The role of seed phytic acid levels in promoting black rice growth, nutrient use efficiency, and yield under low-input conditions

Black rice is cultivated in Southeast Asia’s upland and lowland area, where yields are often limited by low soil fertility, phosphorus (P) deficiency, and limited external inputs. Phytic acid (PA)—the principal storage form of P in rice seeds—represents more than 70% of the total seed P. Data on the effects of seed PA levels on the agronomic performance of black rice, especially under upland field conditions, are scarce. This study explored the effect of seed PA concentration on the early growth, nutrient uptake, and yield performance of black rice under both pot and upland field conditions. In pot experiments, we tested three levels of seed PA (low, moderate, and high) at different soil P applications (control, low P, and high P). A complementary field trial in Luang Prabang, Laos, evaluated the effects of seed PA and nitrogen (N) application (0 or 30 kg N ha^-1) under rainfed conditions. Results demonstrated that high-PA seeds significantly improved early seedling vigor, shoot and root biomass, and nutrient uptake, particularly under conditions of low or no external P supply. At maturity, high-PA plants yielded 35% more grain than that yielded by low-PA plants in pots and exhibited a 47% yield advantage in upland fields. Low N input did not affect grain yield but notably reduced grain PA levels under upland conditions. Overall, the findings indicate that seed PA concentration is a key physiological trait that enhances the adaptation and productivity of black rice in nutrient-poor upland systems.

1 Introduction

Rice (Oryza sativa L.) is a vital staple for over 90% of Southeast Asia’s population and key source of income for smallholder farmers in Laos, where rice is cultivated across diverse ecosystems. Specifically, approximately 89% of rice is grown in lowland areas under irrigated, bunded, or rainfed systems, whereas upland rice, accounting for approximately 11% of the total, is grown on sloping, unbunded fields primarily through traditional slash-and-burn methods in the north (Mullis and Prasertsri, 2019). Although upland rice is crucial for regional food security and cultural heritage, its productivity remains low, averaging only 2.0 tons per hectare—roughly half that of lowland rice—mainly due to limited fertilizer use and reliance on rain-fed, nutrient-poor soils (Roder, 2001; Lao Statistics Bureau, 2019).

Among the upland rice varieties, black rice stands out due to its notable nutritional profile, which is rich in anthocyanins, flavonoids, and phenolics, giving it its distinctive pigmentation and confer health benefits, such as antioxidant properties, that may protect against chronic diseases, such as heart disease, diabetes, and certain cancers (Lobo et al., 2010; Goufo and Trindade, 2014; Kushwaha, 2016; Oo et al., 2025). In Laos, black rice is mainly cultivated in the rainfed upland regions in the north as well as under rainfed conditions in lowland areas often on acidic soils with limited nitrogen (N) and phosphorus (P) availability (Saito et al., 2006a). These challenging soil and climate conditions often result in poor seedling establishment and reduced yields especially in traditional systems relying on local landraces and minimal external inputs (Saito et al., 2006b; Asai et al., 2009a, 2009b). Therefore, enhancing seedling vigor and early nutrient uptake are critical strategies for improving black rice performance under such conditions.

One promising but insufficiently explored approach involves improving seed quality through accumulation of stored nutrients. Phytic acid (myo-inositol hexakisphosphate; PA) is the main storage form of P in rice seeds, representing over 70% of seed P (Raboy, 2000; Karmakar et al., 2020; Silva et al., 2021). While PA has been negatively viewed due to its antinutritional effects in human and animal diets, it plays an essential physiological role during germination, providing P, inositol, and minerals that support early seedling growth and root development (Raboy, 2003). Recent research suggests that higher seed PA levels may enhance early vigor in crops especially under nutrient-deficient or stress-prone conditions (Kolawole and Kang, 1997; Ros et al., 1997; White and Veneklaas, 2012; Oo et al., 2023a). This is particularly relevant in the case of upland rice systems in Laos, where P deficiency and soil acidity often hinder nutrient uptake during early growth stages, negatively impacting yields (Saito et al., 2006a, 2006b). Improved early germination and seedling vigor can also help mitigate early season nutrient stress and moisture shortages, which are becoming more frequent owing to reduced rainfall and shifting climate patterns.

Therefore, seed PA content may serve both as a physiological trait that promotes early growth and as a biochemical marker for selecting genotypes with higher yield potential (Takai et al., 2025). However, empirical data on the impact of seed PA levels on black rice performance under upland conditions remain limited. To address this gap, this study examined how seed PA concentrations influence early seedling growth and nutrient uptake as well as the consequent effects on yield in black rice grown under nutrient-deficient conditions. According to our hypothesis, black rice with higher seed PA should exhibit greater seedling vigor, enhanced nutrient acquisition, and higher yields. The findings can guide seed-based nutrient management strategies and support the development of resilient black rice varieties that are suitable for upland cultivation.

2 Methods

2.1 Pot experiments 1

2.1.1 General

Pot experiments were conducted at the Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan (36° 3′ 14.25″ N, 140° 4′ 47.77″ E), during the 2022 rice growing season (May to October). During the experiments, the average daily temperature ranged from 20.6 to 29.1°C. A factorial design was used with three seed PA levels (low PA (LPA), moderate PA (MPA), and high PA (HPA)) and three levels of P treatments (control, low P, and high P) with four replicates each. P was applied as triple superphosphate at 0 and 34 mg P₂O₅ and 84 mg P₂O₅ per pot.

The black rice variety Asamurasaki was used, with seed PA concentrations previously established under different growth conditions, i.e., low-, medium-, and high-P applications: 15.5, 24.7, and 35.4 mg g⁻¹ (LPA, MPA, and HPA, respectively), all with similar seed weight (Oo et al., 2023b) (Supplementary Table S1). Soil was collected from the JIRCAS farm, air-dried, and sieved (8-mm mesh). Soil characteristics were as follows: 69.2% sand, 29.4% silt, 1.4% clay, pH (H₂O) of 5.78, EC 3.82 mS m⁻², and oxalate-extractable P 400 mg kg⁻¹ (Oo et al., 2023b). Each 1 kg of soil was placed in a 1-L pot that had been pretreated with 100 mg N (NH₄NO₃) and 100 mg K (K₂SO₄) to avoid N and K deficiencies.

Seeds from each PA level were sown in trays, and after 21 days, seedlings were carefully transplanted (two per pot), maintaining saturating conditions. Previous studies showed significant differences in seedling vigor: shoot lengths of 31.09, 35.14, and 35.54 cm and shoot biomass of 39.7, 48.6, and 71.3 mg per seedling for LPA, MPA, and HPA, respectively (Oo et al., 2023a).

2.1.2 Early growth assessment—35 days after transplantation

Plant height and tiller number per pot were measured 35 days after transplantation (DAT). Shoots were harvested, oven-dried at 70°C for three days, and weighed for biomass. Dried shoot samples were analyzed for P concentration using the molybdate blue method (Murphy and Riley, 1962) after dry ashing at 550°C for 2 h and acid digestion. N concentration was measured using a Sumigraph NC-TRINITY analyzer (Sumika Chemical Analysis Service, Osaka, Japan). Shoot P and N uptake were calculated by multiplying the concentrations by the biomass.

Subsequently, roots were washed, preserved in 50% ethanol, scanned at 600 dpi, and analyzed using the WinRhizo Pro software (Regent Instruments, Canada). Following Kano-Nakata et al. (2019), roots were categorized as lateral or nodal (<0.2 or 0.2–2.0 mm diameter, respectively) and eventually dried and weighed.

2.2 Pot experiments 2

2.2.1 General

A second set of pot experiments at JIRCAS used 3 kg of similar soil in Wagner pots that were 20 cm in height and 16 cm in diameter. Treatments included two P levels (100 and 250 mg P₂O₅ per pot as triple superphosphate) and three seed PA levels, with five replicates. N and K were added uniformly (300 mg N and 300 mg K₂O per pot). Two 21-days-old seedlings per pot were transplanted, and the pots were saturated until harvest.

2.2.2 Yield assessment

At maturity, panicles were counted, and grains were separated and air-dried for weight measurement. The straw was oven-dried at 70°C for three days to determine the biomass.

2.3 Field experiments

2.3.1 General

In 2024, a field trial was conducted during the rainy season at the Upland Agricultural Research Center, Luang Prabang, northern Laos (19° 44′ 09.6″ N, 102° 09′ 19.4″ E). The study region is characterized by Orthic Acrisol soils with moderate acidity, low nutrient availability, and poor water retention (Matsuo et al., 2015b). Upland rice in the region is typically grown under rain-fed, low-input conditions (Roder, 2001; Saito et al., 2006a). During the upland rice growing season, i.e., from June to October, the average air temperature is 25.8°C, and the rainfall amount is 1,000 mm. The experimental soil was classified as clay loam, with a slightly acidic pH (5.3), low total N content (2.3 g kg^-1), carbon content of 24.9 g kg^-1, and available P content of 8.1 mg kg^-1.

The black rice variety Kampeng—a tropical japonica landrace rich in functional grain components (Asai et al., 2020)—was selected due to its adaptability to upland field conditions. Seeds from plants grown under no-, moderate-, and high-P treatments were used to obtain seeds with different PA levels (Supplementary Table S1). Prior to sowing, all the weeds and shrubs were manually removed; however, no land preparation was conducted. No external P fertilization was applied; however, N fertilizer treatment was included, as N is also a key limiting factor for black rice production in northern Laos. The experiment adopted a split-plot design, with three replicates. N application (0 or 30 kg N ha⁻¹ as urea) served as the main plot factor, and seed PA concentration (LPA, MPA, and HPA) was the subplot factor. The plot size was 1.5 × 1.5 m. Seeds were sown using dibble sticks, according to local practices, at a spacing of 25 × 25 cm with 5–8 seeds per hill. N was applied once near the hills after seeds were sown in the N-treated plots. Weed control was performed manually as needed, and no pesticides were applied because of the absence of pest damage.

2.3.2 Growth and yield evaluation

Plant height and tiller number were recorded 40 and 60 days after sowing. Although flowering time was monitored, all plots flowered simultaneously, and no treatment effect was observed. At maturity, grains and straw from each plot were harvested. The grains were air-dried and expressed as rough grain weight per pot. Rice straw was oven-dried at 70°C for two days to determine shoot dry weight.

2.3.3 Quantification of PA in rice grains

PA concentrations in field-harvested grains were determined at JIRCAS, Japan, using a modified protocol adapted from Matsuo et al. (2005a).

2.4 Statistical analysis

Data were analyzed using the JMP software (v14.0.0; SAS Institute Inc., Tokyo, Japan). Two-way analysis of variance (ANOVA) tested the effects of P/N application and seed PA level, with Student’s t-tests comparing LPA and HPA under zero P. Treatment means were compared using Tukey’s HSD test at a 5% significance level.

3 Results

3.1 Early growth performance—pot experiments 1

Seedling vigor 35 days after transplanting was influenced significantly by seed PA, P application, and their interaction (Figure 1; Supplementary Table S2). Without P application, overall plant growth was limited due to low native soil fertility. Despite these nutrient-deficient conditions, seedlings from HPA seeds exhibited greater tiller number, plant height, and shoot biomass than those of seedlings from MPA and LPA seeds.

Figure 1

Figure 1. Early rice growth affected by seed phytic acid concentration under different soil P levels at 35 days after transplanting in pot experiments 1. **p < 0.01. Different letters indicate significant differences at p < 0.05 by Tukey’s HSD test. ^†(t-test: p < 0.05): the effect was significant between LPA and HPA under control (no P). LPA, low phytic acid; MPA, moderate phytic acid; HPA, high phytic acid. P, PA, and P × PA indicate the effect of P treatment, phytic acid, and their interaction, respectively.

The positive effect of HPA was further enhanced by increased P supply. Specifically, under low-P conditions, HPA plants showed a 104% increase in shoot biomass relative to that of LPA plants, and this increase was 55% under high-P conditions. Across all P levels, HPA plants consistently showed superior early growth traits, indicating that higher seed PA concentrations contribute to improved early vigor—particularly under moderately favorable nutrient conditions.

3.2 Shoot nutrient uptake

Shoot N and P uptake mirrored the trends observed for biomass accumulation, being significantly affected by seed PA and P application as well as their interaction (Figure 2). Compared with that in LPA plants, shoot N uptake in HPA plants increased by 71.5%, 111.6%, and 92.5% under no-, low-, and high-P treatments, respectively. Similar trends were observed for shoot P uptake, with HPA plants consistently outperforming both LPA and MPA plants across all P regimes. Specifically, compared with that in LPA plants, shoot P uptake in HPA plants increased by 82.4%, 132.9%, and 39.3% under no-, low-, and high-P treatments, respectively. MPA plants exhibited intermediate nutrient uptake values; however, these were not significantly different from those of LPA plants. These results suggest that higher seed PA content supports improved early nutrient acquisition—especially under P-deficient or low-input conditions.

Figure 2

Figure 2. Nutrient uptake of rice plants affected by seed phytic acid concentration under different soil P levels at 35 days after transplanting in pot experiments 1. **p < 0.01. Different letters indicate significant differences at p < 0.05 by Tukey’s HSD test. ^†(t-test: p < 0.05): the effect was significant between LPA and HPA under control (no P). LPA, low phytic acid; MPA, moderate phytic acid; HPA, high phytic acid. P, PA, and P × PA indicate the effect of P treatment, phytic acid, and their interaction, respectively.

3.3 Root morphology and biomass

Root traits were also significantly influenced by seed PA and P application as well as their interaction (Supplementary Table S3). Under both low- and high-P conditions, HPA plants developed longer lateral and nodal roots, greater root surface area, and significantly higher root biomass than those of LPA and MPA plants. HPA root biomass was 109.6% and 61.3% greater than that of LPA plants under low- and high-P conditions, respectively. Although MPA plants showed modest increases in all root parameters compared with those of LPA plants, the differences were not significant. Overall, enhanced seed PA concentrations facilitate early root development, contributing to superior nutrient uptake and growth.

3.4 Yield components and grain production—pot experiments 2

Panicle number, straw biomass, and grain yield at harvest were significantly influenced by seed PA and P application; however, no significant interaction was observed between the two factors (Figure 3). Across all P levels, HPA plants consistently produced more panicles and straw biomass than those produced by LPA plants. Consequently, HPA grain yield was 35% higher than that of LPA plants. Although MPA plants showed panicle numbers comparable with those of HPA plants, the grain yield of MPA plants remained slightly lower, suggesting that the advantages conferred by higher PA concentrations persisted until maturity.

Figure 3

Figure 3. Panicle number, straw and grain yield affected by seed phytic acid concentration under different soil P levels in pot experiments 2. *p < 0.05, **p < 0.01, ns, not significant at 5% level. Different letters indicate significant differences at p < 0.05 by Tukey’s HSD test. LPA, low phytic acid; MPA, moderate phytic acid; HPA, high phytic acid. P, PA, and P × PA indicate the effect of P treatment, phytic acid, and their interaction, respectively.

3.5 Growth and yield under upland conditions

In the field trial under rainfed upland conditions, N application (30 kg N ha⁻¹) did not lead to significant differences in rice growth or shoot biomass; however, the increase in grain yield was marginally significant (p = 0.08) (Table 1). Despite the lack of statistical significance, consistent improvements in tiller number, plant height, and straw biomass were observed in the N-treated plots.

Table 1

Table 1. Plant growth, yield and grain phytic acid (PA) concentrations affected by N application and seed phytic acid concentration under upland field conditions in northern Laos.

Notably, seed PA concentration affected black rice performance significantly under field conditions, as observed in the pot experiment. HPA plants had greater tiller number and plant height 60 days after sowing than those of LPA plants. The enhanced early vigor translated into significantly higher straw and grain yields. Specifically, the grain yield of HPA plants increased by 47% compared with that of LPA plants. MPA plants exhibited no significant differences in yield or early growth compared with those of LPA plants, underscoring the unique advantage of high seed PA concentrations.

3.6 Grain PA concentration

Grain PA concentration was significantly lower under 30 kg N ha⁻¹ (13.8 mg g⁻¹) compared with that under 0 kg N ha⁻¹ (16.3 mg g⁻¹) (p < 0.01), indicating that N application reduced PA accumulation in rice grains (Table 1). However, seeds with different PA levels showed no significant differences in PA accumulation in rice grain (14.9, 15.9, and 14.5 mg g^-1 for LPA, MPA, and HPA, respectively). In addition, no significant interaction between N treatment and PA level was observed, suggesting that the effect of N on PA accumulation in rice grain was consistent across all levels of seed PA.

4 Discussion

According to the results, black rice with higher concentrations of PA in its seeds demonstrated superior early growth, nutrient uptake, and grain yield under pot-transplanted and direct-seeded rain-fed upland conditions. Furthermore, the results support our hypothesis: Increased seed PA enhances seedling vigor and facilitates adaptation to nutrient-deficient environments, such as the upland fields in northern Laos. Notably, the benefits were most pronounced under low- to moderate-P conditions, underscoring the potential of seed-based characteristics to alleviate early nutrient stress in low-input agricultural systems.

Seed PA plays a dual role. Although it is often criticized for its anti-nutritional properties in human and animal diets (Vats and Banerjee, 2004; Raboy, 2020), it is a critical reservoir of P during germination (Raboy, 2003). In this study, the improved early vigor of HPA seedlings—reflected in increased shoot biomass, tiller number, and plant height—aligns with previous research showing that seed P reserves can influence seedling establishment significantly under nutrient-limited conditions (Kolawole and Kang, 1997; Ros et al., 1997; White and Veneklaas, 2012; Oo et al., 2023a). The enhanced root development observed in the HPA plants further supports the view that high internal P reserves stimulate early root growth, facilitating greater soil exploration and nutrient uptake (Wen et al., 2017; Oo et al., 2023a). This early advantage is particularly vital in upland soils, where P availability is often limited by strong P fixation and low organic matter content (Saito et al., 2006a).

Notably, although increasing the external P supply improved growth across all seed PA levels, the relative benefit of HPA levels persisted. Under both low- and high-P applications, HPA plants showed significantly higher shoot and root biomass, N and P uptake, and more developed root systems than those of LPA plants. This suggests that seed PA does not merely substitute for external P but may also interact with soil nutrients to enhance early-stage metabolic efficiency. The findings are consistent with reports that genotypes with higher seed P reserves tend to outperform others even when soil fertility is moderate (Rose and Raymond, 2020). Additionally, given the weak or inconsistent responses of MPA plants across treatments, it appears that only sufficiently high PA concentrations confer such physiological benefits, emphasizing the need for targeted trait selection in breeding programs.

Globally, many rice-growing regions suffer P deficiency (Navea et al., 2024). This is particularly evident in upland systems, where rice is directly seeded and external inputs are limited (Haefele et al., 2014; Rose and Raymond, 2020). In our field trials in northern Laos, HPA seeds consistently produced higher grain yields even in the absence of significant responses to N fertilization. This suggests that the early vigor advantage conferred by high seed PA supports better crop establishment and resource use efficiency, which are especially critical in environments characterized by low soil fertility, erratic rainfall, and limited nutrient mobility (Asai et al., 2009a, b; Saito et al., 2006a). Because we applied only 30 kg N ha^-1 of minimal fertilizer soon after seed sowing, there is a high risk of N loss due to runoff from precipitation under the slash-and-burn system on steep slopes in upland farming; consequently, the effect of N fertilizer application on grain yield was not significant. The stable yield advantage of HPA seeds, regardless of N input, underscores the potential of enhancing intrinsic seed nutrient reserves to buffer early-stage stress and improve stand uniformity. Considering that upland rice farmers often operate under socioeconomic constraints that limit fertilizer use (Roder, 2001; Asai et al., 2009a, b; Rose and Raymond, 2020), selecting for physiological traits, such as PA accumulation, offers a practical, low-cost strategy to enhance productivity in low-input systems.

In addition to enhancing early growth and yield under upland field conditions, N application also influenced grain PA levels. Specifically, applying 30 kg N ha⁻¹ reduced grain PA concentration significantly compared with that of the no-N treatment likely due to a dilution effect associated with increased grain biomass or changes in internal nutrient partitioning. The results of this study are consistent with those of Su et al. (2022), who showed that N application decreased PA content in rice grain. However, grain PA concentrations did not differ significantly among the seed PA levels, and no interaction between N and seed PA levels was observed. This indicates that the reduction in PA content with N was consistent, regardless of the initial seed PA levels. The findings suggest that moderate N inputs can improve yield while maintaining or lowering grain PA concentrations, offering a dual benefit for productivity and nutritional quality. In upland systems where fertilizer use is limited, this reinforces the value of intrinsic seed traits, such as PA content, which supports both agronomic performance and more favorable grain composition.

While our findings emphasize the benefits of high-PA seeds in enhancing growth and performance, it is crucial to acknowledge the role of low-PA genotypes, which may also exhibit favorable traits under specific conditions. Although our research did not directly compare these LPA lines, emerging evidence suggests that certain LPA genotypes can perform well in diverse environments (Elgorashi Bakhite et al., 2021). To provide a more comprehensive perspective, future studies should investigate these variations, highlighting the strengths of our focus on high PA genotypes while also candidly discussing the limitations of this approach. By addressing both high- and low-PA concentrations, we can gain a deeper understanding of their respective impacts on plant performance and navigate the complexities of nutrient dynamics, thereby broadening the applicability of our findings within seed physiology and agricultural practices.

Overall, this study provides empirical evidence supporting seed PA as a beneficial trait that could be exploited to enhance early vigor and yield performance in black rice under upland and low-input conditions. Although further research is required to assess the trade-offs related to human nutrition and identify genetic factors regulating PA accumulation, our findings suggest that seed PA concentration could serve as a useful biochemical marker in breeding programs aimed at improving rice productivity in marginal environments. Recently, a quantitative trait locus increasing seed PA concentration has been detected in black rice in Laos (Takai et al., 2025). Future studies should also investigate the interaction between seed PA and other seed components (e.g., micronutrients and antioxidants) by using large numbers of black and white rice genotypes and validate the performance of HPA genotypes across different agroecological zones and seasons.

Data availability statement

The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding authors.

Author contributions

AZO: Conceptualization, Data curation, Investigation, Methodology, Project administration, Visualization, Writing – review & editing. HA: Conceptualization, Data curation, Investigation, Methodology, Project administration, Visualization, Writing – review & editing. KS: Data curation, Investigation, Methodology, Supervision, Writing – review & editing. BV: Investigation, Methodology, Supervision, Writing – review & editing. TT: Methodology, Supervision, Writing – review & editing. JM: Conceptualization, Data curation, Methodology, Writing – review & editing. HS: Conceptualization, Methodology, Supervision, Writing – review & editing. KV: Methodology, Project administration, Supervision, Writing – review & editing.

Funding

The author(s) declared financial support was received for this work and/or its publication. This research was supported by the JIRCAS research program “Indigenous Crops and Food Design” and a JSPS KAKENHI grant (JP22K05942).

Acknowledgments

We are grateful to Ms. Emiko Kojima and Ms. Mari Momma of the Japan International Research Center for Agricultural Sciences (JIRCAS) for performing the analysis.

Conflict of interest

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Generative AI statement

The author(s) declared that generative AI was not used in the creation of this manuscript.

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Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fagro.2026.1743691/full#supplementary-material

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