Genome-wide identification and analyses of ZmAPY genes reveal their roles involved in maize development and abiotic stress responses

Abstract

Apyrase is a class of enzyme that catalyzes the hydrolysis of nucleoside triphosphates/diphosphates (NTP/NDP), which widely involved in regulation of plant growth and stress responses. However, apyrase family genes in maize have not been identified, and their characteristics and functions are largely unknown. In this study, we identified 16 apyrases (named as ZmAPY1-ZmAPY16) in maize genome, and analyzed their phylogenetic relationships, gene structures, chromosomal distribution, upstream regulatory transcription factors and expression patterns. Analysis of the transcriptome database unveiled tissue-specific and abiotic stress-responsive expression of ZmAPY genes in maize. qPCR analysis further confirmed their responsiveness to drought, heat, and cold stresses. Association analyses indicated that variations of ZmAPY5 and ZmAPY16 may regulate maize agronomic traits and drought responses. Our findings shed light on the molecular characteristics and evolutionary history of maize apyrase genes, highlighting their roles in various biological processes and stress responses. This study forms a basis for further exploration of apyrase functions in maize.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01474-9.

Keywords: Abiotic stress response; Apyrase; Association analysis; Maize; Metabolic.

Fig. 1

Phylogenetic analysis, chromosomal distribution and collinearity analysis of ZmAPY genes A Phylogenetic analysis of APYs from Z. mays, A. thaliana and O. sativa. A total number of 16 ZmAPYs from maize, 7 AtAPYs from Arabidopsis and 9 OsAPYs from rice were used to construct the phylogenetic tree. All APY transporter members were classified into four groups. Group I-III and outgroup are distinguished by different colors. B Chromosomal distribution and collinearity analysis of ZmAPY genes. The chromosomal location of each ZmAPY gene was mapped according to the maize genome. The chromosome number is indicated next to each chromosome. The syntenic ZmAPY gene pairs are connected by orange lines

Fig. 2

Exon–intron structure and conserved motifs of ZmAPY gene family A Exon–intron structures of ZmAPY genes. Red boxes represent exons (CDS), black lines represent introns, and blue boxes represent 5’ and 3’UTR regions. 0, 1 and 2: Intron phase, defined as the position of the intron within a codon, as introns are located either between codons (phase 0) or within codons (phase 1 and 2). B Predicted conserved protein domains of ZmAPY proteins. The black lines represent the length of each protein sequence, and the conserved protein kinase domains are depicted with colored boxes. blue boxes represent transmembrane region and yellow boxes represent GDA1_CD39 domain

Fig. 3

Expression analysis of ZmAPY genes in different tissues The genes were labeled on the left and the tissues were displayed at the top of each column. The gene expression values are reported as square root transformations of the fragments per kilo bases per million mapped reads (FPKM). Different colors in map represent FPKM values, as shown in the bar to the right

Fig. 4

Prediction of upstream regulators of APY genes A Upstream regulators of ZmAPYs were predicted by ChIP-seq data of 104 transcription factors and planttfdb software. Orange dots represent ZmAPYs and blue dots represent potential upstream regulators of ZmAPY genes. The red line connects the transcription factors and ZmAPY genes that may have regulatory relationship analyzed by ChIP-seq data, while the blue line connects the transcription factors and ZmAPY genes that may have regulatory relationship predicted by planttfdb software. B Correlation analysis between the expression levels of potential upstream regulators nacttf78, zim36, bzip79, cchh26 and ZmAPYs. The P values were calculated by test of correlation coefficient

Fig. 5

Expression analysis of ZmAPYs under drought, cold, heat stresses A Expression analysis of ZmAPY genes under three different drought degree stresses. B Expression analysis of ZmAPY genes under cold and heat stresses. The genes were labeled on the left and the abiotic stresses were displayed at the top of each column. The FPKM / TPM values of the ZmAPY genes were used to draw a heat map by using HEMI. C qRT-PCR in analyzing the expression of ZmAPYs under drought, cold and heat stress. Statistical significance was determined by Student’s t test: “*”P < 0.05 and “**”P < 0.01

Fig. 6

ZmAPYs was associated with agronomic traits and drought resistance of maize A. Association of SNPs from ZmAPY16 with plant height. chr9_124751424 is most significantly associated with plant height compared with other SNPs. SNPs significant associated with plant height (p < 0.01) were marked in red. B-E Genetic variation of ZmAPY16 (chr9_124751424) regulates plant length (B), ear-height (C), drought resistance (D) and ZmAPY5 expression (E) in maize. F Association of SNPs from ZmAPY5 with day to silking (DTS). Chr1_54070081 is most significantly associated with DTS compared with other SNPs. SNPs significant associated with DTS (p < 0.01) were marked in red. G-I Genetic variation of ZmAPY5 (chr1_54070081) regulates silking period (G), drought resistance (H) and ZmAPY5 expression (I) in maize. Statistical significance was determined by Student’s t test

Fig. 7

Genetic variation in the ZmAPYs regulate the content of drought-induced metabolites A Co-localization analysis of mQTLs with ZmAPY genes. The red lines represent the collinearity relationship of mQTLs under drought stress with ZmAPY genes, while the blue lines represent the collinearity relationship of mQTLs under control conditions with ZmAPY genes. B Genetic variations in the ZmAPY gene region regulate the contents of metabolites induced by drought. Statistical significance was determined by Student’s t test