Leaf transcriptomic response mediated by cold stress in two maize inbred lines with contrasting tolerance levels

Yu, Tao; Zhang, Jianguo; Cao, Jingsheng; Cai, Quan; Li, Xin; Sun, Yan; Li, Sinan; Li, Yunlong; Hu, Guanghui; Cao, Sen; Liu, Changhua; Wang, Gangqing; Wang, Lishan; Duan, Yajuan

doi:10.1016/j.ygeno.2021.01.018

Cited by 27 publications

(24 citation statements)

References 62 publications

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“…To the best of our knowledge, this is among the first studies to profile a broad set of maize inbred lines at the seedling stage with varying levels of resistance to cold stress in the field. Previous research has usually profiled two samples with differing tolerances to specific environmental stress [45]. As a result, our study provides valuable insight into the in-depth characterization of the molecular responses of maize seedlings to cold stress, because, to date, there remains a scarcity of data on the expression patterns of critical genes and pathways across a gradient of various genotypes with varied responses to specific stress conditions.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

Waititu

Cai

Sun

et al. 2021

Genes

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Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C2H2, were strongly altered by cold stress. Moreover, the tolerant lines’ 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines’ 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

Waititu

Cai

Sun

et al. 2021

Genes

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“…In our study, we demonstrated that cold-tolerant maize had higher POD activity than cold-sensitive maize. The maize antioxidant stress pathway is a known important mechanism underlying cold tolerance ( Özlem et al, 2013 ; Zhang et al, 2020 ; Yu et al, 2021 ). Most research on antioxidant enzymes has so far focused on maize catalase, which removes excess H 2 O 2 from mitochondria and protects plants from cold stress ( Prasad, 1997 ).…”

Section: Discussionmentioning

confidence: 99%

Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping

Jin

Zhang

et al. 2021

Front. Plant Sci.

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Maize (Zea mays L.) is a tropical crop, and low temperature has become one of the main abiotic stresses for maize growth and development, affecting many maize growth processes. The main area of maize production in China, Jilin province, often suffers from varying degrees of cold damage in spring, which seriously affects the quality and yield of maize. In the face of global climate change and food security concerns, discovering cold tolerance genes, developing cold tolerance molecular markers, and creating cold-tolerant germplasm have become urgent for improving maize resilience against these conditions and obtaining an increase in overall yield. In this study, whole-genome sequencing and genotyping by sequencing were used to perform genome-wide association analysis (GWAS) and quantitative trait locus (QTL) mapping of the two populations, respectively. Overall, four single-nucleotide polymorphisms (SNPs) and 12 QTLs were found to be significantly associated with cold tolerance. Through joint analysis, an intersection of GWAS and QTL mapping was found on chromosome 3, on which the Zm00001d002729 gene was identified as a potential factor in cold tolerance. We verified the function of this target gene through overexpression, suppression of expression, and genetic transformation into maize. We found that Zm00001d002729 overexpression resulted in better cold tolerance in this crop. The identification of genes associated with cold tolerance contributes to the clarification of the underlying mechanism of this trait in maize and provides a foundation for the adaptation of maize to colder environments in the future, to ensure food security.

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“…Total RNA was extracted using a biospin plant total RNA extraction kit (Bioflux, Beijing, China) according to the manufacturer’s protocols. Libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s, mRNA library construction, and Illumina sequencing was performed as described previously (Yu et al, 2021).…”

Section: Methodsmentioning

confidence: 99%

“…Index of the reference genome (http://www.maizesequence.org/index.html) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (B73 v4) using Hisat2 v2.0.5 (Yu et al, 2021). Differential expression analyses of two conditions/groups (three biological replicates per treatment) were performed using the DESeq2 R package (1.16.1).…”

Section: Methodsmentioning

confidence: 99%

Photosynthesis and antioxidant metabolism modulate the low-temperature resistance of seed germination in maize

Meng

Wen

Zhang

2021

Preprint

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Spring maize is usually subjected to low-temperature stress during seed germination, which retards seedling growth even if under a suitable temperature. However, the mechanism underlying maize seed germination under low-temperature stress modulating seedling growth after being transferred to normal temperature is still ambiguous. In this study, we used two maize inbred lines with different low-temperature resistance (SM and RM) to investigate the mechanism. The results showed that the SM line had higher lipid peroxidation and lower total antioxidant capacity and germination percentage than the RM line under low-temperature stress, which indicated that the SM line was more vulnerable to low-temperature stress. Further transcriptome analysis revealed that seed germination under low-temperature stress caused down-regulation of photosynthesis related gene ontology (GO) terms in two lines. Moreover, the SM line displayed down-regulation of ribosome and superoxide dismutase (SOD) related genes, whereas genes involved in SOD and vitamin B6 were up-regulated in the RM line. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that photosynthesis and antioxidant metabolism related pathways played important roles in seed germination in response to low-temperature stress, and the photosynthetic system displayed a higher damage degree in the SM line. Both qRT-PCR and physiological characteristics experiments showed similar results with transcriptome data. Taken together, we propose a model for maize seed germination in response to low-temperature stress.

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Leaf transcriptomic response mediated by cold stress in two maize inbred lines with contrasting tolerance levels

Cited by 27 publications

References 62 publications

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping

Photosynthesis and antioxidant metabolism modulate the low-temperature resistance of seed germination in maize

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