RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

Ya, Liu; Zhou, Miaoyi; Gao, Zhaoxu; Ren, Wen; Yang, Fan; He, Hang; Zhao, Jiuran

doi:10.1371/journal.pone.0143128

Cited by 40 publications

(47 citation statements)

References 74 publications

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“…Thus, this is the first investigation revealing the conserved versus non-conserved genetic reprograming in the fungus during the mycorrhizal symbiosis. The non-conserved fungal genes, among others, were related to the auxin hormone pathway, which is known to be involved in the development of arbuscules [36], glutathione-S-transferases that could be involved in heavy metal binding [37] and MAP Kinases which are known to play a role in the response to biotic and abiotic stresses [38, 39]. These results demonstrate that the two AMF strains could have different symbiotic strategies and that these strategies could be modified in presence of a different host plant.…”

Section: Discussionmentioning

confidence: 99%

Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

Mateus¹,

Masclaux

Aletti³

et al. 2018

Preprint

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Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

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Section: Discussionmentioning

confidence: 99%

Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

Mateus¹,

Masclaux

Aletti³

et al. 2018

Preprint

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“…It was functionally annotated using the MapMan annotation and cross-referenced to Affymetrix microarray probes using the publicly available Affymetrix information file Release 35. To this aim, data from Zheng et al (2010) was obtained from GEO and analyzed using ROBINA (Lohse et al, 2012), and RNASeq results from the supplement of Liu et al (2015) were integrated using a custom script.…”

Section: Candidate Genesmentioning

confidence: 99%

Genome-wide analysis of yield in Europe: allelic effects as functions of drought and heat scenarios

et al. 2016

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Assessing the genetic variability of plant performance under heat and drought scenarios can contribute to reduce the negative effects of climate change. We propose here an approach that consisted of (1) clustering time courses of environmental variables simulated by a crop model in current (35 years 3 55 sites) and future conditions into six scenarios of temperature and water deficit as experienced by maize (Zea mays L.) plants; (2) performing 29 field experiments in contrasting conditions across Europe with 244 maize hybrids; (3) assigning individual experiments to scenarios based on environmental conditions as measured in each field experiment; frequencies of temperature scenarios in our experiments corresponded to future heat scenarios (+5°C); (4) analyzing the genetic variation of plant performance for each environmental scenario. Forty-eight quantitative trait loci (QTLs) of yield were identified by association genetics using a multi-environment multi-locus model. Eight and twelve QTLs were associated to tolerances to heat and drought stresses because they were specific to hot and dry scenarios, respectively, with low or even negative allelic effects in favorable scenarios. Twenty-four QTLs improved yield in favorable conditions but showed nonsignificant effects under stress; they were therefore associated with higher sensitivity. Our approach showed a pattern of QTL effects expressed as functions of environmental variables and scenarios, allowing us to suggest hypotheses for mechanisms and candidate genes underlying each QTL. It can be used for assessing the performance of genotypes and the contribution of genomic regions under current and future stress situations and to accelerate breeding for drought-prone environments.With climate changes, crops will be subjected to more frequent episodes of drought and high temperature that may threaten food security (IPCC, 2014). Reducing the impacts of these effects is an urgent priority that (not exclusively) involves the genetic progress of plant performance under heat and drought stresses (Tester and Langridge, 2010;Lobell et al., 2011). Because hundreds of new genotypes of most cereals are commercialized every year, a generic approach is needed to avoid an endless series of experiments assessing the performances of the newly released genotypes. A systematic exploration of the natural genetic diversity used in breeding can provide information usable for large groups of genotypes. This entails the identification, among the thousands of accessions existing in gene banks, of allelic variants exhibiting specific adaptation traits by addressing three questions: (1) Is there a genetic variability for yield and related traits in dry and hot environments? (2) Can this genetic variability be dissected into the effect of genomic regions (quantitative trait loci, QTLs), and (3) have these genomic

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“…Presumably, the expression of targeted genes was under a low level of suppression imposed by miR319 under drought condition. Indeed, one of three genes GRMZM2G115516 was up-regulated >4 times on drought ( Table S11 ) (L iu et al . 2015).…”

Section: Resultsmentioning

confidence: 99%

Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

Zheng

Zeng

et al. 2018

Preprint

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Small RNAs (sRNAs) are short noncoding RNAs that play roles in many biological processes, including drought responses in plants. However, how the expression of sRNAs dynamically changes with the gradual imposition of drought stress in plants is largely unknown. We generated time-series sRNA sequence data from maize seedlings under drought stress and under well-watered conditions at the same time points. Analyses of length, functional annotation, and abundance of 736,372 non-redundant sRNAs from both drought and well-watered data, as well as genome copy number and chromatin modifications at the corresponding genomic regions, revealed distinct patterns of abundance, genome organization, and chromatin modifications for different sRNA classes of sRNAs. The analysis identified 6,646 sRNAs whose regulation was altered in response to drought stress. Among drought-responsive sRNAs, 1,325 showed transient down-regulation by the seventh day, coinciding with visible symptoms of drought stress. The profiles revealed drought-responsive microRNAs, as well as other sRNAs that originated from ribosomal RNAs (rRNAs), splicing small nuclear RNAs, and small nucleolar RNAs (snoRNA). Expression profiles of their sRNA derivers indicated that snoRNAs might play a regulatory role through regulating stability of rRNAs and splicing small nuclear RNAs under drought condition.

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RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize

Cited by 40 publications

References 74 publications

Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

Genome-wide analysis of yield in Europe: allelic effects as functions of drought and heat scenarios

Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

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