Rice Landraces Research Articles

Investigating Microbial Diversity in the Endosphere and Rhizoplane of Three Aromatic Rice Landraces: Implications for Biological Nitrogen Fixation.

Biological nitrogen fixation (BNF) occurring in the rhizosphere is a sustainable source of nitrogen for plants. BNF in cereal crops can be promoted by inoculation of a single or consortium of associative and endophytic diazotrophs. Creating a successful nitrogen-fixing biofertilizer necessitates the study of the core microbiome of the plant rhizosphere and the functional relationship of the members. This study compares the endosphere and rhizoplane microbial diversity of three aromatic landraces and one high-yielding variety of rice using culture-independent methods. The V3-V4 variable regions of 16S rRNA were used for amplicon sequencing of soil DNA. Patescibacteria, Planctomycetota, and Proteobacteria were the predominant phyla in all four genotypes. Richness (Chao-1 and ACE) and microbial diversity indices (Shannon and Simpson indices) showed that microbial diversity among the genotypes varies subtly at the phylum level. Beta diversity analysis with the phylum identified and comparisons of the microbiome at the genus level revealed a more prominent effect of plant genotype on microbial diversity. Canonical component analysis drew a correlation between microbial diversity in each genotype with the sugar and N content of these landraces. Paraburkholderia was identified as one of the major OTUs among the known nitrogen fixing followed by Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group, Azospirillum, Hebarspirillum, and Azotobacter.

Analysis of inter-varietal hybridization in rice (Oryza sativa L.) indicate transgressive segregation

Traits under continuous stabilizing selection may yield transgressive phenotypes in suitable cross combinations. Farmers maintained Njavara (Oryza sativa L. landrace Njavara), a poor yielding medicinal rice landrace in Kerala state over centuries for medicinal applications using short duration (60-70 days) as a selection criterion. This implies that the heading date together with several of the yield related traits, which are co-controlled by pleiotropism, were under constant stabilizing selection in Njavara. We examined the level of transgression in 13 yield related traits in F2 populations raised from crosses between Njavara and a high yielding hybrid variety Jyothi. The cross yielded transgressive phenotype in all of the 13 traits in F2 populations. Difference in the genetic architecture between Njavara and Jyothi due to the difference in the selection pressure experienced by them may have contributed to the excessive transgression observed in the study. The results highlight the value of unattractive poor yielding land races in providing alleles to lift yield barrier in high yielders, and suggest the need to examine the genetic architecture of the trait of interest in parental lines for better genetic advancement in crop improvement programmes.

Effects of germination and gamma irradiation on physico-chemical and cooking qualities of pigmented red rice landrace: Ahu

The rice quality is influenced by various post-harvest treatments, including germination and gamma irradiation. The study investigates the combined effects of germination and gamma irradiation on the physico-chemical and cooking qualities of Ahu, a red rice landrace. The samples were subjected to germination for 0, 24, 48 and 72 hours and subsequently irradiated with gamma rays at doses of 0, 1, 2, 5 and 10 kGy. Post-treatment, samples were analyzed for proximate and mineral composition. Cooking quality parameters including cooking time, water absorption, and texture were also assessed. At a radiation dose of 2 kGy, both protein and carbohydrate content increased; however, they declined at higher doses. The ash content depicted a reduction with increased doses of radiation. Micronutrient composition remained largely unaffected by the irradiation process. Gamma irradiation also influenced cooking quality: water uptake ratio increased, while the optimum cooking time decreased at higher doses. Additionally, an upsurge of amylose content was demonstrated with increasing radiation levels, resulting in softer cooked rice. Thus, it can be attributed that dual processing of rice can effectively modify starch properties, rendering it a viable method for enhancing the textural and functional qualities.

Divergence and convergence in epiphytic and endophytic phyllosphere bacterial communities of rice landraces.

Phyllosphere-associated microbes can significantly alter host plant fitness, with distinct functions provided by bacteria inhabiting the epiphytic (external surface) vs endophytic niches (internal leaf tissue). Hence, it is important to understand the assembly and stability of these phyllosphere communities, especially in field conditions. Broadly, epiphytic communities should encounter more environmental fluctuations and frequent immigration, whereas endophytic microbiota should face stronger host selection. As a result, we expect greater variability in epiphytic than endophytic communities. We analyzed the structure and stability of leaf phyllosphere microbiota of four traditionally cultivated rice landraces and one commercial variety from northeast India grown in the field for 3 consecutive years, supplemented with opportunistic sampling of eight other landraces. Epiphytic and endophytic bacterial communities shared dominant core genera such as Methylobacterium and Sphingomonas. Consistent with an overall strong environmental effect, both communities varied more across sampling years than across host landraces. Seeds sampled from a focal landrace did not support vertical transmission of phyllosphere bacteria, suggesting that both types of communities are assembled anew each generation. Despite these points of convergence, epiphytic communities had distinct composition and significantly higher microbial load and were more rich, diverse, modular, and unstable than endophytic communities. Finally, focused sampling of one landrace across developmental stages showed that the divergence between the two types of communities arose primarily at the flowering stage. Thus, our results show both convergent and divergent patterns of community assembly and composition in distinct phyllosphere niches in rice, identifying key bacterial genera and host developmental stages that may aid agricultural interventions to increase rice yield.IMPORTANCEPhyllosphere (leaf-associated) microbes significantly impact plant fitness, making it crucial to understand how these communities are assembled and maintained. While many studies have analyzed epiphytic (surface) phyllosphere communities, we have a relatively poor understanding of endophytic communities which colonize the very distinct niche formed inside leaf tissues. We found that across several rice landraces, both communities are largely colonized by the same core genera, indicating divergence at the species level across the two leaf niches and highlighting the need to understand the mechanisms underlying this divergence. Surprisingly, both epiphytic and endophytic communities were only weakly shaped by the host landrace, with a much greater role for environmental factors that likely vary over time. Thus, microbiome-based agricultural interventions for increasing productivity could perhaps be generalized across rice varieties but would need to account for the temporal instability of the microbiota. Our results thus highlight the importance of data sets such as ours-with extensive sampling across landraces and years-for understanding phyllosphere microbiota and their applications in the field.

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 landraces in Nepal

Assessment and characterization of agro-morphological characteristics of rice landraces 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.