Optimizing Sowing and Flooding Depth for Anaerobic Germination-Tolerant Genotypes to Enhance Crop Establishment, Early Growth, and Weed Management in Dry-Seeded Rice (Oryza sativa L.)

Genome-Wide Association Study of Early Vigour-Related Traits for a Rice (Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions

Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.

Screening of potential donors for anaerobic stress tolerance during germination in rice

The rising cost of transplanting rice has made direct seeding an affordable alternative for rice establishment, particularly in Africa. However, direct seeding, while cost-effective, faces crop establishment challenges due to flooding. Uncontrolled water, driven by erratic rains in low-lying areas or uneven fields, limit germination. Rice possesses the unique ability of anaerobic germination, enabling it to sprout and emerge in oxygen-deprived conditions. Understanding rice's response to anaerobic stress during germination is crucial for resilience breeding. Africa, although relying on direct seeding, has made limited progress in addressing flooding during germination compared to Asia. Anaerobic stress tolerance ensures successful crop emergence even in oxygen-limited environments and can help suppress weeds, a significant challenge in direct-seeded rice cultivation. This study aims to contribute by screening for potential rice donors exhibiting anaerobic stress tolerance. We screened 200 rice genotypes at Sokoine University of Agriculture (SUA) in Morogoro, Tanzania, primarily focusing on landraces with untapped potential. Using an alpha lattice design, we conducted two anaerobic experiments in September and October 2022, adding 7 cm of standing water immediately after dry seeding for flooded and maintaining a 2 cm water level after germination in the control for duration of 21 days. We identified potential donors based on selection index computed from genomic estimated breeding values (GEBVs) using eight variables: germination at 14 DAS, germination at 21 DAS, seedling height at 14 DAS, seedling height at 21 DAS, shoot dry matter at 21 DAS, root dry matter at 21 DAS, culm diameter at 21 DAS, and root length at 21DAS. Ten genotypes emerged as the most promising, exhibiting at least 70% germination in floodwater at 21 DAS and greater selection indices. These genotypes were like: Afaa Mwanza 1/159, Rojomena 271/10, Kubwa Jinga, Wahiwahi, Magongo ya Wayungu, Mpaka wa Bibi, Mwangaza, Tarabinzona, IB126-Bug 2013A, and Kanamalia with respective percentages of 75, 74, 71, 86, 75, 80, 71, 80, 70, and 73. These findings contribute to global efforts to mitigate the impacts of flooding during germination. These donors, will be potential to enrich the gene pool for anaerobic germination, providing valuable resources for breeding for flooding tolerance.

Medium-Term Effects of Sprinkler Irrigation Combined with a Single Compost Application on Water and Rice Productivity and Food Safety

Traditional rice (Oryza sativa L.) management (tillage and flooding) is unsustainable due to soil degradation and the large amount of irrigation water used, an issue which is exacerbated in the Mediterranean region. Therefore, there is a need to explore rice management strategies in order to improve water-use efficiency and ensure its sustainability. Thus, field experiments were conducted to determine the medium-term effects of different irrigation and tillage methods combined with a single compost application on water and rice productivity, as well as food safety in a semiarid Mediterranean region. The management systems evaluated were: sprinkler irrigation in combination with no-tillage (SNT), sprinkler irrigation in combination with conventional tillage (ST), which were implemented in 2015, and flooding irrigation in combination with conventional tillage (FT), and their homologues (SNT-C, ST-C, and FT-C) with single compost application in 2015. In reference to rice grain yield, the highest values were observed under ST treatment with 10 307 and 11 625 kg ha^-1 in 2018 and 2019 respectively; whereas between FT and SNT there were no significant differences, with 8 140 kg ha^-1 as mean value through the study. Nevertheless, sprinkler irrigation allowed saving 55% of the total amount of water applied in reference to flooding irrigation. Furthermore, the highest arsenic concentration in grains was found under FT but it decreased with compost application (FT-C) and especially with sprinkler irrigation, regardless of tillage management systems. However, sprinkler irrigation favors the cadmium uptake by plants, although this process was reduced under SNT in reference to ST, and especially under amended compost treatments. Therefore, our results suggested that a combination of sprinkler irrigation and compost application, regardless of the tillage system, could be an excellent strategy for rice management for the Mediterranean environment in terms of water and crop productivity as well as food safety.

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice

The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

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.

Seed priming with selenium: Effects on germination, seedling growth, biochemical attributes, and grain yield in rice growing under flooding conditions

Prevalent irregular rainfall, flooding for weed control, and unleveled fields in the middle and lower reaches of the Yangtze River all contribute to flooding stress on germination and growth of direct-seeded rice (Oryza sativa L.). Herein, some experiments were conducted so as to assess the effects of seed priming with selenium (Se) on the germination and growth of rice under hypoxia. The experiment was arranged in a completely randomized factorial design with two factors and five replicates. Factors included Se concentration (0, 30, and 60 μmol/L) and duration of flooding stress (0, 2, 4, and 8 days). The experimental results showed that Se accelerated seed germination and increased emergence index and final emergence percentage. Additionally, Se increased shoot and root lengths and dry weights, but high Se concentration (60 μmol/L) reduced 18-day-old seedling dry weight under long-term flooding (8 days). Furthermore, Se reduced malondialdehyde content and increased starch hydrolysis efficiency in seeds, superoxide dismutase, peroxidase, catalase, and glutathione peroxidase activities and seedling soluble protein and total chlorophyll contents. Se improved seedling total Se and organic Se contents while increasing total dry weight and yield. Notably, the highest yield was obtained after a 4-day flooding period. Although Se priming favored rice seedling emergence and growth under flooding conditions, Se concentrations equal or above 60 μmol/L increased the risk of seedling death during long-term flooding (≥8 days).

Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice

Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms.

Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice

Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.

Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F_2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R² values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice

Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.

Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater

Crops with resilience to multiple climatic stresses are essential for increased yield stability. Here, we evaluate the interaction between two loci associated with flooding survival in rice (Oryza sativa L.). ANAEROBIC GERMINATION 1 (AG1), encoding trehalose 6-phosphate phosphatase 7 (TPP7), promotes mobilization of endosperm reserves to enhance the elongation of a hollow coleoptile in seeds that are seeded directly into shallow paddies. SUBMERGENCE 1 (SUB1), encoding the ethylene-responsive transcription factor SUB1A-1, confers tolerance to complete submergence by dampening carbohydrate catabolism, to enhance recovery upon desubmergence. Interactions between AG1/TPP7 and SUB1/SUB1A-1 were investigated under three flooding scenarios using four near-isogenic lines by surveying growth and survival. Pyramiding of the two loci does not negatively affect anaerobic germination or vegetative-stage submergence tolerance. However, the pyramided AG1 SUB1 genotype displays reduced survival when seeds are planted underwater and maintained under submergence for 16 d. To better understand the roles of TPP7 and SUB1A-1 and their interaction, temporal changes in carbohydrates and shoot transcriptomes were monitored in the four genotypes varying at the two loci at four developmental timeponts, from day 2 after seeding through day 14 of complete submergence. TPP7 enhances early coleoptile elongation, whereas SUB1A-1 promotes precocious photoautotrophy and then restricts underwater elongation. By contrast, pyramiding of the AG1 and SUB1 slows elongation growth, the transition to photoautotrophy, and survival. mRNA-sequencing highlights time-dependent and genotype-specific regulation of mRNAs associated with DNA repair, cell cycle, chromatin modification, plastid biogenesis, carbohydrate catabolism and transport, elongation growth, and other processes. These results suggest that interactions between AG1/TPP7 and SUB1/SUB1A-1 could impact seedling establishment if paddy depth is not effectively managed after direct seeding.