Genome-wide identification of sucrose non-fermenting-1-related protein kinase genes in maize and their responses to abiotic stresses

Abstract

IntroductionProtein kinases play an important role in plants in response to environmental changes through signal transduction. As a large family of protein kinases, sucrose non-fermenting-1 (SNF1)-related kinases (SnRKs) were found and functionally verified in many plants. Nevertheless, little is known about the SnRK family of Zea mays.MethodsEvolutionary relationships, chromosome locations, gene structures, conserved motifs, and cis-elements in promoter regions were systematically analyzed. Besides, tissue-specific and stress-induced expression patterns of ZmSnRKs were determined. Finally, functional regulatory networks between ZmSnRKs and other proteins or miRNAs were constructed.Results and DiscussionIn total, 60 SnRK genes located on 10 chromosomes were discovered in maize. ZmSnRKs were classified into three subfamilies (ZmSnRK1, ZmSnRK2, and ZmSnRK3), consisting of 4, 14, and 42 genes, respectively. Gene structure analysis showed that 33 of the 42 ZmSnRK3 genes contained only one exon. Most ZmSnRK genes contained at least one ABRE, MBS, and LTR cis-element and a few ZmSnRK genes had AuxRR-core, P-box, MBSI, and SARE ciselements in their promoter regions. The Ka:Ks ratio of 22 paralogous ZmSnRK gene pairs revealed that the ZmSnRK gene family had experienced a purifying selection. Meanwhile, we analyzed the expression profiles of ZmSnRKs, and they exhibited significant differences in various tissues and abiotic stresses. In addition, A total of eight ZmPP2Cs, which can interact with ZmSnRK proteins, and 46 miRNAs, which can target 24 ZmSnRKs, were identified. Generally, these results provide valuable information for further function verification of ZmSnRKs, and improve our understanding of the role of ZmSnRKs in the climate resilience of maize.

Mining genic resources regulating nitrogen‐use efficiency based on integrative biological analyses and their breeding applications in maize and other crops

“…We found that ZmCKX1 0 ( Zm00001eb040280 ) encoding cytokinin dehydrogenase and an auxin‐responsive gene, ZmIAA20 ( Zm00001eb213730 ) were located in 195–213.2 Mb and 4.4–39.3 Mb hotspots on chromosomes 1 and 5, respectively (Figure 3e; Table S9). Besides, ZmCIPK44 ( Zm00001eb163480 ) was reported to respond to abiotic stresses via an ABA‐dependent pathway (Feng et al., 2022). Therefore, these phytohormones‐related genes may play important roles in response to N stress.…”

“…Besides, ZmCIPK44 (Zm00001eb163480) was reported to respond to abiotic stresses via an ABA-dependent pathway (Feng et al, 2022). Therefore, these phytohormones-related genes may play important roles in response to N stress.…”

Genome-wide diversity in lowland and highland maize landraces from southern South America: population genetics insights to assist conservation

“…The second gene, Zm00001d015765, is an ortholog of Arabidopsis AtSWC4, which suppresses the expression of FT (florigen) and accelerates flowering time when knocked down (Gómez-Zambrano et al, 2018). Additionally, three outlier SNPs were found within genes whose expression is modified under stress conditions (Supplementary table 8A): the gene Zm00001d020497, identified as cipk28 (calcineurin B-like-interacting protein kinase28), has been observed to exhibit responses to both salt and drought stresses (Chen et al, 2013; Feng et al, 2022). Similarly, Zm00001d047587 encodes a glucose-6-phosphate dehydrogenase (G6PDH3) and has demonstrated induction under osmotic and cold stress (Li et al, 2023).…”