Dataset Information

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture.

ABSTRACT: The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.

SUBMITTER: Panda S

PROVIDER: S-EPMC8199995 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture.

Panda Siddharth S Majhi Prasanta Kumar PK Anandan Annamalai A Mahender Anumalla A Veludandi Sumanth S Bastia Debendranath D Guttala Suresh Babu SB Singh Shravan Kumar SK Saha Sanjoy S Ali Jauhar J

International journal of molecular sciences 20210604 11

The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to hig ...[more]

PMID: 34199720

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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.

Dataset Information

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture.

Publications

Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture.

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