Aerobic rice genotypes displayed greater adaptation to water-limited cultivation and tolerance to polyethyleneglycol-6000 induced stress

RNA-seq reveals the involvement of key genes for aerobic adaptation in rice

Adaptation of rice to the aerobic condition is needed to cope with the water scarcity as well as to ensure sustainable yield in future. To understand the molecular mechanisms responsible for aerobic adaptation in rice, we performed RNA-seq analysis of root and shoot i.e. developing panicle tissues at panicle initiation stage in two cultivars adapted to aerobic (CR Dhan 202) and traditional transplanted anaerobic (BPT 5204) conditions. The RNA-seq data emanated from 1.65 billion clean reads with approximately 37 million reads per sample. The number of differentially expressed transcripts was higher in the root than that in the shoot under both aerobic and anaerobic conditions. The transcription factors viz. MADS4, MADS5, MADS6, MADS7, MADS15 and transporters involved in sugar (SWEET3A) and nutrient uptake (PHT1;6, MDR-like ABC and vacuolar iron transporter homolog 2) were highly and uniquely expressed in the aerobic adapted cultivar (AAC) CR Dhan 202 under aerobic condition indicating their role in adaptation. The hormones such as ethylene and abscisic acid might be significantly involved in imparting aerobic adaptation. The higher expression of root related genes in the AAC under aerobic conditions suggests the involvement and sensitivity of roots to the water limiting condition. The metabolic activities are also more pronounced in the roots which impart rigorous plant establishment under the aerobic condition. The presence of alternative splice variants in the transcripts viz. Tetratrico peptide repeat (TPR) domain containing protein and GOLDEN2-LIKE1 (GLK1) additionally confirms that post transcriptional regulation is also crucial for aerobic adaptation. The QTLs related to root traits and stress tolerance harboring the uniquely expressed genes, which were identified in the present study can be deployed in molecular breeding programs to develop elite, high yielding aerobic rice cultivars.

Studies on root anatomy, morphology and physiology of rice grown under aerobic and anaerobic conditions

With the changing climate and rainfall abrasions, there is a gradual shift in the system of rice cultivation from traditional transplanted anaerobic to aerobic system. Studies on the root anatomical and morpho-physiological traits provide insights about the adaptation under aerobic conditions. We investigated the root anatomical and morpho-physiological traits in anaerobic (BPT 5204) and aerobic (CR Dhan 202) adapted rice genotypes grown under anaerobic and aerobic conditions. It was observed that the formation of fewer aerenchyma, thickened root and larger xylem area were critical anatomical traits associated with aerobic adaptation as compared to anaerobic conditions. The root length of CR Dhan 202 significantly increased under aerobic condition which may be attributed to its aerobic adaptation in terms of water acquisition. The photosynthetic rate was significantly higher in CR Dhan 202 as compared to that of BPT 5204 under the aerobic condition. The morpho-physiological results showed that the root length, total dry weight and photosynthetic rate are the key parameters for imparting aerobic adaptation. These root anatomical and morpho-physiological traits associated with the adaptation can be used as screening criteria for phenotyping and selection of genotypes suitable for aerobic system of cultivation. Such study is expected to expedite the development of rice aerobic varieties in aerobic breeding programmes.

Superior adaptation of aerobic rice under drought stress in Iran and validation test of linked SSR markers to major QTLs by MLM analysis across two years

Drought is one of the biggest challenges for rice (Oryza sativa L.) production in rainfed areas. Developing "aerobic rice" cultivars could be a valuable alternative to irrigated/rainfed areas. During 2010-2013, 115 rice genotypes, including non-local cultivars and aerobic rice genotypes, were evaluated and 31 rice genotypes were screened, while 21 Iranian lowland rice cultivars (52 genotypes) were investigated under non-stress and drought conditions at the University of Guilan, Rasht, Iran, in 2014 and 2017. The results revealed the superiority of high yielding genotypes, namely Neda (6.202 t ha^- 1), IR82639-B-B-140-1 (6.020 t ha^- 1), and IR82635-B-B-82-2 (5.75 t ha^- 1) under non-stress, Panda (4.512 t ha^- 1), and IR82639-B-B-140-1 (4.08 t ha^- 1), under drought stress conditions. Based on the molecular markers evaluation using identified SSR markers linked to major QTLs different important traits specially drought stress, IR 82639-B-B-140-1 showed the highest genetic distance with high-quality Iranian lowland cultivars, which could be considered as a donor for the development of new cultivars. Moreover, the assignment of rice genotypes based on Jaccard distance clustering was in agreement with the grouping of structure analysis. The validation test using MLM analysis in this natural population revealed the most important significant associations that were identified under drought conditions. These are: the associations between RM306, RM319, RM511, RM28166, and RM11943 with different grain yield (GY)-related traits simultaneously and stable across both years. These markers, which were verified in a natural population across 2 years, could be considered as the potential markers for use in marker-assisted breeding and to improve the grain yield of rice.

Weeds in a Changing Climate: Vulnerabilities, Consequences, and Implications for Future Weed Management

Whilst it is agreed that climate change will impact on the long-term interactions between crops and weeds, the results of this impact are far from clear. We suggest that a thorough understanding of weed dominance and weed interactions, depending on crop and weed ecosystems and crop sequences in the ecosystem, will be the key determining factor for successful weed management. Indeed, we claim that recent changes observed throughout the world within the weed spectrum in different cropping systems which were ostensibly related to climate change, warrant a deeper examination of weed vulnerabilities before a full understanding is reached. For example, the uncontrolled establishment of weeds in crops leads to a mixed population, in terms of C3 and C4 pathways, and this poses a considerable level of complexity for weed management. There is a need to include all possible combinations of crops and weeds while studying the impact of climate change on crop-weed competitive interactions, since, from a weed management perspective, C4 weeds would flourish in the increased temperature scenario and pose serious yield penalties. This is particularly alarming as a majority of the most competitive weeds are C4 plants. Although CO2 is considered as a main contributing factor for climate change, a few Australian studies have also predicted differing responses of weed species due to shifts in rainfall patterns. Reduced water availability, due to recurrent and unforeseen droughts, would alter the competitive balance between crops and some weed species, intensifying the crop-weed competition pressure. Although it is recognized that the weed pressure associated with climate change is a significant threat to crop production, either through increased temperatures, rainfall shift, and elevated CO2 levels, the current knowledge of this effect is very sparse. A few models that have attempted to predict these interactions are discussed in this paper, since these models could play an integral role in developing future management programs for future weed threats. This review has presented a comprehensive discussion of the recent research in this area, and has identified key deficiencies which need further research in crop-weed eco-systems to formulate suitable control measures before the real impacts of climate change set in.