Enhanced photosynthesis endows seedling growth vigour contributing to the competitive dominance of weedy rice over cultivated rice

Harnessing weedy rice as functional food and source of novel traits for crop improvement

A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.

A. G, Chandran M. A. S, Shankar AK, S. S, Kumar M, Raju BMK, Jyothilakshmi N, Santosh S, Venkatesh G, Sriram K, Sunitha B, G. K P, Bag S, Rao MS, Singh VK. Diversified legume-oilseed cropping system for synergistic enhancement of yield and water use efficiency in rainfed areas of semi-arid tropics

This study explores the development of diversified legume-oilseed cropping systems aimed at enhancing yield and water-use efficiency in rainfed areas of semi-arid tropics. Dryland agriculture, often limited by mono-cropping practices and erratic rainfall, necessitates innovative approaches for crop intensification and sustainability for the future. The integration of legumes and oilseeds into double cropping systems offers a viable solution for optimizing land use and improving productivity under precipitation-limited conditions. The research was conducted at the Gungal Research Farm of ICAR-Central Research Institute for Dryland Agriculture during the 2022-2024 cropping seasons. Six cropping systems, with and without rainwater management, were evaluated. Key findings indicate that rainwater management especially during the flowering and pod filling stage significantly enhanced crop growth, biomass accumulation, and overall yield, with safflower and sesame showing the highest adaptability to moisture stress. In terms of green gram equivalent yield, cowpea-sesame system with rainwater management achieved the highest yields, recording 1655 kg ha-1 in 2022 and 1362 kg ha-1 in 2023, highlighting the critical role of rainwater management in enhancing crop productivity in semi-arid regions. The study identified a diversified legume-oilseed cropping system as a means to achieve sustainable agricultural production in semi-arid regions.

Comparison of leaf anatomical structure and photosynthetic characteristics between weedy rice and cultivated rice at the seedling stage

To explore the internal factors related to the strong growth and competitive ability of weedy rice during the seedling period, we collected two biotypes of Japonica weedy rice from Northeast China, four biotypes of Indica weedy rice from Eastern China and Southern China, and two biotypes of cultivated rice, Zhendao-8 (ZD-8) and Shanyou-63 (SY-63), which were used as controls in a pot experiment. Under homogeneous garden planting conditions, we measured the vascular bundle size (VBS), vascular bundle number (VBN), leaf thickness (LT), air cavity size (ACS), stomatal size (SS), stomatal density (SD), net photosynthetic rate (Pn) and stomatal conductance (Gs) of the weedy and cultivated rice biotypes. A comprehensive analysis was performed to explore the correlation between the seedling leaf structure and the photosynthetic indices of the biotypes. The results showed the following: (1) At the seedling growth stage, the leaf structure parameters of weedy rice were significantly greater than those of ZD-8 and SY-63. (2) The Pn and Gs of weedy rice were significantly positively correlated with VBS, VBN, LT, ACS, and SD. Thus, the leaf structural features of weedy rice provide the anatomical basis for the stronger Pn and establish a strong competitive physiology at the seedling stage. Therefore, the prevention and elimination of weedy rice should start at the seedling stage.

Phenotypic Characteristics and Occurrence Basis of Leaf Necrotic Spots in Response of Weedy Rice to Imazethapyr

Weedy rice is the most challenging weed species to remove in rice production. We found a novel phenotype of seedling leaves which rapidly generates necrotic spots in response to imidazolinone herbicides in weedy rice, but its influencing factors and formation basis are still unknown. In this study, we used the leaf necrotic spot-producing type of weedy rice as the material. First, leaf necrotic spots were defined as physiological and vacuole-mediated cell necrosis by microscopic examination. The imazethapyr concentration was positively correlated with the degree of necrotic spots occurring, while the action site was in accordance with necrosis using herbicide stability tests combined with fluorescence parameters. Furthermore, transcriptome analysis revealed significant differences in the gene expression of endoplasmic reticulum stress and the lipid metabolism membrane structure damage pathway during necrosis, as confirmed by transmission electron microscopy. The light-temperature test also showed that high temperature and intense light could promote the appearance of necrotic spots. These experimental results are helpful in clarifying the process and basis of imazethapyr in inducing the rapid generation of necrotic spots in rice leaves and providing new insight into understanding the mechanism of response to imidazolinone herbicides and the control of weedy rice.

Evaluating the effect of grafting methods and rootstocks through the analysis of chlorophyll a fluorescence

This study evaluated the side-cleft grafting in native species of the genus Piper (Piper aduncum L., Piper hispidum Sw., and Piper tuberculatum Jacq.) with BRS Kottanadan pepper cultivar as rootstocks (Experiment 1). The top-cleft grafting was evaluated in native species Piper arboreum Aubl., P. aduncum, and P. tuberculatum with Balankotta pepper cultivar as graft using black pepper cv. Bragantina (Experiment 2). Black pepper cv. Bragantina autograft was considered as control. The rootstock P. tuberculatum showed initial incompatibility with the cv. Bragantina, with survival of about 34.8% (side) and 62.5% (top) and total inhibition of graft shooting. The side and top graft on P. aduncum resulted in 84.0 and 47.5% of survival, respectively. The JIP-test parameters indicated better photochemical efficiency in the species grafted using the method of side-cleft grafting. Finally, the initial compatibility was associated with greater survival, shooting, and better energy flow through the electron transport chain.

Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance

Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.

Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds

Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.

Structural breakdown and phytotoxic assessments of PE degradation through acid hydrolysis, starch addition and Pseudomonas aeruginosa bioremediation

Vast amounts of plastic waste are causing serious environmental issues and urge to develop of new remediation methods. The aim of the study is to determine the role of inorganic (nitric acid), organic (starch addition), and biological (Pseudomonas aeruginosa) soil amendments on the degradation of Polyethylene (PE) and phytotoxic assessment for the growth of lettuce plant. The PE-degrading bacteria were isolated from the plastic-contaminated soil. The strain was identified as Pseudomonas aeruginosa (OP007126) and showed the highest degradation percentage for PE. PE was pre-treated with nitric acid as well as starch and incubated in the soil, whereas P. aeruginosa was also inoculated in PE-contaminated soils. Different combinations were also tested. FTIR analysis and weight reduction showed that though nitric acid was efficient in degradation, the combined application of starch and bacteria also showed effective degradation of PE. Phytotoxicity was assessed using morphological, physiological, and biochemical parameters of plant. Untreated PE significantly affected plants' physiology, resulting in a 45% reduction in leaf chlorophyll and a 40% reduction in relative water content. It also had adverse effects on the biochemical parameters of lettuce. Bacterial inoculation and starch treatment mitigated the harmful impact of stress and improved plants' growth as well as physiological and biochemical parameters; however, the nitric treatment proved phytotoxic. The observed results revealed that bacteria and starch could be effectively used for the degradation of pre-treated PE.

A non-chemical weed control strategy, introducing duckweed into the paddy field

BACKGROUND

Herbicide resistance in weeds and environmental pollution resulting from excessive application of chemical herbicides keeps increasing. Development of environment-friendly and effective weed management strategies are required for sustainable agricultural production. In this study we investigated the effects of duckweeds (Landoltia punctata (G. Meyer) Les & D. J. Crawford and Spirodela polyrhiza (Linnaeus) Schle iden) introduction on the weed community and rice growth in paddy fields.

RESULTS

The study was conducted in the two rice-growing seasons (2018 and 2019) with three treatments: rice grown without duckweed introduction (CK), with L. punctata introduction (LP), and with S. polyrhiza introduction (SP). On average, LP and SP significantly reduced total weed density by more than 90% and 97%, respectively. Early in the rice-growing season, both duckweed species completely prevented weed growth. Further, both species significantly promoted rice plant growth in the advanced stages. SP significantly improved grain yield of rice by 23%. Light transmittance, temperature of the floodwater and soil, floodwater pH, and dissolved oxygen content significantly decreased following introduction of the duckweeds, indicating that the duckweeds introduction might inhibit weeds growth by altering environmental factors.

CONCLUSION

This study provides a possible environment-friendly way to inhibit weed biomass in the paddy field by introducing duckweeds and interpreted the possible reasons of the impacts of duckweed on environmental variables. Weed control is beneficial for rice growth. Duckweed coverage might be limited in open fields and the associated practice requires additional investigation. © 2022 Society of Chemical Industry.

The Rapid Cytological Process of Grain Determines Early Maturity in Weedy Rice

Shorter grain-filling period and rapid endosperm development endow weedy rice (WR) with early maturity compared to cultivated rice (CR). However, the role of the cytological features and antioxidative enzyme system during grain development are largely unexplored. We selected four biotypes of WR and their associated cultivated rice (ACR) types from different latitudes to conduct a common garden experiment. The difference in the cytological features of endosperm between WR and ACR was compared by chemical staining, and the cell viability and nuclear morphometry of endosperm cells were observed by optical microscopy. Furthermore, antioxidative enzyme activity was measured during grain filling. Anatomic observation of endosperm shows that the development process of endosperm cell in WR was more rapid and earlier than that in ACR. The percentage of degraded nuclei of WR was 2-83% more than that of ACR. Endosperm cells in WR lost viability 2-6 days earlier than those in ACR. The antioxidant enzyme activity of WR was lower than that of ACR during grain filling. The ability of WR to scavenge reactive oxygen species (ROS) was weaker than that of ACR, which may contribute to the rapid cytological process in the endosperm cells of WR. The rapid cytological process and weaker ability to scavenge ROS in endosperm cells may contribute to early maturity in WR.

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

Another choice for measuring tree photosynthesis in vitro

BACKGROUND

In the case of tall trees in the field or in rugged terrain where an instrument cannot be placed operationally, beveling is a popular method used to measure in vitro photosynthesis. However, some studies and our own research have shown that net photosynthesis values measured in vitro are generally significantly lower than values measured in situ.

METHODS

To develop a more accurate and applicable method for in vitro determination of photosynthesis, we evaluated five different methods for preparing detached tree branches to measure photosynthesis and gas exchange in vitro (beveling, cracking, splitting, girdling, and immersion in salicylic acid solution). Ten common tree-species were used.

RESULTS

By comparing light response curves and water-status data, we found that (1) it is possible, to some extent, to substitute in vitro measurement of photosynthetic characteristics of tree species for in situ measurement, provided a suitable treatment is employed; (2) the beveling method is likely to underestimate photosynthetic potential of some trees; (3) after cracking application, most detached branches effectively continued to absorb water; and (4) measurements obtained using detached tree-branches processed by the cracking method were closer to those obtained in situ in intact trees; (5) some tree species (Diospyros kaki, Eriobotrya japonica) appeared to be particularly sensitive to the cracking method, and their in-vitro maximum net photosynthesis rate (P max) was significantly less than the in-situ value (P < 0.05).

DISCUSSION

Our findings provide a methodological support for comprehensive and accurate measurement of plant functional traits. The use of the cracking method contributes to feasibility and reliability of the measurement of photosynthetic parameters in tall trees, thus providing more accurate photosynthetic parameters for the analysis of trade-off strategies at the leaf level.

Contrasting patterns of variation in weedy traits and unique crop features in divergent populations of US weedy rice (Oryza sativa sp.) in Arkansas and California

BACKGROUND

Weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. Weedy rice is a conspecific weed of rice (Oryza sativa) worldwide. We used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct US weedy rice populations persist in rice fields in different locations under contrasting management regimes. Further, we used a representative subset of 15 sequence-tagged site fragments of expressed genes from global Oryza to assess genome-wide sequence variation among populations.

RESULTS

Crop hull color and crop-overlapping maturity dates plus awns, seed (panicle) shattering (> 50%), pigmented pericarp and stature variation (30.2% of total phenotypic variance) characterize genetically less diverse California weedy rice. By contrast, wild-like hull color, seed shattering (> 50%) and stature differences (55.8% of total phenotypic variance) typify genetically diverse weedy rice ecotypes in Arkansas.

CONCLUSION

Recent de-domestication of weedy species - such as in California weedy rice - can involve trait combinations indistinguishable from the crop. This underscores the need for strict seed certification with genetic monitoring and proactive field inspection to prevent proliferation of weedy plant types. In established populations, tillage practice may affect weed diversity and persistence over time. © 2017 Society of Chemical Industry.

Divergent functions of the GAGA-binding transcription factor family in rice

OsGBPs are a small family of four genes in rice (Oryza sativa L.) that function as transcription factors recognizing the GAGA motif; however, their functions in plant growth and development remain unclear. Here we report the functions of OsGBPs in plant growth and grain development. Knock-down and knock-out of OsGBP1 promoted seedling growth and enhanced grain length, whereas overexpression of OsGBP1 exhibited the opposite effect on seedling growth and grain length, indicating that OsGBP1 repressed grain length and seedling growth. In addition, overexpression of OsGBP1 led to delayed flowering time and suppressed plant height. OsGBP1 could regulate OsLFL1 expression through binding to the (GA)₁₂ element of its promoter. In contrast, OsGBP3 induced grain length and plant height. Grain length and plant height were decreased in OsGBP3RNAi lines and were increased in OsGBP3 overexpression lines. We also found a synergistic effect of these two genes on grain width and plant growth. RNAi of both OsGBP1 and OsGBP3 resulted in severe dwarfism, compared with RNAi of a single gene. These results suggest the presence of functional divergence of OsGBPs in the regulation of grain size and plant growth; these results enrich our understanding of the roles of GAGA-binding transcription factors in the regulatory pathways of plant development.

Early flowering and rapid grain filling determine early maturity and escape from harvesting in weedy rice

BACKGROUND

Early maturity is an important trait that is essential to the survival of weedy rice. To explore the mechanism of early maturity in weedy rice, the reproductive development of a large sample of weedy rice accessions and cultivars was compared in a common garden study. A selected sample of both weedy and cultivated rice was sown at different dates in two years to study in more detail their flowering and grain-filling patterns.

RESULTS

The weedy rice from three major cropping regions matured 7-8 days earlier than their associated cultivars. Representative weedy rice accessions planted on conventional sowing dates flowered 3-26 days earlier than cultivars; delayed sowing caused divergence in the flowering regimes in weedy rice. However, regardless of the sowing date, weedy rice filled its grain 7-21 days faster than cultivars in both study years. Vegetative and reproductive traits of weedy and cultivated rice have different patterns of variation with delayed planting.

CONCLUSION

Early maturity is an essential factor determining the persistence of weedy rice by contributing to the escape of its seed from being harvested with the rice crop. Both early flowering and shorter grain-filling stages determine early maturity, and flowering is more plastic than grain filling. © 2017 Society of Chemical Industry.