Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance

Zhang, Xiaojing; Liu, Xuyang; Zhang, Dengfeng; Tang, Huaijun; Sun, Boxing; Li, Chunhui; Hao, Luyang; Liu, Cheng; Li, Yongxiang; Shi, Yunsu; Xie, Xiaoqing; Song, Yifu; Wang, Tianyu; Yu, Li

doi:10.1371/journal.pone.0179477

Cited by 54 publications

(56 citation statements)

References 83 publications

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“…ARFs play key roles in plant growth and development through the regulation of expression of auxin response genes which can include transcription factors (Li et al 2016). They are also thought to contribute to drought tolerance (Feng et al 2015; Zhang et al 2017). In maize shoots, Feng et al (2015) indeed showed that the expression of ZmGH3.8 was induced by auxin and reduced under polyethylene glycol treatment.…”

Section: Discussionmentioning

confidence: 99%

“…In maize shoots, Feng et al (2015) indeed showed that the expression of ZmGH3.8 was induced by auxin and reduced under polyethylene glycol treatment. More recently, Zhang et al (2017) identified 13 ARFs as differentially expressed between a drought tolerant and a drought sensitive maize line under different drought scenarios. The second region is located on chromosome 5 where we identified two transcription factors, a SBP gene (GRMZM2G111136) and a C2C2-CO-like gene (GRMZM2G148772), as candidate genes underlying QTLs for key plant growth and transpiration traits, pQTLs for seven proteins and coQTLs for three modules.…”

Section: Discussionmentioning

confidence: 99%

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A systems genetics approach reveals environment-dependent associations between SNPs, protein co-expression and drought-related traits in maize

Blein-Nicolas¹,

Negro²,

Welcker³

et al. 2019

Preprint

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The evolution of maize yields under drought is of particular concern in the context of climate change and human population growth. To better understand the mechanisms associated with the genetic polymorphisms underlying the variations of traits related to drought tolerance, we used a systems genetics approach integrating high-throughput phenotypic, proteomics and genomics data acquired on 254 maize hybrids grown under two watering conditions. We show that water deficit, even mild, induced a strong proteome remodeling and a reprogramming of the genetic control of the abundance of many proteins. We identify close co-localizations between QTLs and pQTLs, thus highlighting environment-specific pleiotropic loci associated to the co-expression of drought-responsive proteins and to the variations of phenotypic traits. These findings bring several lines of evidence supporting candidate genes at many loci and provide novel insight into the molecular mechanisms of drought tolerance.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A systems genetics approach reveals environment-dependent associations between SNPs, protein co-expression and drought-related traits in maize

Blein-Nicolas¹,

Negro²,

Welcker³

et al. 2019

Preprint

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“…ZmWRKY40 432 (GRMZM2G120320, rank 9) was shown to confer drought resistance when it was 433 overexpressed in A. thaliana (Wang et al, 2018b). ZmXLG3b (GRMZM2G429113, 434 rank 1), encoding a guanine nucleotide-binding protein predicted to be involved in the 435 response to desiccation, was found to be downregulated in the drought-tolerant 436 H082183 line but upregulated in the drought-susceptible maize line Lv28 under 437 severe drought stress versus control conditions (Zhang et al, 2017). Moreover, 438…”

Section: Exploration Of New Maize Genes Predicted To Be Involved In Bmentioning

confidence: 99%

Using single-plant -omics in the field to link maize genes to functions and phenotypes

Cruz

Meyer

Ampe

et al. 2020

Preprint

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13Most of our current knowledge on plant molecular biology is based on experiments in 14 controlled lab environments. Over the years, lab experiments have generated 15 substantial insights in the molecular wiring of plant developmental processes, stress 16 responses and phenotypes. However, translating these insights from the lab to the 17 field is often not straightforward, in part because field growth conditions are very 18 different from lab conditions. Here, we test a new experimental design to unravel the 19 molecular wiring of plants and study gene-phenotype relationships directly in the 20 field. We molecularly profiled a set of individual maize plants of the same inbred 21 background grown in the same field, and used the resulting data to predict the 22 2009; Atkinson and Urwin, 2012; Nelissen et al., 2014; Nelissen et al., 2019). It has 102 been advocated that to close this lab-field gap, more -omics data and associated 103 phenotypic data should be generated on field-grown plants (Alexandersson et al., 104 2014; Nelissen et al., 2019;Zaidem et al., 2019). Several pioneering studies have 105 already investigated how gene expression is related to environmental stimuli in the 106 field (Nagano et al., 2012; Richards et al., 2012; Plessis et al., 2015). Large-scale 107 studies relating field-generated transcriptomes to field phenotypes are however still 108 lacking. 109Here, we propose a new strategy for studying the wiring of plant pathways and traits 110 directly in the field, involving -omics and phenotype profiling of individual plants of the 111 same genetic background grown in the same field. Uncontrolled variations in the 112 micro-environment of the individual plants hereby serve as a perturbation 113 mechanism. Our expectation is that, in addition to stochastic effects, the individual 114 plants will be subject to subtly different sets of environmental cues, and will in 115 response exhibit different molecular profiles and phenotypes. The aim of this study is 116to investigate to what extent we can use such individual plant differences in the field 117 to link genes to biological processes and field phenotypes. Earlier, we found that 118 gene expression variations among individual Arabidopsis thaliana plants grown under 119 the same stringently controlled lab conditions contain a lot of information on the 120 molecular wiring of the plants, on par with traditional expression profiles of pooled 121 plant samples subject to controlled perturbations (Bhosale et al., 2013). If even gene 122 expression variability among lab-grown plants contains functionally relevant 123 information, the molecular and phenotypic variability among field-grown plants may 124 contain a wealth of information on processes occurring in the field. 125We profiled the ear leaf transcriptome, ear leaf metabolome and a number of 126 phenotypes for individual field-grown maize plants of the same inbred line (Zea mays 127 B104), and used the resulting data to predict the function of genes and to 128 quantitatively predict individ...

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“…These findings suggest that altered lncRNAs may be involved in "plant hormone signal transduction" and regulated differently in the two genotypes. The up-regulation of ABF in response to drought stress can trigger stomatal closure and seed dormancy [94]. The down-regulation of ABF in response to re-watering led to weakened ABA signal, which may alleviate rapeseed seedling growth inhibition by ABA.…”

Section: Gibberellin (Ga) Plays An Important Role In All Stages Of Plmentioning

confidence: 99%

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

Tan

et al. 2020

Preprint

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Background: Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs’ response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage. Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA- mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5,175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 TFs corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes. Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs which were co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response. Conclusions: The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

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Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance

Cited by 54 publications

References 83 publications

A systems genetics approach reveals environment-dependent associations between SNPs, protein co-expression and drought-related traits in maize

A systems genetics approach reveals environment-dependent associations between SNPs, protein co-expression and drought-related traits in maize

Using single-plant -omics in the field to link maize genes to functions and phenotypes

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

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