Chromatin-Level Differences Elucidate Potential Determinants of Contrasting Levels of Cold Sensitivity in Maize Lines

Abstract

Maize is a subtropical, cold-sensitive species. However, some varieties of this species have the potential to withstand long-term low temperatures, even at the seedling stage. The molecular basis of this phenomenon has not been determined. In a chromatin-level study, we compared the cold-stress reaction of seedlings of two maize inbred lines showing contrasting levels of cold sensitivity. The cold-tolerant line was selected based on field data and previous physiological and transcriptomic level studies. The first condition of gene expression—chromatin accessibility—was assessed by formaldehyde-aided isolation of regulatory elements method and DNA sequencing. Potentially expressed genes and cis-regulatory sequences open for interaction with transcription factors have been defined. The results of this study suggest that during cold stress, the tolerant maize line shifted resources from growth to defense. This shift was shown by potential hormone-level events—degradation of growth-promoting gibberellins and synthesis of jasmonic and abscisic acids. This finding is congruent with the xeromorphic morphology of seedlings of the cold-tolerant line and their ability to regrow when stress ceases. It is a common reaction of cold-tolerant maize lines. Moreover, in the cold-tolerant line, several genes from the low-temperature signaling pathways were potentially expressed. Additionally, numerous stress-response AP2/EREBP-binding cis-motifs were accessible in the cold-tolerant line. Differently in the cold-sensitive B73 line, MADS-binding cis-motifs were the most abundant. Development of the photosynthetic apparatus is crucial for the survival of maize seedlings at low temperature. Our results suggest efficient photosynthesis in seedlings of the cold-tolerant line, as was described earlier in physiological-level analyses.

Can we improve the chilling tolerance of maize photosynthesis through breeding?

“…Although several of the photosynthetic and photoprotective responses to chilling have already been used for genetic mapping studies, this is not the case for variation in antioxidant capacity in response to chilling. Candidate genes involved in antioxidant capacity were identified both as a result of mapping variation in chilling tolerance indices ( Huang et al , 2013 ) and by making transcriptomic comparisons between tolerant and sensitive lines ( Sobkowiak et al , 2014 ; Jończyk et al , 2021 ), but their involvement awaits further experimental verification since antioxidant capacity was not directly measured in any of these studies. Following up this work with direct measurements of antioxidant capacity, or with genetic mapping of variation in antioxidant capacity in response to chilling may provide another piece of the puzzle as we move towards a more complete understanding of chilling-tolerant photosynthesis in maize.…”

Multi-omics revolution to promote plant breeding efficiency

“…To illustrate the effect of abiotic stresses on A. thaliana two different techniques, FAIRE-seq and Dnase-seq were used to capture the open chromatin states ( Raxwal et al., 2020 ). Moreover, chromatin accessibility analysis in maize cold tolerant lines during stress has revealed the re-allocation of resources from growth to defense ( Jonczyk et al., 2020 ). To investigate the relationship between chromatin characteristics and gene expression in grapevine, chromatin accessibility was determined using ATAC-seq, Hi-C, and ChIP-seq ( Schwope et al., 2021 ).…”

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

“…To validate the expression of our cold-responsive DEGs, we planted B73 and CIMBL116 maize inbred lines, which have previously been reported as being cold-sensitive andtolerant lines, respectively [25,26]. The seeds from these two maize inbred lines were provided by the Chinese Academy of Agricultural Sciences' crop science institute).…”