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.

Joram Kiriga Waititu,Yinglu Sun,Ying Sun,Quan Cai,Congcong Li,Huan Wang,Jun Liu,Chunyi Zhang

doi:10.3390/genes12101638

Abstract

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.

Highlights

Licensee MDPI, Basel, Switzerland.Maize (Zea mays L.) is the world’s most commonly grown cereal crop, with an estimated global annual production of about 1186.86 million metric tons in 2020/2021 [1].The high dependence on maize for human, animal, and industrial consumption makes it one of the most critical food crops
The tolerant lines maintained a strong vigor with higher survival rates, while the majority of the sensitive line seedlings died and had yellow spots on the leaves
Genes associated with G-protein-coupled receptors (GPCRs), Ca2+ signaling, protein kinases, and reactive oxygen species (ROS) may have played a significant role in rapid sensing and signaling, whereas genes associated with hormones, such as abscisic acid (ABA) and jasmonic acid (JA), may have played a role in signaling and cross-talk between diverse stimuli

Summary

Introduction

Licensee MDPI, Basel, Switzerland.Maize (Zea mays L.) is the world’s most commonly grown cereal crop, with an estimated global annual production of about 1186.86 million metric tons in 2020/2021 [1].The high dependence on maize for human, animal, and industrial consumption makes it one of the most critical food crops. Maize (Zea mays L.) is the world’s most commonly grown cereal crop, with an estimated global annual production of about 1186.86 million metric tons in 2020/2021 [1]. Maize growth and yield are highly dependent on sufficient environmental factors [2]. Weather caused by global warming is projected to increase the incidence of abiotic stresses, such as drought, cold, and freezing during the planting, flowering, and grain-filling stages, in many corn-growing areas [3]. These abiotic stresses typically serve as crucial impediments to maize production and geographical distribution [4] and restrict agricultural yields worldwide

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