Project description:BackgroundAnaerobic germination is a critical trait for rice cultivation, particularly in regions that experience flooding or waterlogging immediately after sowing. Under direct-seeded conditions, where rice is sown directly into the field without prior transplantation, the ability of seeds to germinate in anaerobic (oxygen-deficient) conditions becomes essential for successful crop establishment. This trait is especially relevant in areas prone to waterlogging, were traditional methods of rice cultivation, such as puddled transplanting, may be less viable. Understanding the genetic basis of anaerobic germination can lead to the development of rice varieties that are better adapted to such challenging conditions, thus supporting more sustainable agricultural practices.ResultsIn this study, a nested association mapping (NAM) population consisting of 384 breeding lines was utilized to identify genomic regions associated with anaerobic germination in rice. Through comprehensive analysis, 19 significant marker-trait associations (MTAs) were identified, including 12 associations specifically linked to percent seed germination under anaerobic conditions. These associations were distributed across six different chromosomes: 3, 4, 5, 6, 7, and 9. Notably, a cluster of single nucleotide polymorphisms (SNPs) spanning a 6.9 Mb genomic region on chromosome 3 (from 21,089,181 to 28,017,712 bp) was consistently associated with percent germination at 15 and 21 days after sowing over multiple years. Similarly, a 6.4 Mb genomic segment on chromosome 6 (from 18,028,538 to 24,492,161 bp) was also associated with percent germination at the same time points. Specific SNPs within this region, namely S6_18028538 and S6_24492161, were linked to germination at 15 and 21 days, respectively. In addition to these findings, one MTA was identified for days to 50% flowering on chromosome 1, and six MTAs were identified for grain yield across chromosomes 1, 2, 5, 8, and 10. The breeding lines that exhibited both high and stable yields, along with anaerobic germination traits, have the potential to be particularly valuable in genomics-assisted breeding programs aimed at improving rice varieties for flood-prone areas.ConclusionsThis study provides crucial insights into the genetic basis of anaerobic germination in rice, highlighting specific genomic regions associated with this trait under direct-seeded conditions. The identification of significant MTAs across multiple chromosomes, particularly the consistent associations found on chromosomes 3 and 6, underscores the potential for developing rice varieties with enhanced tolerance to anaerobic conditions. The high-yielding breeding lines identified in this research, which also exhibit strong anaerobic germination traits, represent valuable genetic resources for breeding programs. These findings support the use of direct-seeded rice (DSR) as a sustainable alternative to traditional puddled transplanting, particularly in regions prone to flooding, thereby contributing to the development of more resilient rice cultivation practices.

Project description:The rise of direct-seeded rice cultivation as a suitable alternative to transplanted puddled rice depends on developing genotypes with high seedling emergence under deep sown conditions. Two rice genotypes (IRGC 128442 and PR126) were screened for contrasting seedling emergence and subjected to high-throughput RNA sequencing under varying sowing depths (4 cm and 10 cm) and time intervals (5, 10, and 15 days after sowing). On average, a total of 2702 differentially expressed genes were identified across twelve inter- and intra-genotypic pairwise differential expression analyses, with a false discovery rate ≤ 0.05 and log2 fold change ≥ ± 2. The DEGs specifically showing differential expression under deep-sowing stress were prioritized and further refined based on their corresponding gene ontology terms, gene set enrichment analysis and KEGG and plant reactome pathway. From this pool of DEGs, 24 genes were validated using qRT-PCR. Among these, two genes (LOC_Os04g51460 and LOC_Os02g45450) contribute to cell wall remodelling and membrane stability, while three genes (LOC_Os04g48484, LOC_Os06g04399, and LOC_Os07g15440) play key roles in mitigating abiotic stress. Transcriptional regulators (LOC_Os06g33940 and LOC_Os01g45730) drive stress responses and growth. Notably, high fold changes in LOC_Os03g22720 and LOC_Os07g01960 underscore their importance in early stress responses and metabolic adjustments. The transcriptome analysis also highlighted the role of 29 heat shock proteins in response to deep sowing stress. Differential expression of key components in the abscisic acid (ABA)-mediated signalling pathway such as OsABI5 (LOC_Os01g64000), phosphatase 2C-like (PP2C) (LOC_Os09g15670) and OsPYL (LOC_Os06g36670) indicated downregulation of ABA signalling in the genotype IRGC 128442. Additionally, a role for miRNA-mediated regulation of auxin response factors was hypothesized in seedling emergence regulation. The study brings us closer to understanding the genetic control of seedling emergence under deep sown conditions. Functional validation of the key candidate genes and pathways could provide new targets for genetic improvement, potentially contributing to the development of rice cultivars optimized for direct-seeded rice cultivation.

Project description:Integrated pest management (IPM) is a comprehensive approach to managing diseases, focusing on combining various strategies to reduce pathogen populations effectively and in an environmentally conscious way. We investigated the effects of IPM on beneficial microbial populations and its relationship with pathogen populations in both direct-seeded rice (DSR) and transplanted rice (TR) systems. This study demonstrates that IPM practices have significantly higher populations of beneficial microbes, such as Trichoderma harzianum and Pseudomonas fluorescens, and lower level of the pathogen Fusarium verticillioides compared to non-IPM (farmer practices). The average mean population of T. harzianum was 6.38 × 103 CFU/g in IPM compared to 3.22 × 103 CFU/g in non-IPM during 2019 in TR at Bambawad. P. fluorescens mean population in 2019 was significantly higher in IPM (4.67 × 103 CFU/g) than in non-IPM (3.82 × 103 CFU/g) at the Karnal location in DSR. The F. verticillioides populations were significantly lower in IPM fields (9.46 × 103 CFU/g) compared to non-IPM fields (11.48 × 103 CFU/g) during 2017 at Haridwar in TR. Over three years, a significant increase in the populations of beneficial microbes in IPM plots was observed in all three locations of both TR and DSR, highlighting the sustainable impact of IPM practices. Disease dynamics analysis revealed that IPM effectively managed key diseases in both DSR and TR systems, with significant correlations between microbial density and disease severity. A significant positive correlation was recorded between F. verticillioides population and bakanae incidence at all three locations. Sheath blight incidence was negatively correlated with P. fluorescens population in both TR and DSR. In DSR, bacterial blight and brown spot diseases are reduced with the increased population of T. harzianum. Bioagents T. harzianum and P. fluorescens reduced disease incidence, underscoring the role of beneficial microbes in disease suppression and their importance for sustainable production using IPM practices.

Project description:With the changing climatic conditions and reducing labor-water availability, the potential contribution of aerobic rice varieties and cultivation system to develop a sustainable rice based agri-food system has never been more important than today. Keeping in mind the goal of identifying high-yielding aerobic rice varieties for wider adaptation, a set of aerobic rice breeding lines were developed and evaluated for grain yield, plant height, and days to 50% flowering in 23 experiments conducted across different location in Philippines, India, Bangladesh, Nepal, and Lao-PDR between 2014 and 2017 in both wet and dry seasons. The heritability for grain yield ranged from 0.52 to 0.90. The season-wise two-stage analysis indicated significant genotype x location interaction for yield under aerobic conditions in both wet and dry seasons. The genotype × season × location interaction for yield was non-significant in both seasons indicating that across seasons the genotypes at each location did not show variability in the grain yield performance. Mean grain yield of the studied genotypes across different locations/seasons ranged from 2,085 to 6,433 Kg ha-1. The best-fit model for yield stability with low AIC value (542.6) was AMMI(1) model. The identified stable genotypes; IR 92521-143-2-2-1, IR 97048-10-1-1-3, IR 91326-7-13-1-1, IR 91326-20-2-1-4, and IR 91328-43-6-2-1 may serve as novel breeding material for varietal development under aerobic system of rice cultivation. High yield and stable performance of promising breeding lines may be due to presence of the earlier identified QTLs including grain yield under drought, grain yield under aerobic conditions, nutrient uptake, anaerobic germination, adaptability under direct seeded conditions, and tolerance to biotic stress resistance such as qDTY 2.1 , qDTY 3.1 , qDTY 12.1 , qNR 5.1 , AG 9.1 , qEVV 9.1 , qRHD 1.1 , qRHD 5.1, qRHD 8.1 qEMM 1.1 , qGY 6.1 , BPH3, BPH17, GM4, xa4, Xa21, Pita, and Pita2. The frequency of xa4 gene was highest followed by qAG 9.1, GM4, qDTY 3.1 , qDTY 2.1 , qGY 6.1, and qDTY 12.1.

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Empirical evidence for economic viability of direct seeded rice in peninsular India: An action-based research

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