Modern Rice Varieties Research Articles

Salt-responsive miRNA-SSR markers from Dongxiang wild rice: characterization and potential application in exploring salt-tolerant genetic resources

Abstract MicroRNAs (miRNAs) play important roles in regulating salt tolerance in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). The development of salt-responsive miRNA-simple sequence repeat (SSR) markers will significantly bolster research on DXWR, providing novel tools for exploring salt-tolerant genetic resources and advancing the development of salt-tolerant rice varieties. In the present study, a total of 137 miRNA-SSR markers were successfully developed, specifically derived from miRNAs responsive to salt stress in DXWR. Subsequently, a subset of 20 markers was randomly selected for validation across three distinct DXWR populations, along with 35 modern rice varieties. Notably, 13 of these markers exhibited remarkable polymorphism. The polymorphic markers collectively amplified 52 SSR loci, averaging four alleles per locus. The polymorphism information content values associated with these loci spanned from 0.23 to 0.70, with a mean value of 0.49. Particularly noteworthy is the miR162a-SSR marker, which demonstrated distinct allelic patterns and holds potential as a diagnostic marker for discriminating the salt-tolerant rice varieties from the non-tolerant varieties. This study provides a valuable tool for genetic analysis and precision breeding, facilitating the identification and utilization of valuable salt-tolerant genetic resources.

Factors Influencing Farmers’ Behavior Towards Modern Rice Varieties in Bangladesh

Factors Influencing Farmers’ Behavior Towards Modern Rice Varieties in Bangladesh

The wall-associated kinase GWN1 controls grain weight and grain number in rice.

Grain size is a crucial agronomic trait that determines grain weight and final yield. Although several genes have been reported to regulate grain size in rice (Oryza sativa), the function of Wall-Associated Kinase family genes affecting grain size is still largely unknown. In this study, we identified GRAIN WEIGHT AND NUMBER 1 (GWN1) using map-based cloning. GWN1 encodes the OsWAK74 protein kinase, which is conserved in plants. GWN1 negatively regulates grain length and weight by regulating cell proliferation in spikelet hulls. We also found that GWN1 negatively influenced grain number by influencing secondary branch numbers and finally increased plant grain yield. The GWN1 gene was highly expressed in inflorescences and its encoded protein is located at the cell membrane and cell wall. Moreover, we identified three haplotypes of GWN1 in the germplasm. GWN1hap1 showing longer grain, has not been widely utilized in modern rice varieties. In summary, GWN1 played a very important role in regulating grain length, weight and number, thereby exhibiting application potential in molecular breeding for longer grain and higher yield.

Drought tolerance improvement for grain yield of a modern rice variety based on morphological and physiological response

Growth of rice (Oryza sativa L.) is severely affected by drought stress, which leads to decreased rice production in rainfed ecosystems worldwide. Particularly, modern rice varieties are more susceptible to drought stress rather than traditional rice varieties. In the present study, a modern short-term rice variety, ADT37, abundantly cultivated in the Cauvery delta region of the southern part of India, was improved for grain yield by introducing qDTY1.1 through the conventional backcross method. Positive F1 progenies were identified using RM431 linked with qDTY1.1 in PCR amplification. In phenotypic selection, rice progenies with suitable plant height to avoid linkage drag as well as high degree of drought tolerance to manage the drought stress were selected and advanced through the backcrossing process up to the BC3 generation. Finally, two near isogenic lines with equal plant height to the recurrent parent and high degree of drought tolerance were selected. A positive effect of qDTY1.1 on plant height and fertile seeds was revealed. In the future, the selected superior near isogenic lines would be useful to rice researchers and farmers facing unexpected water crises. Moreover, the morphological marker associated with the performance of crops according to the intensity of stress will support climate resilient agriculture.

Assessment of Nutrient Minerals and Potentially Toxic Elements in a Bangladesh-Origin Rice Cultivar (Oryza sativa cv. BR11) and Associated Health

Rice contributes significantly to both food security and livelihoods in Bangladesh. Despite challenges such as an immense population growth rate and decreased arable land since gaining independence, Bangladesh has attained self-sufficiency in rice production by adopting modern rice varieties (MRVs). However, not all introduced MRVs have gained widespread acceptance among farmers due to concerns about productivity and profitability. Notably, BR11, an MRV, stands out as a prominently adopted rice cultivar during the Aman rice-growing season. This study aims to assess the levels of essential nutrient minerals (Na, K, Ca and Mg) and potentially toxic elements (PTEs) (Cd, Cu, Pb, Ni, Co, Fe, Mn, Zn, Cr) in the BR11 rice cultivar and also to evaluate associated health risks. The concentrations of Na, K, Ca and Mg (mg 100 g–1) in the sampled BR11 rice cultivar were found to be 4.4 ± 2.4, 108.5 ± 24.9, 3.4 ± 0.4 and 4.5 ± 1.1, respectively. Among the PTEs, Cd, Pb, Ni, Co, or Cr contents were below the detection limit, while Fe, Mn, Zn and Cu contents (mg kg–1) were 12.0 ± 4.0, 9.2 ± 1.5, 18.7 ± 2.7 and 2.9 ± 1.0. Comparisons of PTE contents in BR11 rice cultivars exposed to industrial activities with those cultivated in non-industrial zones did not reveal any statistically significant variations (p < 0.05). The estimated daily intake of nutrient minerals through the consumption of BR11 rice was significantly below the daily recommended dietary reference intakes. Likewise, the accumulation of PTEs in the BR11 rice cultivar was well below the maximum allowable concentrations recommended by WHO or FAO. Health risk assessments, involving the computation of non-carcinogenic and carcinogenic risks, did not indicate any concerning risk scenarios associated with the consumption of the BR11 rice cultivar. The data suggests that BR11 is a safe MRV for daily consumption, affirming its suitability for inclusion in the daily diet.

Molecular Diversity Analysis of Some Selected Brri Developed Rice Varieties Using Ssr Markers

Molecular characterization of 26 modern rice varieties of Bangladesh was performed using 52 simple sequence repeat markers (SSRs) to estimate the genetic diversity and to reveal genetic relationships among rice cultivars. A total of 156 alleles were detected where the number of alleles per locus generated by each marker varied from 2 to 7, with an average of 3. The band size for a given microsatellite locus ranged from 79 to 278 bp. The polymorphism information content (PIC) for the SSR loci ranged from 0.08 to 0.79, with an average of 0.35. RM566 was the best marker for identification and variability assessment of varieties as revealed by PIC values. A UPGMA dendrogram generated using the NTSYS-pc revealed four clusters with a similarity coefficient of 0.55, whereas phylogenetic cluster analysis of the SSR data based on Nei-genetic distance divided the varieties into three groups. Two- and three-dimensional graphical views of principal coordinate analysis showed the spatial distribution of the varieties and revealed that BRRI dhan56, BRRI dhan51, BRRI dhan52, BRRI dhan61, BRRI dhan62 and BRRI dhan66 were found far away from the centroid of the cluster. The findings of this study are helpful for varietal identification, background selection during backcross breeding and for selecting the suitable genetically diverse parents for crossing programs. SAARC J. Agric., 21(2): 1-14 (2023)

Impact of Submergence1 (Sub1) Locus in Genetic Background of Modern Rice Varieties (Oryza sativa L.)

Aim: To improve submergence stress tolerance of modern rice varieties (ADT36 and ADT37) through selection of superior rice lines.
 Study Design: Backcross method.
 Place and Duration of Study: This effort was taken in Nethouse of Kandaswami Kandar’s College, Namakkal District, Tamil Nadu, India. This process was completed in four years from 2019 to 2022.
 Methodology: Here, widely cultivated two short-term rice varieties (ADT36 and ADT37) were selected to improve submergence tolerance based on polymorphism at phenotypic and genotypic level. Then, they were improved through backcrossing with respective recurrent parent by selection of superior rice lines compared to parental lines under submergence condition. Likewise, this process was advanced up to BC3F2 generation.
 Results: In this study, a number of two NILs for ADT36 rice variety (ADT36- F12-5-19.18 and ADT36- F15-2-5.17) and five NILs for ADT37 rice variety (ADT37- F113-27-5.2, ADT37- F113-27-5.5, ADT37- F115-2-1.10, ADT37- F115-2-1.14 and ADT37- F115-2-2.14) are selected as superior lines.Selected rice lines exhibited more than 60% submergence tolerance than donor parent. This result indicates the adaptation of Sub1 locus into new genetic background of ADT36 and ADT37 rice variety under submergence condition.
 Conclusion: Improvement process of rice lines under stress condition results in identification of highly active rice lines. Thus, selected submergence tolerant rice lines would be a boon to the rice farmers who are facing crop lose due to frequently occurring cyclones in the Cauvery delta region.

Identification of rice blast resistance genes Pi-1, Pi-2, Pi-33, Pi-40, Pi-ta, Pi-b

Rice is a valuable crop used for food throughout the world. To develop modern, productive and disease resistant rice varieties, it is necessary to accelerate the breeding process using molecular biology methods. The purpose of the current study was to identify alleles of six blast resistance genes (Pi-1, Pi-2, Pi-33, Pi-40, Pi-ta and Pi-b) in the selected rice samples using MAS (marker-associated selection method). The objects of the study were 446 breeding rice samples sent to the laboratory of cell breeding for analysis by breeders from the laboratory for rice breeding and seed production of the FSBSI «ARC «Donskoy». Identification of genes in them was carried out differentially and was determined by the pedigree of the samples. In order to determine the alleles of the blast resistance genes Pi-1, Pi-2 and Pi-33, all 446 samples were studied, for the Pi-40 gene there were studied 20 samples, for the Pi-ta gene there were studied 316 samples. For DNA extraction, there was used a Russian-made kit ‘DNA-Extran-3’. PCR was performed using specific primers of the target genes. Identification of reaction products was performed on agarosegels after photographing in ultraviolet light. As a result of the study, there were identified the rice samples which carried from 1 to 5 blast resistance genes in various combinations. There have been identified 14 samples that possess a set of 5 resistance genes, such as 2723, 2724, 2727, 2728, 2729, 2730, 2733, 2735, 2736, 5007, 5671, 5673, 5450/2 and 2450/2. The information obtained from the results of the study could then be used by breeders to use valuable genotypes as donors in crosses, as well as to select promising breeding material resistant to blast disease.

Functional traits of field-droughted contrasting rice genotypes reveal multiple independent genomic adaptations and metabolic responses

Drought is the most critical environmental stress limiting crop productivity and yield. Rice is one of the top leading food crops worldwide and modern rice varieties are notably drought-sensitive due to their high-water requirements. Generating drought-resilient varieties and fine-tuning their yield performance are time-consuming tasks that could be achieved by exploiting the genetic diversity expressed by the wild ancestors of current-day crop species. We conducted a large-scale field experiment, imposing pre-flowering and post-flowering water shortages on 20 Oryza genotypes. Using detailed agro-physiological, isotopomics, and metabolite characterization of different Asian and African rice accessions, we shed light on the evolutionary biases that have evolved into the spectrum of strategies used to adapt to drought and have added to the rice knowledge base. We find that relevant decreases in photosynthetic rates (linked with stomatal opening) that differed between genotypes. We also identified genotypic differences in core C and N metabolism, and central metabolic pathways, highlighting the possible mechanisms of drought tolerance. Additionally, data suggest strong genetic associations of several amino acids that are significantly enriched during drought. We provide strong evidence of the distinctiveness of agro-physiological and metabolic pathway behaviors to drought across the use of diverse germplasm resources. Also, the resulting data provide insight into the wide variety of germplasm responses triggered by drought.

Joint decision-making, technology adoption and food security: Evidence from rice varieties in eastern India

This study investigates the effect of married couples’ joint decision-making on rice variety selection on rice productivity—a measure of food security. The study uses the 2016 Rice Monitoring Survey and the endogenous switching regression (ESR) method. Results show that rice farms with joint decision-makers (husband and wife) would have higher yields, particularly in households that adopted MRVGen1 (before 1986) rice varieties. Thus, families with joint-decision making have higher food security. Intervention programs for food insecurity should acknowledge and incorporate information regarding the persons responsible for making rice varietal decisions and the characteristics of modern rice varieties to ensure food security.

EFFECT OF PLANTING DENSITY, SEEDLING NUMBERS, AND AGE AT TRANSPLANTING ON YIELD AND YIELD COMPONENTS OF LOCAL TRADITIONAL RICE VARIETY

Sarawak currently has the ability to establish itself as a producer of unique traditional rice that is designated with a geographical indicator (GI) due to its wide variety of traditional rice. The traditional rice varieties are diverse in grain shape, aroma, colour, texture and eating quality. However, because of traditional cultivars’ longer maturation and photoperiod-sensitive, Sarawak only grows rice once a year. Compared to modern rice varieties, it also needs a distinct approach to fertilization management. Therefore, to ensure that the rice plant receives the nutrients it requires and does not receive too much fertilizer, which would cause vigorous droopy leaves the rate and timing of fertilizer application are crucial. In addition to reducing the yield, this circumstance will also attract numerous pests and diseases and result in fertilizer waste. Results showed that for Mamut rice, the optimal age and number of seedlings are 30 days and 3 respectively, while for the plant spacing, 30 cm is recommended. Although no specific fertilization rates are carried out, existing subsidized fertilizers showed the best results for Mamut rice with yield recorded at 3.69 t/ha. However, the optimal rate for each element requires a more detailed study since the study was conducted in a controlled manner. Therefore, verification in the farmer’s field is recommended to confirm the findings of these studies.

Endangered indigenous rice varieties as a source of B vitamins for the undernourished population

AbstractBackground and ObjectivesRice is a staple food for half of the world's population and plays an important role to deliver several micronutrients including B vitamins to humans. The present investigation was carried out to detect some B vitamins and estimate their concentrations in 309 traditional indica rice landraces, compared with three modern rice varieties predominantly available in the Indian market.FindingsLiquid chromatographic examination of the rice samples demonstrated that a large number of traditional rice landraces contained considerable amounts of different B vitamins. In the landraces examined, vitamin B1 (thiamine) was recorded to be present in the range of 0.01–10.55 mg/100 g, vitamin B2 (riboflavin) 0.01–2.63 mg/100 g, vitamin B3 (niacin) 0.20–4.52 mg/100 g, vitamin B5 (pantothenic acid) 0.01–18.55 mg/100 g, vitamin B6 (pyridoxine) 0.01–0.86 mg/100 g, and vitamin B7 (biotin) 0.01–5.90 mg/100 g in different rice landraces.ConclusionCompared with traditional rice, modern rice cultivars seem to have substantially lower B vitamin levels. It appears that these vitamin‐rich traditional rice landraces if incorporated into daily diet, may serve to attain nutritional security of the poor.Significance and NoveltyOur results show that many traditional rice landraces are nutritionally superior to any modern rice cultivar, even though traditional rice landraces are normally not in priority for agronomic research and development. This study shows how native rice landraces may be leveraged to constitute novel nutritious diet that could enhance human health.

Relationship between rice grain protein content and key phenotypes in rice

AbstractIn our previous study, it was found that protein content was one of the most important factors affecting rice‐eating quality. Because rice cultivars have different phenotypes, they may also have different protein concentrations and eating quality. Based on published phenotypic and measured protein content of 706 rice (Oryza sativa L.) cultivars [453 tropical indica, (O. sativa indica) 61 tropical japonica (O. sativa japonica), 22 temperate indica, and 169 temperate japonica], we studied the potential relationship between grain protein content and the rice phenotype (culm length, panicle length, thousand grain weight, and grain length) through cluster analysis and canonical correlation analysis. The results demonstrated significant differences between japonica and indica rice, as well as between landrace rice and modern rice varieties. The protein content of japonica (average = 8.76%) was higher than that of indica (average = 8.11%). The protein content of all japonica was negatively correlated with culm length (p = 0.007) and panicle length (p = 0.006). The protein content of all indica was positively correlated with grain length (p = 0.0005) and grain length/width ratio (p = 0.043). Canonical correlation analysis showed that panicle length and grain width had the highest canonical loadings and canonical cross‐loadings on the external phenotype and grain characteristics in rice with different protein contents. Panicle length and grain width could better reflect rice phenotype traits under the identical grain protein content type.

Responses of modern and local Thai rice varieties to the aerobic soil

This study evaluated responses of modern and local Thai rices to find varieties that are suitable for growing in water-limited areas under aerobic and anaerobic soils. Nine rice varieties and two soil water conditions were arranged as a factorial design in a completely random design (CRD) with three replications. The agronomic traits that were measured consisted of 50% flowering date, plant height, yield components, harvest index (HI), and grain yield plant-1. Growing rice under aerobic soil significantly reduced plant height, yield components and grain yield, compared with anaerobic soil. However, the reduction differed depending on the variety. The modern rice varieties tend to be more adapted to the aerobic soils, compared to local. Modern rice varieties, RD29, RD49, and RD57, and a local rice variety, Chiang Phatthalung, tend to be better adapted under aerobic soil. These were clearly indicated by the smallest reduction in some agronomic traits under aerobic compared to anaerobic conditions. The plant height of RD57 was 107.93/ 104.53 cm in anaerobic and aerobic, respectively. The tiller number plant -1 in RD57 was 15.2/ 8.8; panicle number plant -1 in RD57 was 14.67/8.7 and in RD29 12.6/7.7; spikelet number plant -1 in RD57 was 188/203 and RD49 was 185/189; filled grain plant -1 in RD57 was 166.8/161; empty grain plant -1 in Chiang Phatthalung was 76.6/45.87; filled grain (%) in Chiang Phatthalung was 57.3/62.1. A highly significant correlation was found between grain yield and the number of panicle plants-1 (R=0.75; P<0.001) under non-flooded conditions, which indicated that grain yields under aerobic soil largely depended on panicle initiation. Therefore, the panicle initiation stage should first be concentrated under water shortage. Thailand comprises a wide diversity of rice. Therefore, more varieties of both modern and local Thai rice should be studied further

Comparative studies on tolerance of two rice genotypes differing in their salinity tolerance

Salinity is a serious problem affecting one third of the irrigation land and limiting the yield potential of modern rice (Oryza sativa L.) varieties. To increase our understanding of salt tolerance mechanisms in rice for better production, knowledge of salinity effects on rice seedling growth and yield components is inevitable. Despite of large number of studies on salinity tolerance of rice, we have very limited knowledge on the overall effect of salinity on rice seedlings growth. The experiment was carried out to assess the responses of salinity on the growth, nutrient accumulation and yield of rice genotypes BRRI dhan29 (salt-sensitive) and BINA dhan-10 (salt-tolerant). The pot experiment was conveyed at the net house to evaluate the response of two rice genotypes at five levels of salt stresses (0, 25, 50, 75, 100 mM NaCl) at the vegetative stage. After harvesting of rice, electrical conductivity of soil was analyzed. Growth, yield components, grain and straw yields were evaluated. Binadhan-10 showed a higher salt tolerance in physiological parameters of rice than BRRI dhan29. A significant reduction of growth, yield components, grain and straw yields of both rice genotypes was found in response to salt stress. At different salt stress conditions nutrient uptake (NPS) and K+/Na+ ratio was significantly decreased in both rice genotypes. Yet, K+/Na+ ratio was more in salt-tolerant variety than salt-sensitive variety. Asian J. Med. Biol. Res. 2022, 8 (4), 230-239

Characterization of a Novel Weak Allele of RGA1/D1 and Its Potential Application in Rice Breeding

Semi-dwarfing improves the lodging resistance and yield of rice, and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height, resulting in reduced genetic diversity and negative agronomic traits. Thus, exploring alternative sources of dwarfism is imperative for rice breeding. Here, we identified a novel RGA1 allele, d1-w, from a local indica variety Xiaolixiang (XLX) using a map-based cloning approach. Compared with other rice varieties, RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level. The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding. Compared with transgenic XLX plants (XLXD1), XLX exhibited reduced plant height, increased stem strength, lower reactive oxygen species accumulation, delayed senescence, stronger photosynthesis, higher grain yield and quality (including external, milling and nutritional qualities), and enhanced resistance to drought and Rhizoctonia solani. Therefore, we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

Constraints Faced by Rice Growers in Cauvery Delta Zone of Tamil Nadu in Cultivation of TNAU Modern Rice Varieties

The present study was carried out to analyse the constraints faced by rice growers in Cauvery Delta Zone (CDZ) of Tamil Nadu in use of Tamil Nadu Agricultural University (TNAU) modern rice varieties and to elicit suggestions for improving the adoption of TNAU modern rice varieties. Ex-Post Facto Research Design was followed in this study since it aimed to know the constraints faced by the rice growers. The study was conducted during May and June 2022. The selected districts for the study were Thanjavur, Tiruvarur, Nagapattinam and Mayiladuthurai based on maximum area under rice cultivation. From each of the four districts, two blocks were selected and from the selected blocks, two villages from each block were selected for the study based on maximum area under rice cultivation. Based on proportionate random sampling technique, 160 respondents were selected for the study. The responses of the respondents were subjected to frequency and percentage analysis. More than three fourth of the respondents expressed lodging (83.10%) followed by disease infestation (81.90%) and pest infestation (80.60%) as the major constraints. Lack of awareness and knowledge in adopting TNAU modern rice varieties was expressed by around one-third (36.30%) of the respondents. Availability of non-lodging varieties (91.90%), flood tolerant varieties (91.30%), availability of disease-resistant varieties (90.00%), pest-resistant varieties (89.40%) and increasing promotional efforts (85.00%) were the major suggestions given by the rice growers for increasing the use TNAU modern rice varieties.

Development and verification of SSR markers from drought stress-responsive miRNAs in Dongxiang wild rice (Oryza rufipogon Griff.).

Rice production worldwide has continued to decline due to various environmental stresses, with drought stress being a prominent factor, as rice is a semi-aquatic plant. Thus, development of drought stress-resistant rice varieties is of great importance for rice production. In our previous study, we found that microRNAs (miRNAs) play a crucial role in the response to drought stress in Dongxiang wild rice (DXWR) (Oryza rufipogon Griff.). Developing drought stress-responsive miRNA-based single sequence repeat (SSR) markers for DXWR will be of great value for the efficient identification and utilization of miRNA genes to breed drought stress-resistant rice varieties. In this study, ninety-nine novel SSR markers were developed based on the drought stress-responsive miRNAs of DXWR. These markers were distributed in all 12 rice chromosomes, and most were in chromosomes 2 and 6, with di- and tri-nucleotides being the most abundant repeat motifs. Twelve out of fourteen synthesized markers displayed high levels of genetic diversity in the genomes of three populations of DXWR and 40 modern rice varieties worldwide. The number of alleles per locus ranged from 2 to 7, with an average of 4.67; the genetic diversity index ranged from 0.21 to 0.76, with an average of 0.58; and the polymorphism information content value ranged from 0.18 to 0.72, with an average of 0.53. These novel molecular markers developed from the drought stress-responsive miRNAs of DXWR could be additional tools for mapping elite miRNA genes and breeding drought stress-resistant rice varieties.

Efficiency of honeycomb selection design in early segregating generation inADT45 × Nona Bokra cross under salt stress

Salt stress is a major abiotic stress that limits rice productivity worldwide including India. As modern rice varieties are salt sensitive, infusing salt tolerance through breeding is a viable farmer-friendly approach. Breeding salt tolerant rice varieties has been slow due to complexity of the trait and high Genotype x Environment interaction in the salt affected field. Selection practiced in such a situation using conventional selection method, in the presence of competition, would be misleading. On the otherhand, selection is effective in the absence of competition in honeycomb selection and counteracts the disturbing effects of competition on effectiveness of selection. The present study was conducted to test the efficiency of honeycomb selection design in early generation of a rice cross to study genetics of yield and practice selection. All the characters studied in both the design showed non normal distribution except for panicle length in CSD. All the characters studied in both the design had lower coefficient of variation, high mean and high standard deviation in the HSD compared to CSD. Large number of genes with duplicate epistasis governs days to flowering whereas panicle length and single plant yield are governed by few number of genes with complimentary epistasis. Twenty nine F2 plants each in CSD and HSD were selected based on mean and plant index (SPY), respectively. Plants selected in HSD recorded higher percentage of increase over base population compared to CSD and found HSD to be superior to CSD because of enhanced phenotypic expression in the former by eliminating confounding effects of negative correlation between yielding and competitive ability.

Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype.

Phosphorus (P) is an essential plant nutrient. Most rice growing lands lack adequate P, requiring multiple P fertiliser applications to obtain expected yields. However, P fertiliser is environmentally damaging, and already unaffordable to the marginal farmers. This warrants developing P-efficient rice varieties that require less P to produce the expected yield. However, genetic factors underlying P-use efficiency (PUE) in rice remain elusive. Here, we conducted comparative transcriptome analysis using two rice varieties with contrasting PUE; a P-efficient landrace DJ123 and a P-inefficient modern cultivar IR64. We aimed to understand the transcriptomic responses in DJ123 that allow it to achieve a high PUE under low P conditions. Our results showed that both DJ123 and IR64 had replete tissue P concentrations after 48 h of P deprivation. Yet, DJ123 strongly responded to the external low P availability by inducing P starvation-inducible genes that included SPX2, PHO1, PAPs and SQDs, while these genes were not significantly induced in IR64. We envisage that the ability of DJ123 to rapidly respond to low P conditions might be the key to its high PUE. Our findings lay a valuable foundation in elucidating PUE mechanism in rice, thus will potentially contribute to developing P-efficient modern rice variety.