Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars

Moon, Sunok; Chandran, Anil Kumar Nalini; Gho, Yun Shil; Park, Sun A.; Kim, Sung Ryul; Yoo, Yo Han; Jung, Ki‐Hong

doi:10.1016/j.jplph.2017.10.003

Cited by 6 publications

(8 citation statements)

References 111 publications

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“…Recently, we carried out integrated omics analysis of root-preferred genes and identified a OsRNS1 gene showing root-preferred expression patterns in the OsRNS family [40] . To explore the functional roles of OsRNS1 , we first used a gene indexed mutant having T-DNA insertion in the first intron of the gene and analyzed the phenotypes in the homozygous mutant ( osrns1-1; 1A-06714 ).…”

Section: Resultsmentioning

confidence: 99%

“…1 , Fig. 2 ) [40] , [52] . We compared the effect of the root-preferred promoter ( pPer::OsRNS1 ) with that of the ubiquitously expressed promoter ( Ubi1::RNS1 ).…”

Section: Discussionmentioning

confidence: 97%

“…In a previous study, we conducted a genome-wide analysis for root-preferred genes in rice and identified 684 loci with root-preferred expression, which were validated with in silico analysis using meta-expression profiles of both indica and japonica varieties [40] . In this study, loss-of-function mutations of OsRNS1 were confirmed, and one of the root-preferred genes mentioned above was identified, showing defects in root development.…”

Section: Introductionmentioning

confidence: 98%

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Tissue-specific enhancement of OsRNS1 with root-preferred expression is required for the increase of crop yield

Gho

Choi

Moon

et al. 2022

Journal of Advanced Research

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Section: Resultsmentioning

confidence: 99%

“…1 , Fig. 2 ) [40] , [52] . We compared the effect of the root-preferred promoter ( pPer::OsRNS1 ) with that of the ubiquitously expressed promoter ( Ubi1::RNS1 ).…”

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 98%

See 1 more Smart Citation

Tissue-specific enhancement of OsRNS1 with root-preferred expression is required for the increase of crop yield

Gho

Choi

Moon

et al. 2022

Journal of Advanced Research

Self Cite

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“…However, under drought-stress conditions, 8 inside mesodermis-specific, 14 outside mesodermis-specific, and 7 root-preferred genes were found to be upregulated. Besides this, 59 outside mesodermis-specific, 12 inside mesodermis-specific, and 231 whole root-specific transcripts were found to be downregulated [75].…”

Section: Drought Stressmentioning

confidence: 88%

Root System Architecture and Omics Approaches for Belowground Abiotic Stress Tolerance in Plants

2022

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Plant growth and productivity is negatively affected by several abiotic stresses. To overcome the antagonistic effect of a changing environment, plants have evolved several modifications at the physiological as well as molecular levels. Besides being a vital organ for a plant’s nutrient uptake, roots also plays a significant role in abiotic stress regulation. This review provides insight into changing Root System Architecture (RSA) under varying environmental stimuli using high-throughput omics technologies. Several next-generation and high-throughput omics technologies, such as phenomics, genomics, transcriptomics, proteomics, and metabolomics, will help in the analysis of the response of root architectural traits under climatic vagaries and their impact on crop yield. Various phenotypic technologies have been implied for the identification of diverse root traits in the field as well as laboratory conditions, such as root-box pinboards, rhizotrons, shovelomics, ground-penetrating radar, etc. These phenotypic analyses also help in identifying the genetic regulation of root-related traits in different crops. High-throughput genomic as well as transcriptome analysis has led researchers to unravel the role of the root system in response to these environmental cues, even at the single-cell level. Detailed analysis at the protein and metabolite levels can provide a better understanding of the response of roots under different abiotic stresses. These technologies will help in the improvement of crop productivity and development of resistant varieties.

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“…In a study for salinity stress tolerance, quantitative proteome analysis revealed that total of 56 proteins were significantly altered and 16 of them were enriched in the pathways of photosynthesis, antioxidant and oxidative phosphorylation [50]. A study concluded that identification of root hair-preferential genes and in depth analysis of those genes will be a useful reference to accelerate the understanding of root-hair development in rice [68]. Deciphering the underlying miRNAs-based mechanisms for streamlining nutrient uptake and transport would be a giant step towards solving this puzzle [69].…”

Section: Methods Of Developmentmentioning

confidence: 99%

Effect of Climate Change on Rice

Dabi¹,

Khanna²

2018

Agrotechnology

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Climate change has evolved from a subject of future speculation to an inconvenient reality of the present. Given the inseparable link of agriculture with climatic variables, impact of climate change on agriculture and food security has been at the forefront of the research and policy agenda in recent times. Climatic alteration in India is becoming fairly perceptible, and the changes are far more evident than in other parts of the country. As a result of climate change, extreme abiotic factors like high and low temperatures, droughts, salinity, osmotic stress, heavy rains, floods and frost damages are posing serious threats to rice production and also are detrimental for the farmers earning livelihood from rice cultivation. There is a dire need to frame strategies against these stresses, so that in order to cope with such impacts crop improvement will help in finding the sustainable and effective solution against the negative impact of climate change. Advancement in Molecular breeding will help in utilizing the inherent potential of wild species by generating abiotic tolerant lines through introgression. Large screening of tolerance in wild genotypes should be done with the help of molecular markers to identify the underlying QTLs/genes. With the development in the field of bioinformatics, DNA microarrays, mass spectrometry, RNA-Sequencing or other modern high-throughput genomic techniques, it is now feasible to decipher the underlying metabolic pathways through top down approach. The present paper provides an overview of the recent evidences, potential impacts of climate change on rice and also offers its mitigation strategy through crop improvement with special reference to northeast India.

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Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars

Cited by 6 publications

References 111 publications

Tissue-specific enhancement of OsRNS1 with root-preferred expression is required for the increase of crop yield

Tissue-specific enhancement of OsRNS1 with root-preferred expression is required for the increase of crop yield

Root System Architecture and Omics Approaches for Belowground Abiotic Stress Tolerance in Plants

Effect of Climate Change on Rice

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