther culture efficiency. Methods: The cold pre-treatment of panicles at 10℃ were done at different days of intervals viz., 5, 8, 10 and 12 days. The microspores at uninucleate stage were selected and dusted after pre-treatment. The anthers were cultured in N6 basal media supplemented with casein hydrolysate (250 mg/L), proline (250 mg/L), silver nitrate (100 mg/L), maltose (50 g/L) and growth regulators. Result: The 8 days of cold pre-treatment initiated calli in most of the ten genotypes. The days taken for callus induction varied with genotype from 32-55 days. The callus induction frequency ranged from 1.41 to 5.12%. The responsive genotypes (Azucena, Palawan, Nira) on callus induction were studied for their regeneration potential. [ABSTRACT FROM AUTHOR]

BackgroundThe circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group's evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties.ResultsWe generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica-the rice group most closely related to circum-basmati-as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan.ConclusionThe availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.

The photosynthetic capacity of flag leaf plays a key role in grain yield in rice. Nevertheless, there are few studies on the heterosis of the rice flag leaf. Therefore, this study focuses on investigating the genetic basis of heterosis for flag leaf in the indica super hybrid rice combination WFYT025 in China using a high-throughput next-generation RNA-seq strategy. We analyzed the gene expression of flag leaf in different environments and different time periods between WFYT025 and its female parent. After obtaining the gene expression profile of the flag leaf, we further investigated the gene regulatory network. Weighted gene expression network analysis (WGCNA) was used to identify the co-expressed gene sets, and a total of 5000 highly expressed genes were divided into 24 co-expression groups. In CHT025, we found 13 WRKY family transcription factors in SDGhps under the environment of early rice and 16 WRKY family genes in SDGhps of under the environment of middle rice. We found nine identical transcription factors in the two stages. Except for five reported TFs, the other four TFs might play an important role in heterosis for grain number and photosynthesis. Transcription factors such as WRKY3, WRKY68, and WRKY77 were found in both environments. To eliminate the influence of the environment, we examined the metabolic pathway with the same SDGhp (SSDGhp) in two environments. There were 312 SSDGhps in total. These SSDGhps mainly focused on the phosphorus metallic process, phosphorylation, plasma membrane, etc. These results provide resources for studying heterosis during super hybrid rice flag leaf development. [ABSTRACT FROM AUTHOR]

Rice is generally considered a high-glycemic index (GI) food, but numerous studies show that parboiling reduces the GI. There are no studies on GI of Indica and Japonica subspecies parboiled rice grown in Italy. The aim of this study was (1) to evaluate GI in different varieties of parboiled rice (ribe, white and brown long B, basmati, black, red, roma, and arborio); (2) to evaluate GI of same variety of rice subjected to different rice parboiling processes (parboiled ribe and parboiled long B with two different methods: flora and conventional method); (3) to evaluate GI of two by-products of parboiled rice: white and brown rice cake. Participants were 10 healthy individuals (20–30 years old, body mass index 18.5–25 kg/m2). Proximate composition and GI were determined by using standard methods. All parboiled rice assessed is low-GI (brown long B 48.1 ± 6.4 by flora method, ribe 52.0 ± 1.8 GI by flora method, black rice 52.3 ± 7.6 by flora method, long B 52.4 ± 3.9 by flora method, long B 53.4 ± 5.1 by conventional method, ribe 54.4 ± 4.3 GI by conventional method, Roma 54.4 ± 7.9 GI by flora method, and arborio 54.4 ± 7.9 GI by flora method), except red rice that is of medium-GI (56.1 ± 7.0 GI), and both classic and brown cakes that are high-GI (respectively, 83.3 ± 8.9 GI and 102.2 ± 5.5 GI). Parboiled rice is low-GI and so is favorable for the dietary management of metabolic disorders and celiac disease. Clinicaltrials.gov (NCT05333081). [ABSTRACT FROM AUTHOR]

Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars. [ABSTRACT FROM AUTHOR]

Anther culture is an efficient biotechnological tool in modern plant breeding programs to produce new varieties and parental lines in hybrid seed productions. However, some bottlenecks—low induction rate, genotype dependency, albinism—restrict the widespread utilization of in vitro anther culture in rice breeding, especially in Oryza sativa ssp. indica (indica) genotypes, while an improved efficient protocol can shorten the process of breeding. Three different induction media (N6NDK, N6NDZ, Ali-1) and four plant regeneration media (mMSNBK1, MSNBK3, MSNBKZ1, MSNBKZ2) were tested with five indica rice genotypes to increase the efficiency of in vitro androgenesis (number of calli and regenerated green plantlets). The production of calli was more efficient on the N6NDK medium with an average 88.26 calli/100 anthers and N6NDZ medium with an average of 103.88 calli/100 anthers as compared to Ali-1 with an average of 6.96 calli/100 anthers. The production of green plantlets was greater when calli was produced on N6NDK medium (2.15 green plantlets/100 anthers) compared when produced on to N6NDZ medium (1.18 green plantlets/100 anthers). Highest green plantlets production (4.7 green plantlets/100 anthers) was achieved when mMSNBK1 plant regeneration medium was used on calli produced utilizing N6NDK induction medium. In the best overall treatment (N6NDK induction medium and mMSNBK1 plant regeneration medium), four tested genotypes produced green plantlets. However, the genotype influenced the efficiency, and the green plantlets production ranged from 0.4 green plantlets/100 anthers to 8.4 green plantlets/100 anthers. The ploidy level of 106 acclimatized indica rice plantlets were characterized with flow cytometric analyses to calculate the percentage of spontaneous chromosome doubling. Altogether, 48 haploid-, 55 diploid-, 2 tetraploid- and 1 mixoploid plantlets were identified among the regenerant plantlets, and the spontaneous chromosome doubling percentage was 51.89%. Utilization of DH plants have been integrated as a routine method in the Hungarian rice breeding program. The tetraploid lines can be explored for their potential to offer new scopes for rice research and breeding directions in the future. [ABSTRACT FROM AUTHOR]

Arsenic (As) is a worldwide concern because of its toxic effects on crop yield and prevalence in the food chain. Rice is consumed by half of the world's population and is known to accumulate As. The present study reviews the available literatures on As accumulation in different subspecies of rice grains (indica, japonica and aromatic) and performs meta-analyses for grain size and texture; these data include 120 studies conducted over the last 15 years across different parts of the world. Aromatic rice varieties accumulate less As with its 95% confidence interval (CI) being 73.90 – 80.94 μg kg-1 which is significantly lower than the As accumulation by either indica or japonica rice varieties with their overall 95% CI being 135.48 – 147.78 μg kg-1 and 204.71 – 212.25 μg kg-1, respectively. Japonica rice varieties accumulate higher As than indica rice grains and within each subspecies polished and/or shorter rice grains accumulated significantly lower As compared to larger and/or unpolished grains; 95% CIs for the polished indica and japonica rice varieties are seen to be 96.33 – 111.11 μg kg-1 and 203.34 – 211.09 μg kg-1, respectively, whereas the same for unpolished varieties are seen to be 215.99 – 238.18 μg kg-1 and 215.27 – 248.63 μg kg-1, respectively. This shows that rice-based As bioaccumulation in humans could be lowered by increased use of aromatic or polished indica rice varieties, followed by the cultivation of shorter polished grains of japonica rice. These findings will be important to inform policy on rice cultivation and dietary uptake of As for a large portion of the global population. [ABSTRACT FROM AUTHOR]

Abstract Background Many rice transformation protocols have been reported, but optimization is still required to ensure efficient transformation of specific rice accessions. The modified rice transformation protocol presented here builds upon the original protunocol: ‘An improved protocol for efficient transformation and regeneration of diverse Indica rice cultivars’ volume 7, Article number: 49 (2011), Plant Methods. Results Following the aforementioned transformation protocol, calli browning occurred and no Agrobacterium-mediated transformation could be achieved, but this could be remedied by increasing the concentration of l-Proline. Improved callus health lead to successful transformation and proliferation of calli on selection media, but a low frequency of plantlet regeneration occurred when calli were transferred to regeneration media. The efficiency of plantlet regeneration was greatly improved by removing antibiotics from regeneration media, with the presence of escapes selected against during subsequent transfer of plantlets to antibiotic containing rooting media. Transformation of CO39 callus was found to be possible 8 days after callus induction resulting in a time saving of 10 days compared to the original protocol. Conclusions This optimized transformation protocol allows for the generation and survival of healthy CO39 calli, efficient transformation of calli using Agrobacterium, and produces a high frequency of regenerated transgenic plants. These protocol modifications will be useful for optimizing the transformation and regeneration of other recalcitrant Indica rice cultivars, particularly those sensitive to antibiotics during plantlet regeneration.

Among the commercial cannabis varieties, some are high yielders but characterized by a relatively poor root system. Roots absorb water and minerals from the soil, enabling vegetative development that directly affects yield, as vigorous plants have more resources to support reproduction. Moreover, healthy foliage is a primary key to high assimilation rates, leading to better production of photosynthetic products, including cannabinoids and terpenes, which are the main active components of cannabis. We grafted a high-THC variety, named 'Freud Super-Ego' (FSE) onto three chemotypes of rootstocks: high-THC (T), high-CBD (C), and Balanced (B). All the rootstocks had significantly greater root biomass compared to FSE. All the grafting treatments significantly improved FSE's vegetative indices and yield. The best overall vegetative performance – height, stem circumference, number of mature leaves - was that of plants grafted onto the Balanced and high-CBD rootstocks, resulting in high yields as well. However, the greatest number of inflorescences was counted when FSE was grafted onto a high-THC rootstock. According to leaf mineral content analysis, the highest nitrogen and phosphorus levels were found in leaves of FSE grafted on the balanced rootstock. The cannabinoid content profile analysis revealed that all grafting treatments raised the THC level in FSE's inflorescences by 8–12 % in comparison to the non-grafted control, and the THC rootstock led to the highest THC level. The results indicate the importance of grafting in cannabis as a tool to increase the productivity and quality of the product. • Grafting has a high potential in cannabis propagation. • All rootstock chemotypes had significantly positive impacts on the scion. • Both vegetative and reproductive indices were positively affected. • Cannabinoid levels were significantly raised. • The scion's biochemical category was not changed. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is a primary food that is widely consumed throughout the world, especially in Asian countries. The two main subspecies of rice are japonica and indica which are different in physical characteristics. In general, both indica and japonica rice consist of three types of grain colors, namely white, red, and black. Furthermore, rice and rice by-products contain secondary metabolites such as phenolic compounds, flavonoids, and tocopherols that have bioactivities such as antioxidants, antimicrobial, cancer chemopreventive, antidiabetic, and hypolipidemic agents. The existence of health benefits in rice bran, especially as antioxidants, gives rice bran the opportunity to be used as a functional food. Most of the bioactive compounds in plants are found in bound form with cell wall components such as cellulose and lignin. The process of releasing bonds between bioactive components and cell wall components in rice bran can increase the antioxidant capacity. Fermentation and treatment with enzymes were able to increase the total phenolic content, total flavonoids, tocotrienols, tocopherols, and γ-oryzanol in rice bran. [ABSTRACT FROM AUTHOR]

Abstract Background Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established. Results In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism. Conclusions Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.

The photosynthetic capacity of flag leaf plays a key role in grain yield in rice. Nevertheless, there are few studies on the heterosis of the rice flag leaf. Therefore, this study focuses on investigating the genetic basis of heterosis for flag leaf in the indica super hybrid rice combination WFYT025 in China using a high-throughput next-generation RNA-seq strategy. We analyzed the gene expression of flag leaf in different environments and different time periods between WFYT025 and its female parent. After obtaining the gene expression profile of the flag leaf, we further investigated the gene regulatory network. Weighted gene expression network analysis (WGCNA) was used to identify the co-expressed gene sets, and a total of 5000 highly expressed genes were divided into 24 co-expression groups. In CHT025, we found 13 WRKY family transcription factors in SDGhps under the environment of early rice and 16 WRKY family genes in SDGhps of under the environment of middle rice. We found nine identical transcription factors in the two stages. Except for five reported TFs, the other four TFs might play an important role in heterosis for grain number and photosynthesis. Transcription factors such as WRKY3, WRKY68, and WRKY77 were found in both environments. To eliminate the influence of the environment, we examined the metabolic pathway with the same SDGhp (SSDGhp) in two environments. There were 312 SSDGhps in total. These SSDGhps mainly focused on the phosphorus metallic process, phosphorylation, plasma membrane, etc. These results provide resources for studying heterosis during super hybrid rice flag leaf development.

Background: Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes. Methods and results: This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169 bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types. Conclusion: The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties. [ABSTRACT FROM AUTHOR]

Abstract Background Cannabis use is growing domestically due to recent legalization in many jurisdictions. There are two main species of cannabis, Cannabis sativa and Cannabis indica, and thousands of different commercially available cannabis strains. Although there are multiple reports of cannabis allergy in the literature, to our knowledge, there is no prior published report of selective cannabis strain allergy. Case presentation A 31-year-old male was referred for allergy assessment due to several episodes of localized pruritus and erythema after direct contact with various strains of cannabis. He had noted that the severity of his reaction appeared to be strain dependent. He developed a severe local reaction involving bilateral periorbital edema shortly after coming into direct contact with one particular strain of cannabis. He denied any adverse symptoms after inhalation of cannabis. Fresh skin prick testing was performed to various strains of cannabis and had positive testing to the three of the five tested strains. Conclusions We believe this is the first reported case of selective cannabis strain allergy based on patient history and skin prick testing. This case report outlines the variability in different strains of cannabis and stresses the importance of further research into cannabis allergen identification. Multiple cannabis allergens should be included and incorporated into commercial extracts when they become routinely available.

Anther culture is an efficient biotechnological tool in modern plant breeding programs to produce new varieties and parental lines in hybrid seed productions. However, some bottlenecks—low induction rate, genotype dependency, albinism—restrict the widespread utilization of in vitro anther culture in rice breeding, especially in Oryza sativa ssp. indica (indica) genotypes, while an improved efficient protocol can shorten the process of breeding. Three different induction media (N6NDK, N6NDZ, Ali-1) and four plant regeneration media (mMSNBK1, MSNBK3, MSNBKZ1, MSNBKZ2) were tested with five indica rice genotypes to increase the efficiency of in vitro androgenesis (number of calli and regenerated green plantlets). The production of calli was more efficient on the N6NDK medium with an average 88.26 calli/100 anthers and N6NDZ medium with an average of 103.88 calli/100 anthers as compared to Ali-1 with an average of 6.96 calli/100 anthers. The production of green plantlets was greater when calli was produced on N6NDK medium (2.15 green plantlets/100 anthers) compared when produced on to N6NDZ medium (1.18 green plantlets/100 anthers). Highest green plantlets production (4.7 green plantlets/100 anthers) was achieved when mMSNBK1 plant regeneration medium was used on calli produced utilizing N6NDK induction medium. In the best overall treatment (N6NDK induction medium and mMSNBK1 plant regeneration medium), four tested genotypes produced green plantlets. However, the genotype influenced the efficiency, and the green plantlets production ranged from 0.4 green plantlets/100 anthers to 8.4 green plantlets/100 anthers. The ploidy level of 106 acclimatized indica rice plantlets were characterized with flow cytometric analyses to calculate the percentage of spontaneous chromosome doubling. Altogether, 48 haploid-, 55 diploid-, 2 tetraploid- and 1 mixoploid plantlets were identified among the regenerant plantlets, and the spontaneous chromosome doubling percentage was 51.89%. Utilization of DH plants have been integrated as a routine method in the Hungarian rice breeding program. The tetraploid lines can be explored for their potential to offer new scopes for rice research and breeding directions in the future.

The effect of salinity on rice (Oryza sativa L.) cropping systems has been extensively studied in controlled experiments, but little is known about the performance of rice varieties to salt stress under field conditions. The study's purpose was to examine the effect of salinity on agronomic, physiological, and grain quality traits of indica and japonica rice varieties with different sensitivity to salt stress in a three-year (2010–2012) field study under Mediterranean conditions. Treatments consisted of two salinity levels, i.e., high salinity level (HSL, EC between 3.8 to 6.4 dS m-1) and low salinity level (LSL, EC between 0.9 and 1.3 dS m-1), and eight rice varieties arranged in a randomized complete block design in a split-plot arrangement. Rice growth showed an inconsistent response across varieties and years, demonstrating the importance of genotype and environment on rice response to salinity. The detrimental effect of salinity to rice growth was more evident when the weather conditions were favourable for rice production and salt stress was the main limiting factor for plant growth. Averaged across varieties, HSL prolonged the time to heading by 7 to 14 days compared to the LSL treatment. A considerable decrease of dry matter accumulation was observed in salt-sensitive varieties. In addition, salinity stress reduced the number of fertile tillers per plant up to 27% and the grain yield up to 50%. The contribution of pre-anthsesis assimilates to grain yield was increased due to salinity in two of the three years of the experimentation. In tolerant varieties, no differences among salinity levels in grain weight were observed. Salinity had less effect on grain quality. Grain length was similar across salinity treatments, while there was no consistent correlation between salinity level and grain vitreosity. Findings provide suggestive salinity tolerance traits of the studied rice varieties under field conditions that could be exploited for optimizing the performance of rice cropping systems in saline soils.

Background: Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established. Results: In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism. Conclusions: Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions. [ABSTRACT FROM AUTHOR]

The objective of this study was to preliminarily analyze the differences in pathogenicity and physiologic races between Pyricularia oryzae isolates from indica and japonica rice varieties. Five to 7 isolates of P. oryzae from indica and japonica, having good sporulation capacity, were screened out in each experimental year. To determine the pathogenicity of P. oryzae, different kinds of rice varieties were inoculated with mixtures of indica and japonica isolates. A total of 46 isolates, including 23 indica isolates and 23 japonica isolates, were screened out in four years. In total, 1252 rice varieties, including 490 indica, 296 japonica and 466 indica-japonica hybrid rice varieties, were inoculated. Our results suggested that the degree of disease was more severe in most indica varieties infected with indica isolates than in those infected with japonica isolates. That is, indica isolates were more inclined to infect indica varieties. A majority of japonica and indica-japonica hybrid rice varieties infected with japonica isolates showed more severe infection than those infected with indica isolates. In other words, japonica isolates more easily infected japonica and indica-japonica hybrid rice varieties. The differences in quantity among the varieties indicated high resistance to rice blast in the corresponding kinds of rice inoculated with indica and japonica isolates, fully explaining the above viewpoint. Most of the 23 indica isolates belonged to indica races. Among the 23 japonica isolates, half were indica races and half were japonica races. In addition, there were significant differences between the isolates selected in the first two years and those selected in the second two years. The isolates in the first two years were all of indica races, and those of japonica races all appeared in the second two years. The results showed that the race of isolates shared little association with the kind of rice variety collected but was associated with the year of neck blast sample collection. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is a primary food that is widely consumed throughout the world, especially in Asian countries. The two main subspecies of rice are japonica and indica which are different in physical characteristics. In general, both indica and japonica rice consist of three types of grain colors, namely white, red, and black. Furthermore, rice and rice by-products contain secondary metabolites such as phenolic compounds, flavonoids, and tocopherols that have bioactivities such as antioxidants, antimicrobial, cancer chemopreventive, antidiabetic, and hypolipidemic agents. The existence of health benefits in rice bran, especially as antioxidants, gives rice bran the opportunity to be used as a functional food. Most of the bioactive compounds in plants are found in bound form with cell wall components such as cellulose and lignin. The process of releasing bonds between bioactive components and cell wall components in rice bran can increase the antioxidant capacity. Fermentation and treatment with enzymes were able to increase the total phenolic content, total flavonoids, tocotrienols, tocopherols, and γ-oryzanol in rice bran.

Accurate classification tool for screening varieties with superior eating and cooking quality based on its pasting and starch structure properties is in demand to satisfy both consumers’ and farmers’ need. Here we showed the data related to the article entitled “Deploying viscosity and starch polymer properties to predict cooking and eating quality models: a novel breeding tool to predict texture” [1] which provides solution to this problem. The paper compiles all the pasting, starch structure, sensory and routine quality data of the rice sample used in the article into graphical form. It also shows how the data were processed and obtained.

Abstract Background The domestication process of Asian rice (Oryza sativa L.) is complicated. It’s well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice. Results A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima’s D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice. Conclusions Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.

Abstract Background While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. Results Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. Conclusions This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.

Background: Cannabis use is growing domestically due to recent legalization in many jurisdictions. There are two main species of cannabis, Cannabis sativa and Cannabis indica, and thousands of different commercially available cannabis strains. Although there are multiple reports of cannabis allergy in the literature, to our knowledge, there is no prior published report of selective cannabis strain allergy. Case presentation: A 31-year-old male was referred for allergy assessment due to several episodes of localized pruritus and erythema after direct contact with various strains of cannabis. He had noted that the severity of his reaction appeared to be strain dependent. He developed a severe local reaction involving bilateral periorbital edema shortly after coming into direct contact with one particular strain of cannabis. He denied any adverse symptoms after inhalation of cannabis. Fresh skin prick testing was performed to various strains of cannabis and had positive testing to the three of the five tested strains. Conclusions: We believe this is the first reported case of selective cannabis strain allergy based on patient history and skin prick testing. This case report outlines the variability in different strains of cannabis and stresses the importance of further research into cannabis allergen identification. Multiple cannabis allergens should be included and incorporated into commercial extracts when they become routinely available. [ABSTRACT FROM AUTHOR]

Rice straw has an enormous amount of biomass for energy use, but the complexity of the cell wall component hinders technical processes. Although belonging to rice straws, the straws from different varieties should be with different treatment strategies to obtain best energy efficiency. To confirm this hypothesis, 7 different rice varieties (RPY GENG, RIL269, RIL272, RIL31, RIL57, RIL06, LUOHUI 9) with different cell wall traits from RIL population were evaluated for their response toward different pretreatments. For japonica RPY GENG, 2% of H2SO4 acid was best pre-treatment while high acid (5% of H2SO4) pretreatment caused undue loss. For Indica LUOHUI 9 rice, high acid pretreatment was suitable, while RIL57 had maximum of glucose yield with high alkali (10% NaOH) pretreatment. High-concentration alkali pretreatment is the most convenient and effective pretreatment method for the treatment of unknown varieties of rice straws, because the lignin has been removed and has the lowest negative effects on the glucose yield under the high alkali condition. As the RILs used in this study vary considerably in their wall structure, an understanding of their response to different pre-treatments confirms our hypothesis and help us to understand the influence of different wall compositions on the final output.

Moderate soil drying (MD) imposed at the post-anthesis stage significantly improves carbon reserve remobilization in rice stems, increasing grain yield. However, the methylome and transcriptome profiles of carbon reserve remobilization under MD are obscure in indica and japonica rice stems. Here, we generated whole-genome single-base resolution maps of the DNA methylome in indica and japonica rice stems. DNA methylation levels were higher in indica than in japonica and positively correlated with genome size. MD treatment had a weak impact on the changes in methylation levels in indica. Moreover, the number of differentially methylated regions was much lower in indica , indica ting the existence of cultivar-specific methylation patterns in response to MD during grain filling. The gene encoding β-glucosidase 1, involved in the starch degradation process, was hypomethylated and up-regulated in indica , resulting in improved starch to sucrose conversion under MD treatment. Additionally, increased expression of MYBS1 transactivated the expression of AMYC2/OsAMY2A in both indica and japonica , leading to enhanced starch degradation under MD. In contrast, down-regulated expression of MYB30 resulted in increased expression of BMY5 in both cultivars. Our findings decode the dynamics of DNA methylation in indica and japonica rice stems and propose candidate genes for improving carbon reserve remobilization. [ABSTRACT FROM AUTHOR]

Eighty one rice genotypes were studied using 30 SSR markers and data obtained were analyzed using STRUCTURE software which classified the population into two sub groups or subpopulations, designated as subpopulation 1 and 2. Subpopulation 1 mostly comprised of 60 germplasms majority of which are Indica in origin, whereas subpopulation 2 mostly comprised of tropical and temperate Japonica subspecies. Cluster analysis was performed using UPGMA and Dendrogram was constructed which consisted of 4 clusters comprising of Indica accessions in majority and 3 clusters of tropical and temperate Japonica subspecies, thereby suggesting large diversity in the population. [ABSTRACT FROM AUTHOR]

There is a growing interest in the production of hemp for the extraction of cannabidiol (CBD) due to reported therapeutic benefits. Recent policy reform has permitted state hemp pilot programs, including the land grant research institutions, the ability to investigate the potential of growing and harvesting Cannabis sativa plants (<0.3% tetrahydrocannabinol) for these purposes in the U.S. There are vast gaps of knowledge regarding the fertility requirements of hemp cultivars grown in a horticultural production setting for floral attributes such as the cannabinoid constituents. Foliar tissue analysis provides an avenue to determine adequate ranges for nutrient uptake and estimating fertilizer requirements prior to visual symptoms of deficiency or toxicity. To facilitate a survey range of elemental nutrient acquisition in hemp cultivars propagated for CBD production, foliar analysis was executed using the most recently mature leaves (MRML) of mother stock plants. All plants were maintained in the vegetative stage for twelve weeks, prior to initiation of cutting for clone harvesting. A total of thirteen cultivars were utilized to broaden previously reported baseline survey ranges. Significant differences were found among all thirteen cultivars in accumulation of both micro and macro essential nutrients, widening the range of the fertility requirements of Cannabis plants grown in this production model for CBD harvesting. [ABSTRACT FROM AUTHOR]

There are different appraisal criteria for the reference of rice varieties to the group of cultivars with high quality. In India, Bangladesh and the Philippines the people prefer the high amylose varieties which are boiled soft. The starch properties are the key factor for the nutritional and culinary qualities of the cooked rice, and the quantity of proteins and their amino acid composition affect its nutritional value. The starch in the grain kernels is the 6-carbon sugars, polymerized into the granules of starch endosperm. One part of spare starch in grains presents the direct chains of amylose; the other part is the amylopectin with the branched molecular structure. The starch of the gluten or waxy rice completely consists of the amylopectin. The groats of the varieties with high content of amylose (more than 25%) isn’t boiled soft and can be used for pilaf and other cuisines where it’s important to preserve the integrity of a kernel and its attractive appearance. In Russia we cultivated only low-amylose varieties with its content of 1519%, but the last time there is a necessity to develop domestic varieties with the amylose content more than 20% and the varieties with higher content of gluten. The samples of the sub type indica of foreign breeding have been involved in the hybridization as the donors of the trait. Despite the high content of bare kernels of the intersubspecific hybrids, the second generation of the hybrids produces the highly productive and more promising plants for further hybridization. The analysis of the breeding material showed the possibility to grow the varieties with the long and large kernels with the different rate of maturity. During the control trial and competitive variety testing we selected the samples with the content of amylose more than 20%.

The gene tms5 , which controls thermo-sensitive genic male sterility (TGMS), has been widely used in two-line hybrid rice breeding in China. The tms5 lines have two sources, namely, AnnongS-1 (AnS) and Zhu1S (ZhS) and, interestingly, are commonly subject to an alteration at cds.71. However, whether cds.71 acts as a mutation hotspot is unknown. Herein, another tms5 mutant named T98S (induced from T98B by irradiation) was used to explore this. First, the gene of tms(t) responsible for T98S was fine-mapped on chromosome 2 based on an F2 group of T98S/R893. In T98S, the candidate gene TMS5 (LOC_Os02g12290.1) mutated at cds.71 with a transversion from cytosine (C) to adenine (A), as also observed in AnS and ZhS. Moreover, the entire coding sequence of TMS5 from T98B converted T98S from sterile to fertile by Agrobacterium tumefaciens -mediated transformation, confirming that T98S is controlled by tms5. Next, detection on nearly 40,000 single nucleotide polymorphisms (SNPs) on Rice 56K SNP Array revealed T98S was 99.99% similar to T98B but only 72.84% and 77.47% similar to AnS and ZhS, respectively, demonstrating that T98S originated from T98B rather than from existing tms5 lines. Furthermore, the cds.70 was found to exist as a T/G haplotype, and it was T rather than G that helped to induce a TGMS trait. The T frequency was 67.52% in indica rice but decreased to 1.75% in japonica rice in 2,644 cultivars tested, which partly explains why tms5 mutants were mostly found in indica lines. Our findings provide evidence that cds.71 may act as a mutation hotspot and clues for breeding TGMS lines in a more efficient way. [ABSTRACT FROM AUTHOR]

The use of ὀνοµαζόµενα at Arr. Ind. 27.1 continues to puzzle scholars. This article uses the textual debate as a jumping-off point to explore Nearchus' presentation of naval guides and their role on Alexander's expedition, something which previous interpretations of the passage have not adequately considered. Through examination of all Nearchan fragments, I argue that providing local place names was a key aspect of a guide's role and significant for navigation. It is also suggested that the use of this verb may additionally refer to the Macedonians' practice of giving places new names or altering indigenous names; in this section, comparative material from New World conquest is brought to bear on the ancient evidence. In light of this analysis, I conclude that the manuscript reading of ὀνοµαζόµενα should be retained. [ABSTRACT FROM AUTHOR]

Summary: In agricultural soils, amino acids can represent vital nitrogen (N) sources for crop growth and yield. However, the molecular mechanisms underlying amino acid uptake and allocation are poorly understood in crop plants. This study shows that rice (Oryza sativa L.) roots can acquire aspartate at soil concentration, and that japonica subspecies take up this acidic amino acid 1.5‐fold more efficiently than indica subspecies. Genetic association analyses with 68 representative japonica or indica germplasms identified rice Lysine‐Histidine‐type Transporter 1 (OsLHT1) as a candidate gene associated with the aspartate uptake trait. When expressed in yeast, OsLHT1 supported cell growth on a broad spectrum of amino acids, and effectively transported aspartate, asparagine and glutamate. OsLHT1 is localized throughout the rice root, including root hairs, epidermis, cortex and stele, and to the leaf vasculature. Knockout of OsLHT1 in japonica resulted in reduced root uptake of amino acids. Furthermore, in 15N‐amino acid‐fed mutants versus wild‐type, a higher percentage of 15N remained in roots instead of being allocated to the shoot. 15N‐ammonium uptake and subsequently the delivery of root‐synthesized amino acids to Oslht1 shoots were also significantly decreased, which was accompanied by reduced shoot growth. These results together provide evidence that OsLHT1 functions in both root uptake and root to shoot allocation of a broad spectrum of amino acids in rice. Significance Statement: Amino acids can serve as important nitrogen sources in agricultural fields, but little is known about the underlying mechanisms of amino acid uptake and allocation in crops. This study conducted genetic association analyses of 15N‐aspartate uptake among rice accessions, combined with genetic and biochemical analyses, and revealed that Oryza sativa Lysine‐Histidine‐type Transporter 1 (OsLHT1) functions in both root uptake and root to shoot allocation of a broad spectrum of amino acids. [ABSTRACT FROM AUTHOR]

Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indica–japonica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4–5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice. [ABSTRACT FROM AUTHOR]

Gene editing by use of clustered regularly interspaced short palindromic repeats (CRISPR) has become a powerful tool for crop improvement. However, a common bottleneck in the application of this approach to grain crops, including rice (Oryza sativa), is efficient vector delivery and calli regeneration, which can be hampered by genotype-dependent requirements for plant regeneration. Here, methods for Agrobacterium-mediated and biolistic transformation and regeneration of indica rice were optimized using CRISPR-Cas9 gene-editing of the submergence tolerance regulator SUBMERGENCE 1A-1 gene of the cultivar Ciherang-Sub1. Callus induction and plantlet regeneration methods were optimized for embryogenic calli derived from immature embryos and mature seed-derived calli. Optimized regeneration (95%) and maximal editing efficiency (100%) were obtained from the immature embryo-derived calli. Phenotyping of T1 seeds derived from the edited T0 plants under submergence stress demonstrated inferior phenotype compared to their controls, which phenotypically validates the disruption of SUB1A-1 function. The methods pave the way for rapid CRISPR-Cas9 gene editing of recalcitrant indica rice cultivars.

the plant Opuntia ficus-indica against the toxicity of carbon tetrachloride (CCl4) in rat males. Seventy five rats were divided into five groups of 15 rats each. The first group was a negative control and the other 60 rats were given 1ml/kg.b.w. CCl4 once each 3 days for 12, 18 and 30 days. Then they This study was designed to investigate the protective effects of the water extract of were divided into four groups, the first group served as positive control (CCl4 only) while the second, third and fourth groups were given 0.25, 0.50 and 1ml/100 gm.b.w. of water extract of the plant daily, respectively. Results indicated that CCl4 caused a significant increase in the activity of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and lactate dehydrogenase (LDH). Furthermore, CCl4 caused a decrease in the concentration of glutathione (GSH) and an increase in the concentration of malondialdehyde (MDA) in the positive control group. As well the groups were treated with plant extract,showeda significant decrease in the levels of ALT, AST, ALP and LDH. Other results is significant increase in GSH and significant decrease in MDA concentration. It was concluded that water extract of the plant Opuntia ficus-indica ameliorated the toxic effects of CCl4. It is concluded from the present study that the Opuntia ficus-indica water extract has a protective effect on the liver also enhancing the antioxidant defense system and suppresses lipid peroxidation.

Abstract Background Asian cultivated rice (Oryza sativa L.), including japonica and indica, is unarguable the most important crop in Asia as well as worldwide. However, a decisive conclusion of its origination and domestication processes are still lacking. Nowadays, the ever-increasing high-throughput sequencing data of numerous rice samples have provided us new opportunities to get close to the answer of these questions. Results By compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice, two types of domesticated regions (DR-I and DR-II) with strong selective sweep signals between different groups were detected. DR-I regions included 28 blocks which significantly differentiated between japonica and indica subspecies, while DR-II regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice, each covered 890 kb and 640 kb, respectively. In-depth analysis suggested that both DR-Is and DR-IIs could have originated from Indo-China Peninsula to southern China, and DR-IIs might be introgressed from indica to japonica. Functional bias with significant positive selection has also been detected in the genes of DR-I, suggesting important role of the selective sweep in differentiation of japonica and indica. Conclusions This research promoted a new possible model of the origin of the cultivated rice that DR-Is in japonica and indica maybe independently originated from the divergent wild rice in the Indo-China Peninsula to southern China, and then followed by frequent introgression. Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.

In Oryza sativa, indica and japonica are pivotal subpopulations, and other subpopulations such as aus and aromatic are considered to be derived from indica or japonica. In this regard, Oryza sativa accessions are frequently viewed from the indica/japonica perspective. This study introduces a computational method for indica/japonica classification by applying phenotypic variables to the logistic regression model (LRM). The population used in this study included 413 Oryza sativa accessions, of which 280 accessions were indica or japonica. Out of 24 phenotypic variables, a set of seven phenotypic variables was identified to collectively generate the fully accurate indica/japonica separation power of the LRM. The resulting parameters were used to define the customized LRM. Given the 280 indica/japonica accessions, the classification accuracy of the customized LRM along with the set of seven phenotypic variables was estimated by 100 iterations of ten-fold cross-validations. As a result, the classification accuracy of 100% was achieved. This suggests that the LRM can be an effective tool to analyze the indica/japonica classification with phenotypic variables in Oryza sativa.

Introduction: The panicle fertilization strategy for japonica and indica rice under wheat straw return (SR) has not been updated, especially on the elaboration of their impacts on spikelet differentiation and degeneration. This study aimed to verify the hypothesis that SR increases spikelet number by reducing spikelet degeneration and to explore the possibility of simplifying panicle fertilization., Methods: In three consecutive years, four varieties of japonica and indica rice were field-grown in Yangzhou, Jiangsu Province, China. Six panicle fertilization rates and split treatments were applied to SR and no straw return (NR) conditions., Results: The results showed that SR promoted rice yield significantly by 3.77%, and the highest yields were obtained under the T2 (split panicle fertilization at the panicle initiation (PI) and spikelet primordium differentiation (SPD) stages) and T1 (panicle fertilization only at the PI stage) treatments, for indica and japonica rice, respectively. Correlation and path analysis revealed that the number of spikelets per panicle was the most attributable to yield variation. SR significantly increased the concentration of alkali hydrolyzable N in the soil 40 days after rice transplantation, significantly increased the nitrogen accumulation per stem (NA) during the SPD-pollen mother cell meiosis (PMC) stage, and increased the brassinosteroids level in the young panicles at the PMC stage. SR also reduced the degeneration rate of spikelets (DRS) and increased the number of surviving spikelets (NSS). The dry matter accumulation per stem was more important to increasing the NA in japonica rice at the PMC stage, whereas NA was more affected by the N content than the dry matter accumulation in indica rice. In japonica rice, panicle N application once only at the PI stage combined with the N released from SR was enough to improve the plant N content, reduce the DRS, and increase the NSS. For indica rice, split application of N panicle fertilization at both the PI and SPD stages was still necessary to achieve a maximum NSS., Discussion: In conclusion, under wheat SR practice, panicle fertilization could be simplified to once in japonica rice with a significant yield increase, whereas equal splits might still be optimal for indica rice., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Shu, Zhang, Wang, Fu, Ding, Yang, Wang, Zhao, Xu, Zhou, Ju, Huang, Yao, Wang and Dong.)