GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings

Ma, Langlang; Zhang, Minyan; Chen, Jie; Qing, Chunyan; He, Shijiang; Zou, Changying; Yuan, Guangsheng; Yang, Cong; Peng, Hua; Pan, Guangtang; Lübberstedt, Thomas; Shen, Yaou

doi:10.1007/s00122-021-03897-w

Cited by 72 publications

(49 citation statements)

References 67 publications

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“…For example, ZmNC2 ( Na + CONTENT 2 ) and ZmNSA1 ( Na + CONTENT UNDER SALINE‐ALKALINE CONDITION ) were identified to confer the natural variation of shoot Na + in maize by using GWAS (Cao et al, 2020; Zhang et al, 2019). Our previous study also decoded the genetic architecture of Na + and K + content in maize seedlings and found seven SNPs controlling Na + /K + in shoot, root K + content, and K + transport coefficient (Ma et al, 2021). However, few studies have attempted to demonstrate the variations of Ca 2+ concentration in response to salt stress.…”

Section: Discussionmentioning

confidence: 90%

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Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Liang

Qing

Liu

et al. 2021

Physiologia Plantarum

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Soil salinization is an important factor threatening the yield and quality of maize. Ca2+ plays a considerable role in regulating plant growth under salt stress. Herein, we examined the shoot Ca2+ concentrations, root Ca2+ concentrations, and transport coefficients of seedlings in an association panel composed of 305 maize inbred lines under normal and salt conditions. A genome‐wide association study was conducted by using the investigated phenotypes and 46,408 single‐nucleotide polymorphisms of the panel. As a result, 53 significant SNPs were specifically detected under salt treatment, and 544 genes were identified in the linkage disequilibrium regions of these SNPs. According to the expression data of the 544 genes, we carried out a weighted coexpression network analysis. Combining the enrichment analyses and functional annotations, four hub genes (GRMZM2G051032, GRMZM2G004314, GRMZM2G421669, and GRMZM2G123314) were finally determined, which were then used to evaluate the genetic variation effects by gene‐based association analysis. Only GRMZM2G123314, which encodes a pentatricopeptide repeat protein, was significantly associated with Ca2+ transport and the haplotype G‐CT was identified as the superior haplotype. Our study brings novel insights into the genetic and molecular mechanisms of salt stress response and contributes to the development of salt‐tolerant varieties in maize.

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Section: Discussionmentioning

confidence: 90%

“…Our previous study also decoded the genetic architecture of Na + and K + content in maize seedlings and found seven SNPs controlling Na + /K + in shoot, root K + content, and K + transport coefficient (Ma et al, 2021).…”

Section: Candidate Gene Association Analysis Revealed the Potentially...mentioning

confidence: 89%

Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Liang

Qing

Liu

et al. 2021

Physiologia Plantarum

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“…Transcriptome profiling has been widely used to analyze saltinduced gene expression in various plants (Zhu et al, 2019;Zhang et al, 2020;Ma et al, 2021). With the aid of RNA sequencing, significant pathways of differentially expressed genes (DEGs) are identified that would otherwise have been overlooked.…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis Unravels Defense Pathways of Fraxinus velutina Torr Against Salt Stress

et al. 2022

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Fraxinus velutina Torr with high salt tolerance has been widely grown in saline lands in the Yellow River Delta, China. However, the salt-tolerant mechanisms of F. velutina remain largely elusive. Here, we identified two contrasting cutting clones of F. velutina, R7 (salt-tolerant), and S4 (salt-sensitive) by measuring chlorophyll fluorescence characteristics (Fv/Fm ratio) in the excised leaves and physiological indexes in roots or leaves under salt treatment. To further explore the salt resistance mechanisms, we compared the transcriptomes of R7 and S4 from leaf and root tissues exposed to salt stress. The results showed that when the excised leaves of S4 and R7 were, respectively, exposed to 250 mM NaCl for 48 h, Fv/Fm ratio decreased significantly in S4 compared with R7, confirming that R7 is more tolerant to salt stress. Comparative transcriptome analysis showed that salt stress induced the significant upregulation of stress-responsive genes in R7, making important contributions to the high salt tolerance. Specifically, in the R7 leaves, salt stress markedly upregulated key genes involved in plant hormone signaling and mitogen-activated protein kinase signaling pathways; in the R7 roots, salt stress induced the upregulation of main genes involved in proline biosynthesis and starch and sucrose metabolism. In addition, 12 genes encoding antioxidant enzyme peroxidase were all significantly upregulated in both leaves and roots. Collectively, our findings revealed the crucial defense pathways underlying high salt tolerance of R7 through significant upregulation of some key genes involving metabolism and hub signaling pathways, thus providing novel insights into salt-tolerant F. velutina breeding.

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“…Co-expression modules have been used to exhibit the interaction relationships between different function-associated genes [ 38 , 39 ]. In total, 8,577 DETs including 7,835 DE-PCTs and 742 DELs were used for constructing the co-expression modules via WGCNA (Table S9).…”

Section: Resultsmentioning

confidence: 99%

“…Generally, the shoot and root growth was more seriously inhibited under salt treatment in the salt-sensitive line BML1234 compared with the salt-tolerant line L2010-3 [ 28 ]. A total of 178 K single nucleotide polymorphisms (SNPs) existed between the two lines [ 39 ]. In the present study, considerable variations in transcript expression levels were found between BML1234 and L2010-3, which coincided with the large genetic variations between the two lines.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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Background Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance. Results The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF. Conclusions The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.

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GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings

Cited by 72 publications

References 67 publications

Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Comparative Transcriptome Analysis Unravels Defense Pathways of Fraxinus velutina Torr Against Salt Stress

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

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