Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Liu, Peng; Zhang, Yinchao; Zou, Chaoying; Yang, Cong; Pan, Guangtang; Ma, Langlang; Shen, Yaou

doi:10.1186/s12864-021-08286-7

Cited by 23 publications

(15 citation statements)

References 97 publications

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“…While lncRNAs serve as important regulators in several vital biological processes and circRNAs functioned as miRNA sponges, transcriptional and splicing regulators, and moderators of primary gene expression in plants ( Lai et al., 2018 ; Waititu et al., 2020 ). Whole-transcriptome sequencing in plants was used to create the global landscape of these mRNAs in plants, such as maize ( Liu et al., 2022a ) Chinese cabbage ( Shi et al., 2022 ) citrus ( Fu et al., 2019 ).…”

Section: Multi-omics Techniques Accelerate the Genetic Dissection Of ...mentioning

confidence: 99%

Multi-omics revolution to promote plant breeding efficiency

Mahmood

Li²,

Fan³

et al. 2022

Front. Plant Sci.

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Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world’s food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

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Section: Multi-omics Techniques Accelerate the Genetic Dissection Of ...mentioning

confidence: 99%

Multi-omics revolution to promote plant breeding efficiency

Mahmood

Li²,

Fan³

et al. 2022

Front. Plant Sci.

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“…Two maize inbred lines, BML1234 (a salt-sensitive line) and L2010-3 (a salt-tolerant line), were selected from the association panel for the transcriptomic analysis. The transcriptome data of 28 sequencing libraries were composed of the roots under a control and salt treatment conditions at different stages (0, 6, 18, and 36 h) as described in our previous studies [ 65 , 66 ]. The dataset can be downloaded from NGDC under the accession number CRA003872.…”

Section: Methodsmentioning

confidence: 99%

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

Liu

Zhu

Líu

et al. 2022

IJMS

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Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding.

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“…To better understand the function of lncRNAs, clustering lncRNAs with highly correlated expression to protein-coding genes using weighted gene co-expression networks, often referred to as “Guilt-by-Association” (GBA), is gaining traction in both plants and animals ( Langfelder and Horvath 2008 ; Liu et al 2022 ; Nolte et al 2022 ; Waseem et al 2022 ; Zhang et al 2022a ). Given similarities in expression profiles across a complex dataset, genes will group together into modules.…”

Section: Novel Approaches For Inferring Functionmentioning

confidence: 99%

Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

Palos

Railey

et al. 2023

The Plant Cell

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Long non-coding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pre-genomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.

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Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress

Cited by 23 publications

References 97 publications

Multi-omics revolution to promote plant breeding efficiency

Multi-omics revolution to promote plant breeding efficiency

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

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