Development of Sustainable Organic Rice Ratoon Production Systems in the Southern US

Main Crop

Agronomic traits:

The analysis of variance (ANOVA) for key agronomic traits including plant height, grain yield, total and whole grain milling yield, grain N content, and total N removal, is summarized in Table 1. Results from both 2023 and 2024 revealed that rotation and cultivar significantly affected plant height, grain yield, and total N removal. Cultivar had a strong influence on the milling quality of the main crop in 2023, while in 2024, only whole grain milling yield was significantly influenced by both rotation and cultivar. Grain N content and N removal were consistently affected by rotation across both years, indicating that the inclusion of cover crops or organic residue contributed to enhanced N dynamics in the soil. Cultivar differences also played a notable role in determining total N removal, reflecting variation in nutrient uptake efficiency between hybrid and inbred varieties. Despite these main effects, no significant interaction was observed between rotation and cultivar for any of the measured agronomic traits.

 Across both 2023 and 2024, cover cropping and cultivar selection significantly influenced plant growth, yield, and nitrogen dynamics in the organic rice system. In 2023, cover cropping increased plant height by 3.8% and grain yield by an impressive 46%, while in 2024, the corresponding increases were 4.9% and 26% (Fig. 2A–B, 4A–B). The hybrid cultivar XP753 consistently outperformed the inbred Presidio, exhibiting 26% and 4.2% greater plant height and 75% and 32.5% higher grain yield in 2023 and 2024, respectively. In terms of milling quality, XP753 had 3.2% higher total and 20% higher whole grain milling yield in 2023, while in 2024, the hybrid advantage persisted with a 4% improvement in whole grain milling yield (Fig. 2C–D, 4D). Although cultivar differences did not significantly affect grain nitrogen (N) content in either year, cover cropping enhanced grain N concentration by 5% in 2023 and 10% in 2024 (Fig. 2E, 4E). Total N removal, calculated as the product of grain yield and N content, reflected these combined effects. In 2023, cover cropping and XP753 removed 54% and 73% more N than winter fallow and Presidio, respectively, while in 2024, the corresponding increases were 42.3% and 23.7% (Fig. 2F, 4F).

Overall, these results highlight the importance of both cultivar selection and rotation management in optimizing productivity and nitrogen utilization in organic rice systems. The consistent effect of rotation on grain N content and N removal further emphasizes the potential of cover cropping and residue incorporation in improving soil fertility and sustaining long-term crop performance.

Table 1: Results of analysis of variance (ANOVA) for agronomic traits of main crop in 2023 and 2024

Fig 2. Effect of rotation (Cover crop vs winter fallow) and cultivar (XP753 vs Presidio) on main crop’s plant heigh (A), grain yield (B), total grain milling yield (C), whole grain milling yield (D), grain N content (E) and N removal (F) in 2023. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation or variety. 

Fig 3. Effect of rotation (Cover crop vs winter fallow) and cultivar (XP753 vs Presidio) soil ammonium nitrogen (NH₄-N) during active tillering and panicle initiation stage in 2023. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation or variety. 

Fig 4. Effect of rotation (Cover crop vs winter fallow) and cultivar (XP753 vs Presidio) on main crop’s plant heigh (A), grain yield (B), total grain milling yield (C), whole grain milling yield (D), grain N content (E) and N removal (F) in 2024. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation or variety. 

Fig 5: Effect of rotation (Cover crop vs winter fallow) and cultivar (XP753 vs Presidio) soil ammonium nitrogen (NH₄-N) during active tillering and panicle initiation stage in 2024. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation or variety. 

Soil N availability:

Soil N availability was assessed during the active tillering and panicle initiation stages in both 2023 and 2024. In both years, a similar trend was observed—cover cropping increased soil N availability during the early growth stage compared to winter fallow plots. However, this positive effect diminished as the crop advanced to the panicle initiation stage. The lack of a consistent difference in N availability later in the season can be attributed to the blanket application of 145 kg N ha⁻¹ to all plots, irrespective of treatment, using Nature Safe®, which likely masked the influence of the cover crop on soil N dynamics (Fig. 3 and 5). Cultivar differences did not significantly affect soil N availability at either growth stage in either year, suggesting that rotation management played a more prominent role than cultivar selection in regulating soil N dynamics under organic production systems. However, the hybrid cultivar XP753 tended to show slightly lower soil N availability during the early growth stage, likely due to its greater early-season N uptake and vigorous growth compared to the inbred Presidio.

Fig 6. Relationship between weed pressure and rice main crop grain yield in 2023 and 2024.

Weed pressure:

In organic cultivation, effective weed management is crucial, presenting a formidable challenge. This is especially pronounced in organic rice cultivation, where weed control is pivotal for crop success. Weed infestation levels during the main rice crop phase exhibited significant variability, ranging from minimal occurrences to extensive infestations across the plots. Consistent with findings in existing literature, the present study also underscores a notable negative correlation between weed pressure and organic rice main crop grain yield (Fig 6). This correlation highlights the importance of implementing effective weed management strategies to mitigate adverse impacts on crop productivity. By recognizing and addressing the detrimental effects of weed pressure, organic rice farmers can enhance the likelihood of achieving optimal yields and ensuring successful crop outcomes. This emphasizes the critical role that weed management plays in the context of organic rice cultivation.

Greenhouse Gas Emissions:

Fig 7. Grwing season emissions of carbon dioxide (CO₂) and methane (CH₄) for rice main crop in 2023 and 2024.  Columns with different letters indicate significant difference at P<0.5 for the interaction effect of rotation and cultivar. 

The GHGs emitted from rice production were CO₂ and CH₄, whereas N₂O emissions were negligible. In both growing years, CO₂ emissions were similar across the different rotation and cultivar combinations. CO₂-C emissions ranged from 3,487 to 4,320 kg ha⁻¹ in 2023 and from 3,255 to 3,830 kg ha⁻¹ in 2024, indicating slightly lower emissions in 2024 compared to 2023. In contrast, methane emissions in 2023 differed significantly among rotation–cultivar combinations. The Presidio cultivar under cover cropping produced the highest CH₄ emissions (258 kg ha⁻¹), while XP753 under winter fallow had the lowest (103 kg ha⁻¹). In 2024, however, there were no significant differences among treatments due to high variability within replications, with CH₄ emissions ranging from 198 kg ha⁻¹ for XP753 under cover cropping to 100 kg ha⁻¹ for XP753 under winter fallow.

To assess the climate impact of these emissions, growing season GHG emissions were converted to global warming potential (GWP) and global warming intensity (GWI). GWP was calculated by converting methane emissions to CO₂-equivalents and adding them to the CO₂ emissions. GWI was calculated by dividing GWP by the grain yield and expressed as kg CO₂-C per kg of grain. In 2023, the lowest GWI (1.24 kg CO₂-C per kg of grain) was observed for the highest-yielding system—hybrid rice under cover cropping—indicating that this combination is the most climate-friendly compared to inbred rice under winter fallow (Fig 8). A similar trend was observed in 2024, though GWI was slightly higher due to lower grain yields that year (Fig 8). Nevertheless, XP753 under cover cropping consistently showed the lowest GWI, suggesting that this cultivar and management system represents the most climate-friendly option for organic rice production across both years.

Fig 8. Bubble plot reveals the means of global warming potential (GWP) and greenhouse gas intensity (GHGI) of rice main crop in 2023 and 2024. The x-axis represents grain yield, y-axis indicates the GWP level, the size of the bubble is proportional to the GHGI.

Ratoon Crop

Agronomic traits:

The ANOVA results revealed that during the 2023 growing season, rotation had a pronounced effect on several measured traits (Table 2). Rotation significantly influenced plant height, grain yield, total grain milling yield, whole grain milling yield, and total nitrogen removal, with the strongest effects observed for plant height and whole grain milling yield. However, rotation did not significantly affect grain N content (p = 0.6960), suggesting that while crop rotation improved growth and yield performance, it did not alter the N concentration in the harvested grain. Cultivar differences were also highly significant for plant height, grain yield, grain N content, and total N removal, indicating that genetic variability strongly influenced plant performance and nutrient uptake. Although cultivar affected whole grain milling yield, its influence on total grain milling yield was not significant. Nitrogen rate effects were generally modest, with only grain N content and total N removal responding significantly to different N fertilization levels, implying that N primarily influenced grain nutritional quality rather than yield or milling traits. The interaction terms among factors were largely non-significant, showing limited evidence of combined or synergistic effects among rotation, cultivar, and N rate treatments in 2023.

In contrast, during the 2024 growing season, the effects of rotation, cultivar, and N rates displayed somewhat different patterns (Table 2). Rotation continued to significantly affect plant height, grain yield, total grain milling yield, and total N removal, confirming its consistent influence on growth and productivity. Cultivar differences were also evident for grain yield, whole grain milling yield, and total N removal, though not for plant height or total milling yield, indicating that genotypic differences were more pronounced for yield-related and quality traits in 2024. Nitrogen rate effects were significant for grain yield, grain N content, and total N removal (p < 0.0001), suggesting a yield response to N fertilization. Among interactions, the cultivar × rotation term significantly affected grain yield and total N removal. All other interaction terms remained non-significant, suggesting that main effects rather than interactions predominantly governed the response of rice growth, yield, and N dynamics in both seasons.

Table 2: Results of analysis of variance (ANOVA) for agronomic traits of ratoon crop in 2023 and 2024 

Cover cropping and cultivar significantly influenced plant growth, grain yield, grain milling yield, and N dynamics in both 2023 and 2024, though the magnitude of responses varied between years. In 2023, cover cropping increased plant height by 6.1% and grain yield by 34% (Fig. 9A and 9B), while the hybrid cultivar XP753 showed an 11% increase in height and a striking 97% increase in grain yield compared to the inbred cultivar Presidio. Cover cropping also resulted in a modest 1.0% increase in total grain milling yield. Consequently, XP753 achieved a higher whole grain milling yield (5.5%) than Presidio, and cover cropping increased whole grain milling yield by 11% (Fig. 9C and 9D). Rotation had no significant effect on grain N content; however, XP753 exhibited an 8.4% higher grain N content than Presidio (Fig. 9E). Correspondingly, cover cropping and XP753 removed 34% and 115% more N, respectively, compared to winter fallow or Presidio (Fig. 9F).The response to nitrogen (N) rates in 2023 indicated that increasing N application led to higher ratoon yields, with the peak achieved at 101 kg N ha⁻¹ and 135 kg N ha⁻¹ after stabilizing from 0 to 68 kg N ha⁻¹ (Fig. 10A). The highest yield of 2.0 Mg ha⁻¹ occurred at 101 kg N ha⁻¹, followed closely by 135 kg N ha⁻¹; both were significantly higher than the 0 kg N ha⁻¹ treatment. Grain N content at 101 kg N ha⁻¹ was slightly lower than at other N rates but was statistically similar. Nitrogen removal followed the pattern of grain yield, peaking at 101 kg N ha⁻¹ at 34 kg N ha⁻¹ (Fig. 10B and 10C).

In 2024, cover cropping continued to enhance growth and yield, though the magnitude differed. Plant height increased by 5%, and grain yield rose by 54% with cover cropping (Fig. 11A and 11B). XP753 showed a 25% increase in grain yield compared to Presidio. Total grain milling yield increased slightly by 1.3% under cover cropping, and XP753 exhibited an 8.1% higher whole grain milling yield than Presidio (Fig. 11C and 11D). Unlike 2023, grain N content was not significantly affected by rotation or cultivar (Fig. 11E). Nonetheless, cover cropping and XP753 still achieved greater N removal, with increases of 35.3% and 22.2%, respectively, compared to winter fallow or Presidio (Fig. 11F). Nitrogen rate effects in 2024 mirrored those of the previous year. Ratoon yield increased with higher N application, peaking at 101 kg N ha⁻¹ and 135 kg N ha⁻¹ (Fig. 12A). The highest yield of 1.7 Mg ha⁻¹ occurred at 101 kg N ha⁻¹, followed by 135 kg N ha⁻¹, both significantly exceeding the 0 kg N ha⁻¹ yield. Grain N content was lowest at 0 kg N ha⁻¹, while N removal closely followed the yield trend, peaking at 26 kg N ha⁻¹ for the 101 kg N ha⁻¹ treatment (Fig. 12B and 12C).

Overall, both years demonstrated that cover cropping and the hybrid cultivar XP753 consistently improved plant growth, grain yield, whole grain milling, and N removal, although the absolute gains varied between years. The response to N application was also consistent, with peak performance observed around 90-100 kg N ha⁻¹, highlighting optimal management strategies for organic rice production.

Fig 9. Effect of rotation (Cover crop vs winter fallow) and cultivar (XP753 vs Presidio) on ratoon crop’s plant heigh (A), grain yield (B), total grain milling yield (C), whole grain milling yield (D), grain N content (E) and N removal (F) in 2023. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation or variety. 

Fig 10. Effect of nitrogen rates on ratoon crop’s yield, grain N content and N removal in 2023. Columns with different letters indicated significant difference at P<0.05. 

Fig 11. Effect of rotation (Cover crop vs winter fallow) and cultivar (XP753 vs Presidio) on ratoon crop’s plant heigh (A), grain yield (B), total grain milling yield (C), whole grain milling yield (D), grain N content (E) and N removal (F) in 2024. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation or variety. 

Fig 12. Effect of nitrogen rates on ratoon crop’s yield, grain N content and N removal in 2024. Columns with different letters indicated significant difference at P<0.05. 

Greenhouse gas emissions:

The GHGs emitted from ratoon rice production were primarily CO₂ and CH₄, whereas N₂O emissions were negligible, similar to the main crop. In both growing years, CO₂ emissions were consistent across rotation, cultivar and N rate combinations, ranging from 878 to 2,312 kg ha⁻¹ in 2023 and from 632 to 1,820 kg ha⁻¹ in 2024, indicating slightly lower emissions in 2024. Methane emissions were generally unaffected by rotation, cultivar, or N application rates due to high variability within replications. The highest CH₄ emission was observed in XP753 under cover cropping with 135 kg N ha⁻¹ (178 kg ha⁻¹), while the lowest occurred in Presidio under winter fallow without N application (86 kg ha⁻¹) in 2023. In 2024 CH₄ emissions ranged between 131 kg ha⁻¹ for XP753 under cover cropping with 135 kg N ha⁻¹ to 66 kg ha⁻¹ for Presidio under winter fallow without N. Overall, there was a general trend in both years indicating that increasing N rates corresponded with higher CO₂ and CH₄ emissions.

Fig 13. Grwing season emissions of carbon dioxide (CO₂) and methane (CH₄) for rice ratoon crop in 2023 and 2024.  Due to large iter replication variation no significant difference was detected. 

To evaluate the climate impact of ratoon rice production, growing season GHG emissions were converted to GWP and GWI similar to main crop. In 2023, the lowest GWI (2.11 kg CO₂-C per kg of grain) was recorded for XP753 under winter fallow without nitrogen application (Fig. 14). In 2024, the lowest GWI (2.09 kg CO₂-C per kg of grain) was observed for Presidio under cover cropping with 135 kg N ha⁻¹. Conversely, the highest GWI in 2023 (6.64 kg CO₂-C per kg of grain) occurred in Presidio under winter fallow without nitrogen, while in 2024 the highest value (4.30 kg CO₂-C per kg of grain) was observed in Presidio under cover cropping without nitrogen (Fig. 14). Among nitrogen rates, the 67 kg N ha⁻¹ treatment consistently exhibited lower GWI values across both rotation and cultivar combinations compared to other N rates, suggesting that moderate N input may optimize productivity while minimizing the carbon footprint of ratoon rice systems.

Fig 14. Bubble plot reveals the means of global warming potential (GWP) and greenhouse gas intensity (GHGI) of rice ratoon crop in 2023 and 2024. The x-axis represents grain yield, y-axis indicates the GWP level, the size of the bubble is proportional to the GHGI.

Pest pressure:

In the ratoon crop, cultivar exerted a significant influence on weed density, with the occurrence of Narrow Brown Leaf Spot (NBLS) and Brown Spot (BS) being further impacted by rotation and cover cropping. Additionally, nitrogen (N) rates also played a role in affecting BS incidence. Notably, only N rates showed significance concerning the occurrence of white heads, as depicted in Table 3. Due to its higher tillering ability, the hybrid cultivar XP753 exhibited lower weed density compared to the inbred cultivar Presidio (Fig 7 A). This trait allows XP753 to effectively compete for space, sunlight, and resources with weeds. Furthermore, cover cropping led to an 8.6% reduction in NBLS and an 8.9% reduction in BS. XP753 also demonstrated a notable reduction in NBLS (39%) and BS (30%), as shown in Figures 7 B and C, respectively. Interestingly, the highest N rate of 135 kg ha^-1 resulted in the greatest number of white heads (Fig 7 D). These findings underscore the multifaceted interactions between cultivar selection, agronomic practices such as cover cropping and rotation, and nutrient management in influencing weed dynamics and pest incidence in ratoon rice cultivation.

Table 3: Results of analysis of variance (ANOVA) for pest incidence in ratoon crop 

Fig 15. Effect of rotation, cultivar and N rates on pest pressure in ratoon rice crop. Columns with different letters indicate significant difference at P<0.5 for the mean effect of either rotation, cultivar or N rate.