IRRI Journal Articles
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Item On-farm nitrogen, phosphorus, and potassium partial balances in three major rice production systems in sub-Saharan Africa(Journal Article, 2025-03-01) Rakotoson, Tovohery; Johnson, Jean-Martial; Senthilkumar, Kalimuthu; Ibrahim, Ali; Saito, KazukiAbstract Context Quantifying nutrient balances in cropping systems is critical for better nutrient management towards efficient and sustainable agriculture. However, information about nutrient balances for rice in major production systems is limited in sub-Saharan Africa (SSA). Objectives This study aimed to assess nitrogen (N), phosphorus (P), and potassium (K) balances in the three major rice production systems in SSA and their relationships with rice yield at different spatial levels. Methods On-farm survey of 1025 farmers’ fields in 32 sites within 19 countries across West, Central, and East Africa, and for three major rice production systems consisting of irrigated lowland, rainfed lowland, and rainfed upland were used to quantify the nutrient partial balances calculated as nutrient inputs minus outputs. Results The study found significant variations in N, P, and K partial balances across regions, countries, and production systems ranging from −209–220 kg ha−1 for N, −39–86 kg ha−1 for P, and −282–163 kg ha−1 for K. Production system was the main source of these variations, while region largely contributed to the P partial balance. The partial balance of all three nutrients was generally negative except for a few sites, with more negative P (70 %) and K (73 %) partial balances compared to the N partial balance (51 %). East Africa had the largest negative partial balances, except for Uganda. Rainfed upland rice was the least sustainable, with negative partial balances of 13, 1, and 13 kg ha−1 for N, P, and K, respectively. There were inconsistent relationships between grain yield and partial nutrient balance. Conclusions N, P, and K partial balances in rice production in SSA largely vary and are mostly outside of acceptable ranges. Irrigated lowland rice is the most sustainable. We identified clusters of combinations of sites and production systems based on yield and nutrient partial balance and suggested research and development strategies for improving yields and optimizing nutrient balances. Implications For comprehensive nutrient balance assessment, future studies should take into account variations in residue management, biological N fixation in lowland rice systems, and organic input.Item Meta-analysis of yield-emission trade-off in direct seeded vs. puddled transplanted rice: Towards a cleaner and sustainable production(Journal Article, 2024-11-20) Reddy, K. Srikanth; Parihar, C.M.; Panneerselvam, P.; Sarkar, Ayan; Patra, Kiranmoy; Bharadwaj, Sneha; Sena, D.R.; Reddy, G. Sreeja; Sinha, Alok; Dhakar, Rajkumar; Kumar, Virender; Nayak, Hari SankarConventional rice production through puddled transplanted rice-PTR is tillage, water, energy, and capital intensive. Furthermore, it is a major contributor to greenhouse gas (GHGs) emissions. In this regard, Direct seeded rice-DSR can be a potential alternative to PTR for reducing GHGs emissions, while sustaining yields. However, depending upon agroclimatic situation, whether the effect of DSR on GHGs emission and yield are consistent or not, as compared to PTR need a comprehensive analysis. To bridge this knowledge gap, we performed a meta-analysis synthesizing 876 paired measurements from 54-peer-reviewed studies to understand how DSR impacts N2O and CH4 emissions, global warming potential-GWP (heat-trapping potential of greenhouse gases compared to CO2), yield and C-footprint-CFP (environmental impact in CO2 eq. due to concerned activity). Compared to PTR, DSR decreased CH4 emissions by 70%, GWP by 37% and CFP by 34%, despite 85% increase in N2O emissions. However, this shift comes with 11% decrease in yield. To decipher the primary factors driving these outcomes, we conducted subgroup analyses by taking environmental conditions and management practices as predictors in a random effect model. Low to medium pH soils, zero tillage, puddled soil (wet DSR), conventional flooding, and high nitrogen rates (>200 kg/ha) are found to be favorable for DSR with comparable yields but posing a discrepancy with environmental sustainability benefits. Therefore, further research to evaluate DSR across agro-ecologies, management practices are needed to optimize yields with lower GWP and CFP.Item Unravelling candidate genes associated with blast disease resistance in an elite green super rice varietal panel using genome-wide association study(Journal Article, 2025-02-02) Saxena, Harshita; Murugaiyan, Varunseelan; Ghimire, Bikash; Robiso, Christian John; De Asis, Erik Jon; Yanoria, Mary Jeanie; Raymer, Paul L.; Bahri, Bochra Amina; Ali, JauharRice blast disease, caused by the filamentous fungus Magnaporthe oryzae, significantly threatens global rice crops leading to yield losses worldwide. Given that existing resistance genes often fail to control rice blast due to the evolution of new virulent strains, identifying novel genes using modern breeding tools to enhance partial resistance is crucial for developing more durable and effective control measures. Here, we used a genome‐wide association study (GWAS) with 2698 high‐throughput single‐nucleotide polymorphism (SNP) markers to analyse 134 rice cultivars from the Green Super Rice breeding programme against two virulent rice blast isolates, M101‐1‐2‐9‐1 (M101) and M64‐1‐3‐9‐1 (M64). GWAS identified 12 potential quantitative trait loci (QTLs) for blast resistance: five against M101 on chromosomes 1, 2, 3, 4 and 7 and seven against M64 on chromosomes 1, 4, 5, 6 and 12, with no QTL in common against both. Notably, qM101_2 is within the 500 kb linkage disequilibrium (LD) block containing the known resistance gene Pib on chromosome 2, and qM64_12.1 and qM64_12.2 are within the Pi‐ta and Ptr gene cluster on chromosome 12. The remaining nine QTLs represented novel blast disease resistance sources. The identified candidate genes, including those encoding nucleotide‐binding site leucine‐rich repeats domains, protein kinases, resistance gene analogues and pathogenesis‐related proteins, may serve as a foundation for further studies to explore their potential role in enhancing disease resistance in rice.Item Yield stability of four staple crops of sub-Saharan Africa: analysis of long-term trials(Journal Article, 2025-02-01) Awio, Thomas; Senthilkumar, Kalimuthu; Ibrahim, Ali; Corbeels, Marc; Saito, KazukiMeeting the food demand of the growing population of sub-Saharan Africa (SSA) requires improvement of agronomic interventions including cropping systems and management practices that can lead to higher and more stable crop production. We reviewed studies on long-term experiments (LTEs) in SSA to assess yield and yield stability of maize, rice, sorghum, and pearl millet, and identify agronomic interventions having higher and more stable crop productivity. We used 558 observations from 58 LTEs across 13 SSA countries. Across crops, mineral fertiliser application significantly (p ≤ 0.04) increased yield and sustainable yield index (SYI) by 48–185% and 49–257%, respectively. Organic inputs significantly (p ≤ 0.04) increased yield of rainfed rice and maize by 21 and 79%, respectively, and SYI of pearl millet and maize by 133 and 125%, respectively. Green manure application (in-situ) considerably enhanced yield and SYI of maize by 207 and 291%, respectively, compared with no application. Combined application of mineral fertiliser and organic input substantially increased yield and SYI of maize by 23–36 and 31–43%, respectively. Conservation tillage practices and intercropping did not increase yield and yield stability. Across crops, irrespective of the agronomic interventions, SYI increased with higher yields, whereas for coefficient of variation only a significant negative relationship was observed for rice. The results of this study suggest that achieving both high yields and high yield stability are not conflicting goals. However, apart from mineral fertiliser, the impact of other agronomic interventions is crop specific. Given the limited availability of data from the crops other than maize, there is a need to establish a new generation of LTEs focusing on these other crops in diverse environments in SSA.Item Eco-optimizing rice-wheat system of Eastern Indo-Gangetic plains of India through resource conservation technologies: insights from field experiments and modeling(Journal Article, 2025-01-31) Reddy, K. Srikanth; Parihar, C. M.; Panneerselvam, P.; Sarkar, Ayan; Nayak, Hari Sankar; Patra, Kiranmoy; Sena, D. R.; Reddy, G. Sreeja; Sinha, Alok; Bharadwaj, Sneha; Kumar, Sunil; Kumar, VirenderIn eastern India, the rice-wheat cropping system (RWCS) faces challenges like poverty, fragmented landholdings, and resource overexploitation, with smallholder farmers prioritizing short-term gains through excessive water and nitrogen use. To address these issues, our study combined field experiments and the DNDC crop simulation model to evaluate the resilience, viability, and environmental sustainability of RWCS under conservation agriculture (CA) with varying irrigation methods and nitrogen rates at the International Rice Research Institute-South Asia Regional Center (ISARC), Varanasi, India. The treatments included: (1) Puddled transplanted rice followed by zero-tilled wheat with flood irrigation (PTR-ZTW-F), (2) Direct-seeded rice followed by ZTW with flood irrigation (DSR-ZTW-F), (3) DSR followed by ZTW with surface drip fertigation (DSR-ZTW-SD), and (4) DSR followed by ZTW with subsurface drip fertigation (DSR-ZTW-SSD), evaluated under 75% and 100% recommended nitrogen dose and nitrogen control plots. The DNDC model accurately predicted soil mineral N (: R2 = 0.74, RRMSE = 52.9%; : R2 = 0.79, RRMSE = 63.5%), water-filled pore space (R2 = 0.85, RRMSE = 20.9%), soil temperature (R2 = 0.91, RRMSE = 4.6%), redox potential (R2 = 0.82, RRMSE = 24.1%), system productivity (R2 = 0.93, RRMSE = 7.8%), and nitrogen uptake (R2 = 0.86, RRMSE = 18.1%). DSR-ZTW systems with drip fertigation significantly enhanced sustainability and productivity compared to PTR-ZTW system, where CH4 emissions were reduced by 70%–80% and global warming potential reduced by 56%, despite higher N2O emissions. Additionally, DSR-ZTW-SSD achieved the highest system yield (12.8 t ha−1), minimized water losses, and improved nitrogen use efficiency. Also, TOPSIS analysis ranked DSR-ZTW-SSDF as the most sustainable system, achieving the highest yield and resource use efficiency, while significantly reducing GHG emissions. The study underscores the potential of integrating CA, drip fertigation, and DSR to enhance productivity, conserve resources, and improve the sustainability of RWCS.Item Development of functional molecular markers for viviparous germination resistance in rice(Journal Article, 2024-12-04) Lee, So-Myeong; Kim, Sung-Ryul; Kang, Ju-Won; Park, Hyeonjin; Cha, Jin-Kyung; Park, Dong-Soo; Cho, Jun-Hyun; Kim, Woojae; Eom, Gyu-Hyeon; Lee, Jong-HeeRice (Oryza sativa) plays a pivotal role in global food security. Understanding the genetics of rice cultivation is crucial, particularly for traits such as viviparous germination, which significantly influences germination and yield. Our research aimed to elucidate the genetic and molecular mechanisms by which the Sdr4 gene influences viviparous germination and to develop novel molecular markers for this gene to enhance breeding strategies against viviparous germination. In all, 683 rice cultivars and 100 F2 plants were used for viviparous germination and genetic analysis using KASP (Kompetitive Allele-Specific PCR) and agarose gel-based markers related to viviparous germination tolerance. We developed and used a polymorphic agarose gel-based marker and a KASP marker targeting the Sdr4 gene. A genetic analysis of field-grown rice cultivars and the F2 population revealed that the two markers on Sdr4 were functional for the genomic selection of SNPs and InDels related to dormancy. The Pearson correlation coefficient (r = 0.74, p-value = 3.31 × 10−8) between the Sdr4-IND KASP marker genotype and viviparous germination rate demonstrated a significant positive correlation, supporting the marker’s utility for selecting rice varieties with diminished viviparous germination. This insight serves as a critical theoretical foundation for breeding strategies for developing early-maturing rice varieties with enhanced resistance to viviparous germination, addressing pivotal challenges in rice cultivation, and ensuring food security.Item Ups and downs in the world rice market(Newsletter, 2024-07-02) Pede, Valerien; Dawe, DavidInternational rice prices have risen substantially. Over the past year, the main factors driving world market prices have been El Niño and the export restrictions from India, the world’s largest rice exporter. Since January 2024, however, prices have declined as El Niño conditions have ended. Fertilizer prices have declined substantially from their peaks in mid-2022 and have stabilized over the past year. These factors give grounds for optimism that international rice prices will stabilize or decline further in the near future.Item World rice market update: more trade, better weather, lower prices(Newsletter, 2024-12-14) Dawe, David; Pede, Valerien Olivier; Antonio, Ronald JeremyGood news: the recent developments in the global rice trading environment and improved weather conditions have lowered world market prices. As these factors lead to lower domestic prices, consumers will find it easier to afford a healthy diet. Improved trade World prices are now back to levels last seen before India’s restrictions were imposed in July 2023 (see the latest data point in Figure 1). This shift is largely influenced by the major rice trade policy changes in both the world’s largest exporter (India) and the world’s largest importer (the Philippines) in the past months. Beginning in late September and continuing over the succeeding weeks, India removed nearly all restrictions on rice exports in the face of large domestic stocks and prospects for an excellent forthcoming crop. These restrictions included a ban on non-basmati non-parboiled rice exports (with some exceptions for countries that needed imports for food security), a minimum export price on basmati rice and an export tax on parboiled rice, paddy, and husked rice.Item Low glycemic index rice: a healthier diet for countering diabetes epidemic in Asia(Journal Article, 2024-11-29) Tiozon, Rhowell Jr; Lenaerts, Bert; Kor, Sakshi; Demont, Matty; Fernie, Alisdair; Sreenivasulu, NeseThe prevalence of type 2 diabetes is rising worldwide, particularly in Asia, where rice is a dietary staple. Hence, it is essential to consume low glycemic index (GI) food. Here, we review the potential of low GI and high resistant starch (RS) of rice to mitigate diabetes risk. Progress has been made in lowering the GI of rice without compromising yield and grain quality through marker-assisted breeding techniques. To enhance RS content, mutation breeding and genome editing were used. Deployment of these new varieties in global food systems remains critical through policy initiatives such as ‘Seeds without Borders’ and the widespread deregulation of genome editing plants that can expedite the wider adoption of low-GI and high-RS rice.Item Low glycemic index rice: a healthier diet for countering diabetes epidemic in Asia(Journal Article, 2024-11-29) Tiozon, Rhowell N.; Lenaerts, Bert; Kor, Sakshi; Demont, Matty; Fernie, Alisdair R.; Sreenivasulu, NeseThe prevalence of type 2 diabetes is rising worldwide, particularly in Asia, where rice is a dietary staple. Hence, it is essential to consume low glycemic index (GI) food. Here, we review the potential of low GI and high resistant starch (RS) of rice to mitigate diabetes risk. Progress has been made in lowering the GI of rice without compromising yield and grain quality through marker-assisted breeding techniques. To enhance RS content, mutation breeding and genome editing were used. Deployment of these new varieties in global food systems remains critical through policy initiatives such as ‘Seeds without Borders’ and the widespread deregulation of genome editing plants that can expedite the wider adoption of low-GI and high-RS rice.Item Incorporating iron fortificant in ultrasonicated waxy rice led to its stickier and firmer characteristics(Journal Article, 2024-12-10) Bonto, Aldrin; Camacho, Drexel; Sreenivasulu, NeseIncorporating iron in milled rice is an excellent recommendation for regaining mineral loss during milling and addressing micronutrient deficiency issues. This paper investigated the waxy rice variety iron fortification on sonicated milled grains and the effects of iron on the textural attributes of cooked fortified rice measured by a texture profile analyzer (TPA). Through enhanced absorption, modified rice grain induced by ultrasonic treatment has successfully increased iron uptake by 13.2% compared to non-sonicated waxy rice, with excellent retention of 99.33% after washing and cooking. The textural hardness of fortified sonicated rice significantly decreased (p < 0.01) by 19%, attributed to the microporous formation after the ultrasonic treatment. The rice stickiness increased by 39.5% after ultrasonication, and iron fortification was associated with the enhancement of the leached amylopectin-iron network resulting in a stronger attraction between the fortified rice and the TPA probe. The improved network formation in fortified rice was confirmed in the increased elastic (G') and viscous (G") moduli during temperature ramp and frequency sweep experiments. The observed impacts of micronutrient fortificants on the textural and rheological attributes may be helpful in the development of rice and rice products with enhanced eating quality.Item A field methodology to advance social equity and transformative adaptation to climate change in smallholder communities(Journal Article, 2024-01-01) Petesch, Patti; Fisher, Eleanor; Bullock, Renee; Olivia, Ebenstål AlmeidaGlobal climate policies recognize the urgent need to address the inequitable impacts of climate change on smallholder agricultural communities, but there is limited understanding of how to accomplish this in practice. We contribute to closing this gap through the design of a participatory qualitative methodology intended to nurture locally-led “transformative adaptation pathways” that strengthen social equity and sustainability. Our conceptual framework draws upon theories of social equity and justice rooted in participatory parity—values and norms that encourage people to interact with one another as equals and synergistically nurture recognitional, distributional, representational and intergenerational equities. Recognizing that social equity is enhanced when poor and vulnerable people gain decision-making power that expands their access to resources and opportunities, we question how people understand and experience social equity and its relationship to their capacity to adapt. We also ask how norms about gender, generation, and socio-economic status shape people's understandings and experiences of social equity and adaptation. To address these questions, we illustrate the methodological approach with evidence gathered from pilot tests conducted in smallholder communities of Kenya and Philippines. Our findings show how understandings of fairness provide a basis for learning, eliciting comparative and contextualized findings that can inform community-based adaptation. Overall, we demonstrate that in the face of social processes that typically fuel inequities, participatory tools and learning tactics can serve to empower low-income women and men to identify, contribute to, and monitor actions that nurture their community's progress towards strong and equitable climate adaptation capacity.Item Data-driven strategies to improve nitrogen use efficiency of rice farming in South Asia(Journal Article, 2025) Coggins, Sam; McDonald, Andrew; Silva, Joao Vasco; Urfels, Anton; Nayak, Hari; Sherpa, Sonam Rinchen; Jat, Mangi Lal; Jat, Hanuman Sahay; Krupnik, Timothy J.; Kumar, Virender; Malik, Ram; Sapkota, Tek; Nayak, Amaresh Kumar; Craufurd, Peter Q.Increasing nitrogen use efficiency (NUE) in agricultural production mitigates climate change, limits water pollution and reduces fertilizer subsidy costs. Nevertheless, strategies for increasing NUE without jeopardizing food security are uncertain in globally important cropping systems. Here we analyse a novel dataset of more than 31,000 farmer fields spanning the Terai of Nepal, Bangladesh's floodplains and four major rice-producing regions of India. Results indicate that 55% of rice farmers overuse nitrogen fertilizer, and hence the region could save 18 kg of nitrogen per hectare without compromising rice yield. Disincentivizing this excess nitrogen application presents the most impactful pathway for increasing NUE. Addressing yield constraints unrelated to crop nutrition can also improve NUE, most promisingly through earlier transplanting and improving water management, and this secondary pathway was overlooked in the IPCC's 2022 report on climate change mitigation. Combining nitrogen input reduction with changes to agronomic management could increase rice production in South Asia by 8% while reducing environmental pollution from nitrogen fertilizer, measured as nitrogen surplus, by 36%. Even so, opportunities to improve NUE vary within South Asia, which necessitates sub-regional strategies for sustainable nitrogen management.Item Agri-Food System Governance in Bangladesh’s Coastal Regions: Why the Socio-Ecological Systems Approach Needs to Be Politicized(Journal Article, 2025-01-07) Joshi, Deepa; Schulze, Paul; Amin, Md Nurul; Gallant, Bryce; Aheeyar, Mohamed; Rahman, Mokhlesur; Garrett, James; Sarker, Mou RaniWhile Bangladesh is reported as doing well in food production, there is increasing concern that this essentially deltaic and highly climate-vulnerable country will face steep challenges in food governance and productivity. Anthropogenic drivers shaped by narrow economic goals and sectoral policies have deeply altered Bangladesh’s food systems since the early 1960s and partly led to adverse outcomes. By combining policy and institutional analysis and primary research in Shyamnagar Upazila in Satkhira District in the southern coastal deltas, we revisit two key transi- tions – poldering and commercial shrimp farming – to reveal how diverse economic, social and political factors have shaped the effi ciency, inclusivity and sustainability of agri-food systems. These complex interactions between agri-food systems, the broader ecology and heterogeneity in poverty, gender and other social identities are poorly understood and accounted for in policies and programme interventions. This has resulted in unequal confl icts and contestations around critical resources, which impact most marginalized groups, also because policy incoherence encourages collusion between local elites and local decision-makers for resource appropriation and control. Conceptually, a social-ecological systems (SES) framework would identify these complexities. However, SES approaches tend to be technocratic and overlook the overtly economic framing of natural resources governance, diversity among local communities, and the politics of resource ap- propriation. This gap can be remedied by merging SES thinking with a critical political ecology lens to trace the historical, scalar and deeply intersectional nature of socio-ecological relations.Item Stochastic simulation to optimize rice breeding at IRRI(Journal Article, 2024-11-01) Seck, Fallou; Prakash, Parthiban Thathapalli; Covarrubias-Pazaran, Giovanny; Gueye, Tala; Diédhiou, Ibrahima; Bhosale, Sankalp; Kadaru, Suresh; Bartholomé, JeromeGenetic improvement in rice increased yield potential and improved varieties for farmers over the last decades. However, the demand for rice is growing while its cultivation faces challenges posed by climate change. To address these challenges, rice breeding programs need to adopt efficient breeding strategies to provide a steady increase in the rate of genetic gain for major traits. The International Rice Research Institute (IRRI) breeding program has evolved over time to implement faster and more efficient breeding techniques such as rapid generation advance (RGA) and genomic selection (GS). Simulation experiments support data-driven optimization of the breeding program toward the desired rate of genetic gain for key traits.Item Weak vs strong knowledge spillover effects. Evidence from geographic distribution of innovative startup in Italy(Journal Article, 2024-08-31) Barboza, Gustavo; Pede, ValerienThis paper introduces the concepts of weak and strong knowledge spillover effects within the context of the Knowledge Spillover Theory of Entrepreneurship. In this context, the fundamental idea of our proposition is to provide a comprehensive analysis of the factors and conditions promoting and supporting entrepreneurship development at the regional and provincial level using a unique unbalanced panel database, consisting of 9242 Italian Innovative startups for the period 2008-2018. In general terms, we argue that the evidence from our unbalanced panel dataset indicates that these dynamics are as follows. First, spillover effects deriving from competition are initially strong at the province level, and later decay to weak spillover effects at the regional level. Second, in terms of specialization (intra-industry) spillover effects, they are initially strong at the provincial level, and later become weak at the regional level. Third, spillover effects deriving from diversity (inter-industry) are predominantly strong at the regional level, yet weak at the provincial level of aggregation. At the provincial level, higher levels of competition result in strong knowledge spillover effects leading to higher new firm formation, with weak knowledge spillover effects deriving from specialization. Furthermore, in line with the Knowledge Spillover Theory of Entrepreneurship, the existence of non-homogeneous distribution of opportunities and related knowledge spillover effects create heterogeneity of patterns of new firm formation across different units of geographic aggregation. These results provide evidence of constraint potential for growth that remains a puzzle and challenge for academics and policymakers.Item RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci(Journal Article, 2024-03-12) Shrestha, Anish M. S.; Gonzales, Mark Edward M.; Ong, Phoebe Clare L.; Larmande, Pierre; Lee, Hyun-Sook; Jeung, Ji-Ung; Kohli, Ajay; Chebotarov, Dmytro; Mauleon, Ramil P.; Lee, Jae-Sung; McNally, Kenneth L.Background As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources. Results We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs. Conclusions RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.Item Machine learning approach for high-throughput phenolic antioxidant screening in black Rice germplasm collection based on surface FTIR(Journal Article, 2024-08-02) Herath, Achini; Tiozon, Rhowell Jr.; Kretzschmar, Tobias; Sreenivasulu, Nese; Mahon, Peter; Butardo, VitoPigmented rice contains beneficial phenolic antioxidants but analysing them across germplasm collections is laborious and time-consuming. Here we utilised rapid surface Fourier transform infrared (FTIR) spectroscopy and machine learning algorithms (ML) to predict and classify polyphenolic antioxidants. Total phenolics, flavonoids, anthocyanins, and proanthocyanidins were quantified biochemically from 270 diverse global coloured rice collection and attenuated total reflectance (ATR) FTIR spectra were obtained by scanning whole grain surfaces at 800–4000 cm−1. Five ML classification models were optimised using the biochemical and spectral data which performed predictions with 93.5%–100% accuracy. Random Forest and Support Vector Machine models identified key FTIR peaks linked to flavonols, flavones and anthocyanins as important model predictors. This research successfully established direct and non-destructive surface chemistry spectroscopy of the aleurone layer of pigmented rice integrated with ML models as a viable high-throughput platform to accelerate the analysis and profiling of nutritionally valuable coloured rice varieties.Item Revisiting FR13A for submergence tolerance: beyond the SUB1A gene(Journal Article, 2024-07-12) Hussain, Waseem; Anumalla, Mahender; Ismail, Abdelbagi M.; Walia, Harkamal; Singh, Vikas Kumar; Kohli, Ajay; Bhosale, Sankalp; Bhardwaj, HansRice landrace FR13A is the original donor of the SUB1A gene. FR13A harbors hidden genetic variation that surpasses the submergence tolerance level of SUB1A. Here, we provide an overview of the unique features of FR13A associated with exceptional recovery ability that have been overlooked since the significant discovery of the SUB1 locus. We present a detailed overview of how to underpin the new genes associated with the recovery ability seen in FR13A. Finally, we propose a unique approach to develop rice cultivars that surpass submergence tolerance beyond the SUB1 locus from FR13A.Item Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content(Journal Article, 2024-08-27) Badoni, Saurabh; Pasion-Uy, Erstelle A.; Kor, Sakshi; Kim, Sung-Ryul; Tiozon, Rhowell N.; Misra, Gopal; Buenafe, Reuben James Q.; Labarga, Luster May; Ramos-Castrosanto, Ana Rose; Pratap, Vipin; Slamet-Loedin, Inez; Steimker, Julia von; Alseekh, Saleh; Kohli, Ajay; Khush, Gurudev S.; Sreenivasulu, NeseTo counter the rising incidence of diabetes and to meet the daily protein needs, we created low glycemic index (GI) rice varieties with protein content (PC) surpassing 14%. In the development of recombinant inbred lines using Samba Mahsuri and IR36 amylose extender (IR36ae) as parental lines, we identified quantitative trait loci and genes associated with low GI, high amylose content (AC), and high PC. By integrating genetic techniques with classification models, this comprehensive approach identified candidate genes on chromosome 2 (qGI2.1/qAC2.1 spanning the region from 18.62 Mb to 19.95 Mb), exerting influence on low GI and high amylose. Notably, the phenotypic variant with high value was associated with the recessive allele of the starch branching enzyme 2b (sbeIIb). The genome-edited sbeIIb line confirmed low GI phenotype in milled rice grains. Further, combinations of alleles created by the highly significant SNPs from the targeted associations and epistatically interacting genes showed ultralow GI phenotypes with high amylose and high protein. Metabolomics analysis of rice with varying AC, PC, and GI revealed that the superior lines of high AC and PC, and low GI were preferentially enriched in glycolytic and amino acid metabolisms, whereas the inferior lines of low AC and PC and high GI were enriched with fatty acid metabolism. The high amylose high protein recombinant inbred line (HAHP_101) was enriched in essential amino acids like lysine. Such lines may be highly relevant for food product development to address diabetes and malnutrition.