Rice Landraces Research Articles

Integrative metabolomic and transcriptional regulation insights reveal salt-tolerance in rice landrace ‘Korgut’ (Oryza sativa L.)

Integrative metabolomic and transcriptional regulation insights reveal salt-tolerance in rice landrace ‘Korgut’ (Oryza sativa L.)

Evaluating the performance of traditional paddy (Oryza sativa L.) landraces under floating cultivation techniques in southern Tamil Nadu

Floating rice cultivation, a novel method, is essential for boosting crop yields and resilience amid climate change using flood-prone and water-saturated environments. This approach leverages aquatic resources such as lakes and reservoirs, enhancing agricultural productivity and ecosystem health. This study was conducted in 2023 at the Department of Agronomy, Agricultural College and Research Institute, Madurai to assess the suitability and production potential of cultivating traditional paddy varieties viz., Chinnar and Chithiraikar under floating conditions. Various substrates including soil, coir pith, wooden chips, sugarcane trash, thermocol, leaf compost, and jute bags were levelled out over paddy seeding trays (60 × 30 cm) and placed over bamboo rafts (120 × 120 cm) which served as the float base. Various parameters viz., germination (%), leaf area index (LAI), vigour index, plant population, dry matter production (g/m2), grain yield (kg/ha) and straw yield (kg/ha) were analysed. Results revealed that better crop establishment and crop growth were highly influenced by nursery and conditions with coconut coir outperforming other substrates. However, findings indicated that thermocol substrate is more productive in realizing higher yield attributes and yield (9.83 g/plant, 9.90 g/plant, respectively) of both Chinnar and Chithiraikar landraces of rice. Thus, floating rice cultivation offers a sustainable way to enhance productivity and adaptability, with traditional paddy varieties suitable for soilless media, though further research is needed to optimize its effectiveness.

An experimental approach to farmer valuation of African rice genetic resources

AbstractGenebanks serve as both providers of valuable traits for breeding programs and repositories of diverse crop genetic material representing society's agricultural heritage. In this study, we use a Becker‐DeGroot‐Marschak mechanism to elicit the willingness‐to‐pay of rice farmers in Côte d'Ivoire for small amounts of African rice (Oryza glaberrima) landraces held by the genebank of the Rice Biodiversity Center for Africa, and for seed of newly developed ARICA rice varieties bred using genebank materials. Using a field experiment, we additionally investigate how randomized exposure to and experimentation with small amounts of African rice landrace seed or seed of advanced rice varieties developed by AfricaRice affect how smallholder rice farmers value these novel genetic resources. Surprisingly, we find that farmers generally value having access to African rice landraces at approximately the same level as for advanced rice varieties (and far above market rates for improved seed), and that those farmers who grew landrace seed in the offseason were willing to pay more than those who did not. Our results demonstrate the additional value provided by the conservation of African rice landrace varieties (apart from their use in breeding) and highlight the importance of experimentation in the adoption process.

Response of Nepalese Rice Landraces to Brown Spot [Bipolaris oryzae (Breda de Haan) Shoemaker] at Rampur, Chitwan, Nepal

Brown spot disease, caused by the fungus Bipolaris oryzae, is a common foliar affliction in rice plants, impacting agricultural yields worldwide. A field experiment was conducted to identify brown spot resistant landraces at Rampur, Chitwan during June to November, 2018. A set of 54 rice genotypes comprising of 52 landraces and two checks (resistant and susceptible) were evaluated for resistance to the disease under field condition in alpha lattice design with three replicates. Area under disease progress curve (AUDPC) values varied significantly among the genotypes. Of the tested 54 genotypes, nine genotypes were found moderately resistant, 38 genotypes susceptible and seven genotypes were found highly susceptible. The maximum incidence (64.9%) of pathogen was found in seed of Hodbachhi followed by Sankharika (64.15%). The minimum average incidence of pathogen was found in check Sabitri (4.05%), which was as par with other 28 genotypes. The yield attributing characters were highly significant among the genotypes. Highest grain yield (1.55 t ha-1) was obtained from Ghusara (1.51 t ha-1) followed by Lalbachhi. Lowest grain yield was obtained from Ghuyeni Saro (0.21 t ha-1) followed by Jaguli Mansuli (0.25 t ha-1). All the yield and yield attributing characters were negatively correlated with AUDPC. Seed-borne infection after harvest was highly significant among the genotypes. The results revealed that among the screened genotypes most of the landraces of rice are susceptible to brown spot.

Enhancing Agro Morphological Traits of three Unique Traditional Rice Landraces of Chhattisgarh through Gamma Ray-Irradiation

Mutation breeding is a simple and effective technique for generating genetic variation within crops. Mutagens such as Gamma radiation induce changes in their DNA that could lead to the development of new traits, such as improved yield or disease resistance. In the present study, Gamma ray mutagenesis was performed on three traditional rice varieties (Gudma dhan, Dawar dhan, and Lohandi dhan) to identify potentially beneficial mutants with desirable agro-morphological agricultural characteristics. The major constraints to address were their tall statures and weak culms, fewer panicles and tillers, and late maturity. Using a fixed dose of 300 Gy, 35 mutants were identified in Dawar dhan, 33 in Gudma dhan, and 21 in Lohandi dhan. The selected mutants showed an average reduction in plant height that ranged from 42.69% to 33.11%, as compared to their respective landraces. Also, a substantial reduction (ranging from 3.08%-10.55%) in days to 50% flowering was observed. Importantly, these mutants showed an increase in yield of 38.11% (Dawar dhan), 32.63% (Gudma dhan), and 7.0% (Lohandi dhan). These findings demonstrate the utility of mutation breeding through Gamma radiation in alleviating the key constraints inherent to traditional rice landraces.

Genotype by Environment Interaction Using AMMI, GGE Biplot and Multivariate Analysis of Nepalese Aromatic Rice Landraces

Aromatic group of rice comprises fine, medium, long and extra-long grain that has rich in agro-biodiversity, carries historical and cultural significance in Nepalese society. The objective was to identify stable, high-yielding aromatic rice landraces for Nepal Thirty aromatic rice landraces including two released varieties as standard checks were evaluated at three locations during 2020 and 2021. The experiment was laid out in a Randomized Complete Block Design with three replications. The combined analysis of variance indicated differences among genotypes and genotype-environment interactions for grain yield. The additive main effects and multiplicative interaction (AMMI) analysis revealed that genotypic effects for 69%, genotype × environment interaction effects for 28% and environmental effects accounted for 3% of the total sum of squares. Similarly, GGE biplot analysis showed that the principal components (PC1 and PC2) accounted for 53% and 47% of the GGE sum of squares, respectively. Based on AMMI1, AMMI2 biplots, and GGE biplots, the genotypes Samba Masuli Sub-1 and Sugandhit Dhan-1 were identified as the high yielding and stable fine and aromatic rice landraces. Other promising genotypes are Damari Dhan, Tilki, Hiupuri, Kalo Basmati, Gouriya, and Brahmamusi Dhan. Specifically, Samba Masuli Sub-1 demonstrated the highest grain yield performance at the NRRP, Hardinath, while Sunaulo Sugandha and Balamsari Dhan excelled in the Tarahara and Khajura environments, respectively. In PCA analysis, four PCs showed significant eigen value >1.0 contributing more than 84% of total variance. Biplot analysis reflected that 1000 grain weight, panicle length, heading and maturity days, and grain yield showed greater variation among the landraces. The results provide a robust basis for the further evaluation and verification of this findings in advance stage trials. The superior and outstanding landraces with higher yields and aroma are potential future varieties that can be either use directly as varieties after selection or utilize in future breeding programs for the development of new aromatic rice varieties.

Exploring Distribution and Evolution of Pi-ta Haplotypes in Rice Landraces across Different Rice Cultivation Regions in Yunnan.

Background: Rice blast, caused by Magnaporthe oryzae, seriously damages the yield and quality of rice worldwide. Pi-ta is a durable resistance gene that combats M. oryzae carrying AVR-Pita1. However, the distribution of the Pi-ta gene in rice germplasms in Yunnan Province has been inadequately studied. Methods: We analyzed the potential molecular evolution pattern of Pi-ta alleles by examining the diversity in the coding sequence (CDS) among rice varieties. Results: The results revealed that 95% of 405 rice landraces collected from different ecological regions in Yunnan Province carry Pi-ta alleles. We identified 17 nucleotide variation sites in the CDS regions of the Pi-ta gene across 385 rice landraces. These variations led to the identification of 28 Pi-ta haplotypes, encoding 12 novel variants. Among these, 5 Pi-ta haplotypes (62 rice landraces) carried R alleles. The evolutionary cluster and network of the Pi-ta haplotypes suggested that the Pi-ta S alleles were the ancestral alleles, which could potentially evolve into R variants through base substitution. Conclusions: This study suggests that Pi-ta alleles are diverse in the rice landraces in Yunnan, and the Pi-ta sites resistant to blast evolved from the susceptible plants of the rice landraces. These results provide the basis for breeding resistant varieties.

Assessment and characterization of agro-morphological characteristics of rice land races in Nepal

Assessment and characterization of agro-morphological characteristics of rice land races in Nepal

Toward an Integrated Social-ecological Assessment of a Traditional Upland Rice-based Agroecosystem in Southern Philippines

Located in Southern Philippines, the Sarangani traditional agroecosystem currently sits at the nexus of ecological devastation, bio-cultural erosion, and pervasive modernization. Upland farms in these remote areas are inhabited predominantly by smallholder tribal households who cultivate rice landraces using traditional farming methods. Integrated agroecosystem assessment revealed Sarangani social-ecological system (SES) components, along with connections and feedback loops that underlie their interactions. DPSIR and CCA jointly identified drivers of change in Sarangani SES, revealed its key features, and investigated the whole gamut of issues impacting it. CCA, based on an Ishikawa cause and effect diagram, identified upland poverty, tribal culture and government mismanagement as root causes of intractable problems in the Sarangani SES while DPSIR successfully gauged the suitability of responses instituted by the local government. Study results can thus be used as bases for policy/programs that will resolve problem root causes in the Sarangani SES. In addition, steps must be undertaken to mitigate the effects of climate change which has proven to be utterly devastating in these vulnerable areas. Finally, for traditional agroecosystems like the Sarangani SES, interventions that uphold human well-being while conserving tribal culture/resources and preserving the environment are therefore warranted. Keywords: social-ecological systems, DPSIR, causal chain analysis, Sarangani, traditional agroecosystem

Differential physiological responses to salt stress in rice landraces in Thailand

Soil salinity is a limitation factor for rice cultivation in the north-eastern Thailand. Understanding the mechanisms of salt stress tolerance is critical for maintaining or improving crop yield under salt stress. Over the past ten years, many landrace rice varieties have been examined for genetic diversity. To utilize the richness of natural resources and to explore novel genetic resources for developing a new variety, evaluating local rice varieties for salinity is still needed. This study investigated the physiological and biochemical responses of 8 landrace rice varieties in comparison to ‘Pokkali’, the standard salt-tolerant rice genotype, to clarify the major salt tolerance mechanisms in the landraces found in Thailand. After being exposed to 120 mM NaCl for 7 days, ‘Pokkali’ expressed physiological parameters in response to salt stress which are indicative of salt tolerance ability including low growth reduction, low Na+/K+ ratio, low chlorophyll degradation and low membrane integrity. In contrast, the landrace varieties displayed varying patterns of response. No landrace variety showed an outstanding ion exclusion mechanism as ‘Pokkali’, as evidenced by the fact that all landrace varieties showed approximately two times higher Na+/K+ ratios than ‘Pokkali’. However, it was found that ‘Surin’ had a similar salt stress response to ‘Pokkali’ (low growth reduction, low chlorophyll degradation, low membrane integrity), except for the markedly increased proline and sugar accumulation, suggesting an osmotic adjustment mechanism. Therefore, this variety could be a potential genetic resource to be developed as a donor for the osmotic adjustment trait to improve salt-tolerant rice in the future.

Scouting rice (Oryza sativa L.) landraces for moisture stress tolerance using morphometric diversity analysis

Climate-change is a major threat to sustainable agriculture. Rice is one of the staple food grains that sustain 2/3rd of global population. Therefore, developing climate-resilient rice genotypes to combat moisture stress and other climate change factors are most important to address the challenges posed by climate change. The vast availability of genetic variance among the rice genotypes for different traits favours the selection of desirable donor parents. A field investigation was carried out to characterize 21 traditional rice landraces under induced moisture stress in 2 environments including induced moisture stress (S) and non-stress (NS). The response to the varied level of environments was observed in terms of biometric and yield parameters followed by multivariate analysis and variability analysis. The study revealed higher phenotypic-coefficient of variation (PCV) and genotypic-coefficient of variation (GCV) for plant height and single plant yield in both environments. High heritability was also recorded in the moisture stressed environment for plant height (98.63 %), single plant yield (98.19 %) and productive tillers (95.12 %), whereas under NS, the heritability is more for single plant yield only (99.56 %). The genotypes formed nine clusters under the S environment, based on the Euclidean distance, of which the three CMS lines segregated in cluster III distinctly. The principal component analysis exhibited three principal components with a cumulative variance of 86.13 % and 86.40 % in the NS and S environments respectively. The traits such as days to 50 % flowering, panicle height, panicle length, grains per panicle, productive tillers, thousand-grain weight and single plant yield were the positive contributors. Spikelet fertility (%) and harvest index were positively correlated with seed yield per plant. Path-coefficient analysis was significant for grain yield, harvest index, spikelet fertility, pollen fertility and plant height and positively influenced by productive tillers plant-1. The study concluded the prospect of using Mattaikar, Rajalakshmi, Mallikar and Kuliyadichan as potential donors for developing upland rice with moisture stress resilience.

Comprehensive phenotyping of SKUAST-K released rice varieties reveals significant role of root traits in drought resilience

The North Western Himalayan region, particularly the Kashmir valley, harbors a rich diversity of rice landraces, yet systematic studies on climate resilience are lacking. The present study was aimed at investigating the root traits and their interplay with shoot morphological and physiological traits under drought stress using seven indica and three japonica rice varieties released by SKUAST-Kashmir and their possible role in adaptive capacity to different environments. Significant variability was observed in root and shoot traits across the varieties. Root traits exhibited a wide phenotypic range, including rooting depth, fresh and dry weight, diameter, length, volume, surface area, and length density. Associations between root and shoot traits were identified, with notable correlations such as shoot weight with root shoot ratio, shoot length with root dry weight, diameter, and surface area, and tiller number with various root traits. Additionally, physiological traits like canopy temperature depression showed significant correlations with root depth and surface area. Principal component analysis (PCA) analysis grouped japonica type varieties together with a notable outlier, Chenab, due to its superior root traits among indica varieties. These findings emphasize the substantial contribution of root traits to productivity and advocate for their integration into varietal development processes. In view of the increasing evidences in crop plants about their role of root traits in defining plant productivity and reproductive fitness, study of root traits could provide valuable insights into the patterns of crop adaptation to diverse areas and growing environments.

Rhizobacterial Community Structure Differs Between Landrace and Cultivar of Rice Under Drought Conditions.

The rhizosphere plays a critical role in crop growth and fitness, particularly under moisture-stress conditions. Modern breeding has diminished the ability of crops to recruit beneficial microbiomes, making them more vulnerable to drought, unlike wild types and landraces that adapt better. This study aims to elucidate how rice landrace and cultivar influence the rhizosphere bacterial communities and biochemical attributes under normal and moisture stress conditions. Rhizospheres of rice landrace, Norungan, and high-yielding cultivar, Co51, were assessed using soil biochemical and 16S rRNA gene sequencing approaches. Drought negatively impacted soil carbon pools, enzymes, and respiration in the rhizospheres of both genotypes. However, Norungan's rhizosphere showed less harm than Co51's. During drought, reductions in soil organic carbon (3.94%), microbial biomass carbon (14.26%), labile carbon (1.94%), dehydrogenase (10.1%), urease (21.27%), phosphatase (9.61%), and respiration rate (15.02%) were more pronounced in Co51 than in Norungan. Alpha diversity of rhizosphere bacterial communities was significantly lower than bulk soil, with drought further reducing diversity in both genotypes. Drought decreased the abundance of Firmicutes and Bacteroidetes in Norungan's rhizosphere while it increased the abundance of Acidobacteria, Actinobacteria, Chloroflexi, and Proteobacteria. Conversely, in Co51's rhizosphere, drought enhanced the abundance of Firmicutes and Bacteroidetes while reducing the abundance of Acidobacteria and Proteobacteria. These results suggest that under moisture-stress conditions, the landrace Norungan recruits less-diversified, specific groups of microorganisms to augment the rhizosphere's functioning. This study underscores the need to develop strategies for cultivars and hybrids with enhanced rhizosphere resilience during drought conditions.

Genetic variation and distribution of different blast resistance genes in landrace rice of Thailand

Genetic variation and distribution of different blast resistance genes in landrace rice of Thailand

Extensive immune receptor repertoire diversity in disease-resistant rice landraces

Plants have powerful defense mechanisms and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice (Oryza sativa) is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in southwest China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasizes the value of standing genetic variation that is maintained in farmer landraces as a resource to make modern crops and agroecosystems less prone to disease. The conservation of landraces is, therefore, crucial for ensuring food security in the face of dynamic biotic and abiotic threats.

QTL detection and candidate gene identification of qCTB1 for cold tolerance in the Yunnan plateau landrace rice.

The online version contains supplementary material available at 10.1007/s11032-024-01488-3.

Yield and growth duration of Maroon rice landraces measured in traditional settings

AbstractRice, the most consumed cereal worldwide, has two domesticated species: Asian and African rice. Commercial cultivars, almost all Asian rice, are mostly selected for high yields. Traditional landraces are often selected for different traits, such as time to maturity or resistance against common stress factors, including bird attacks and poor soils. Maroons, descendants of enslaved Africans in Suriname and French Guiana, cultivate a rich diversity of rice landraces. They categorize landraces into short, medium, and long-maturation and maintain that fast-ripening crops with moderate yields facilitated their flight from enslavement, while once settled in a safe place, there was time for landraces with longer ripening periods and higher yields. Previous authors assumed that all Maroon landraces had low yields (700–1000 kg/ha), but their performance in traditional farming systems had never been investigated. We followed the growth and harvest of 28 Maroon rice landraces and two commercial cultivars in Maroon farmer fields, using traditional farming methods, at three locations. We show that, in farmer-managed fields, Maroon rice can yield 2600 kg/ha (average 1665 kg/ha), without any agrochemicals or machinery. Contrastingly, the commercial cultivars in Maroon farmer fields had a low yield (625–1205 kg/ha), partly due to bird predation. The maturation time varied between 110 and 183 days, but the three Maroon maturation categories showed significant overlap. Our study indicates that Maroon rice performance can only be fairly evaluated if measurements are taken in traditional Maroon farming systems, since this is the environment in which these landraces were originally selected.

Biochemical foundation of the aroma and antioxidant activity of Indian traditional rice landrace Maharaji and the effect of radiation-induced mutagenesis on its metabolome

Maharaji rice, an aromatic variety with medium slender grains, is traditionally cultivated in the central regions of India. This study aimed to identify the biochemical compounds responsible for Maharaji rice's distinctive fragrance and enhance its agro-morphological traits through mutation breeding. Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis, forty major metabolites were identified which may be responsible for its characteristic aroma. The bioactive compounds included terpenes, flavonoids, and amino acids. Maharaji brown rice extract exhibited potent radical scavenging activity. Radiation-induced mutation breeding improved the agro-morphological traits and also triggered biochemical diversification in different mutants. Maharaji Mutant-2 exhibited improved aroma due to higher abundance of aromatic compounds, improved yield and morphological characters as compared to the parent. This study, for the first time identifies the compounds associated with the characteristic aroma of Maharaji rice. Global metabolomics may, therefore, expedite the selection of mutants with suitable aroma and desirable biological properties.

Genotype-specificity in putative competitive endophytes modulated by root exudation of rice

The putative competitive endophytic bacteria with plant-growth-promoting attributes could be potential bio inputs to enhance agricultural sustainability. These special rhizosphere colonizing bacteria possess distinct strategies to enter and colonize the host plant asymptomatically and offer several plant growth-promoting benefits. However, the molecular interaction between the endophyte and host plant remains unclear in many crop spheres. In this study, we categorize putative endophytes in rice into two groups—common endophytes and genotype-specific endophytes—based on their ability to colonize alternative hosts. The putative competitive endophytes of rice landrace Norungan and high-yielding cultivar Co51 were cross-inoculated with each other under gnotobiotic conditions and attempted to re-isolate from the inoculated plants. Two Norungan endophytes (Priestia endophytica NE14 and NE21) and one Co51-endophyte (Peribacillus endoradicis CE10) could not colonize the internal tissues of the alternate hosts, and they were considered as genotype-specific endophytes. In contrast, the rest of the strains could colonize both genotypes (common endophytes). The bait trap assay with flow cytometry revealed that the Norungan root exudate significantly enhanced the chemotactic movement of NE14 and NE21 compared to Co51-endophyte (CE10) and common endophytes (NE09 and CE07). Likewise, the Co51-root exudate triggered high levels of chemotaxis of CE10 but not the others. The root exudates did not alter the growth and biofilm-producing capability of genotype-specific and common endophytes. The cell wall degrading enzyme, pectinase of genotype-specific endophytes (NE14 and NE21), had positively enhanced due to Norungan root exudate but not with Co51 exudate. When the genotype-specific endophytes were inoculated to alternate host, a strain-level difference was observed in the induction of rice defense enzymes. NE14 inoculation in Co51 rice had high levels of peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, and glutathione reductase; NE21 induced high levels of glutathione reductase and peroxidase alone in Co51. Likewise, CE10 triggered relatively high levels of catalase, glutathione reductase, peroxidase, and polyphenol oxidase in Norungan rice. No apparent difference between the two rice genotypes in defense enzymes’ levels was observed due to common endophytes (NE09 and CE07). These results authenticate the occurrence of genotype-specific putative competitive endophytes in rice, and exploring them for crop growth and yield would be a better choice for rice sustainability.

Effect of pigmentation on physical, phytochemical and antioxidant properties of traditional rice landraces from Odisha region (India)

Effect of pigmentation on physical, phytochemical and antioxidant properties of traditional rice landraces from Odisha region (India)