RiceRelativesGD: a genomic database of rice relatives for rice research

Mao, Limin; Chen, Meihong; Chu, Qinjie; Lu, Jia; Sultana, Most. Humaira; Wu, Dongya; Kong, Xiang-Dong; Qiu, Jie; Ye, Chu-Yu; Zhu, Qian‐Hao; Chen, Xi

doi:10.1093/database/baz110

Cited by 13 publications

(8 citation statements)

References 48 publications

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“…The perennial Z. latifolia and annual Z. palustris are used for the commercial production of Chinese and northern wild rice, respectively 2 . Owing to long-term adaptation to environmental changes and resistance to abiotic and biotic stresses, genetic variation and useful gene resources of wild relatives of rice (e.g., Z. latifolia ) have formed and accumulated during evolution 16 . Notably, Z. latifolia has several excellent traits not found in rice, including high protein content, high biomass productivity, deep-water tolerance, and blast resistance 1 , 3 , 17 .…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Ning

Yang

et al. 2022

Commun Biol

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Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7–31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

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Section: Introductionmentioning

confidence: 99%

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Ning

Yang

et al. 2022

Commun Biol

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“…While transcripts involved in wax and terpenoid metabolism were upregulated in Pokkali, transcripts encoding thioredoxin and those related in phenylpropanoid metabolism were upregulated Two rice cultivars, IR36 (salt-sensitive) and Weiguo (salt tolerant), were used for QTL discovery. This resulted in the identification of qRSL7, which have related to relative shoot length (RSL) and situated on chromosome 7 (Li et al, 2018;Mao et al, 2019;Lei et al, 2020). After 36 hours of salt exposure at the budburst stage, RNA sequencing for IR36 and Weiguo identified five differentially upregulated genes in this potential area.…”

Section: Rice Rna-seq For Abiotic Stressrelated Gene Identificationmentioning

confidence: 99%

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

Ahmad

2022

Front. Plant Sci.

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More over half of the world’s population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review

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“…Among the cereals, genome databases are available for rice and maize. Four other data genome databases are available for rice such as Rice Genome Annotation Project (RGAP) ( (accessed on 25 January 2022)), International Rice Informatics Consortium (IRRI) ( (accessed on 2 February 2022)), O. sativa genome database (OsGDB) ( (accessed on 12 February 2022)) and Rice RelativesGD ( (accessed on 17 February 2022)) [ 95 , 96 , 97 ]. All these databases contain annotated genomes of rice, and molecular resources (cDNA full length, gene, EST, markers, and expression data).…”

Section: Functional Genomic Approaches To Identify Stress-responsive ...mentioning

confidence: 99%

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

Rakkammal

Priya

Subramanian

et al. 2022

Plants

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Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

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RiceRelativesGD: a genomic database of rice relatives for rice research

Cited by 13 publications

References 48 publications

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

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