Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An’nong 591 under heat stress

Abstract

Background Heterosis is the superior performance of F 1 hybrids relative to their parental lines for a wide range of traits. In this study, expression profiling and heterosis associated genes were analyzed by RNA sequencing (RNA-Seq) in seedlings of the maize hybrid An’nong 591 and its parental lines under control and heat stress conditions. Results Through performing nine pairwise comparisons, the maximum number of differentially expressed genes (DEGs) was detected between the two parental lines, and the minimum number was identified between the F 1 hybrid and the paternal lines under both conditions, which suggested greater genetic contribution of the paternal line to heat stress tolerance. Gene Ontology (GO) enrichment analysis of the 4518 common DEGs indicated that GO terms associated with diverse stress responses and photosynthesis were highly overrepresented in the 76 significant terms of the biological process category. A total of 3970 and 7653 genes exhibited nonadditive expression under control and heat stress, respectively. Among these genes, 2253 (56.8%) genes overlapped, suggesting that nonadditive genes tend to be conserved in expression. In addition, 5400 nonadditive genes were found to be specific for heat stress condition, and further GO analysis indicated that terms associated with stress responses were significantly overrepresented, and 60 genes were assigned to the GO term response to heat. Pathway enrichment analysis indicated that 113 genes were involved in spliceosome metabolic pathways. Nineteen of the 33 overlapping genes assigned to the GO term response to heat showed significantly higher number of alternative splicing (AS) events under heat stress than under control conditions, suggesting that AS of these genes play an important role in response to heat stress. Conclusions This study reveals the transcriptomic divergence of the maize F 1 hybrid and its parental lines under control and heat stress conditions, and provides insight into the underlying molecular mechanisms of heterosis and the response to heat stress in maize. Electronic supplementary material The online version of this article (10.1186/s12870-019-1878-8) contains supplementary material, which is available to authorized users.

Identification and Characterization of Heat-Responsive miRNAs and their Regulatory Network in Maize

“…For example, 3 genes were found to be involved in the spliceosome pathway. Consistent with many studies, our previous study indicated that heat stress can result in a signi cant increase in the number of alternative splicing (AS) events [32], which can be regulated by different plant developmental stages and environmental stress [55,56]. In addition, one gene was targeted by a DEM (zma-miR169i-3p_R + 1_1) with down-regulated expression, and involved in the mitogen-activated protein kinase (MAPK) signaling pathway that has been demonstrated to play important roles in plant growth and development, and stress response [57].…”

“…In our previously study [32], we reported that maize inbred line CM1 exhibits high tolerance to high temperature stress. To identify miRNAs involved in the response to heat stress, six small RNA libraries were constructed from the leaves of maize inbred line CM1 under heat treatment (MH1, MH2 and MH3) and normal conditions (MC1, MC2 and MC3).…”

“…qRT-PCR reactions were performed according to our previous studies [32]. The 5S rRNA was used as internal control for the expression analysis of miRNAs [32,59]. The relative expression level of the miRNAs was calculated by the 2 -ΔΔCT method [60].…”

Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize

“…Most of the methods detecting variation are based on sequencing data derived either from whole-genome sequencing (WGS) or whole-exome sequencing (WES) [ 10 , 11 ]. In the last few years, NGS approaches in the form of RNA-seq have been co-opted to provide global insights into the gene expression patterns to understand the genetic networks and metabolic pathways involved in maize responses to heat stress [ 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. Apart from gene expression analysis, RNA-seq can also be used to identify genomic variants in expressed genes alongside WGS and WES [ 19 ].…”

Enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of cotton (Gossypium hirsutum) hybrid ‘Huaza Mian H318’ as revealed by genome-wide gene expression analysis

“…In past years, many transcriptome studies have provided insights into the molecular basis of heterosis in different species like rice [8,12], Arabidopsis [13,14] and maize [15,16]. In these studies, a vast number of DEGs associated with different biochemical pathways have been found related to heterosis.…”