Genome-wide identification, expression profiles and regulatory network of MAPK cascade gene family in barley

Abstract

Background: Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley.

Results: Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs.

Conclusion: This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.

Keywords: Barley; Gene family; MAPK cascade; Regulatory network.

Fig. 1

List of barley MAPK signalling components

Fig. 2

The subfamily organizations based on phylogenetic relationships (a), intron-exon structure structures (b) and protein structures (c) analysis of MAPK cascade genes in barley

Fig. 3

Phylogenetic analysis of barley MAPK cascade proteins

Fig. 4

Chromosome locations and duplicated genes pairs of MAPK cascade genes in the barley genome. Each barley chromosome is displayed in different color. Duplicated gene pairs are displayed in corresponding color and linked using lines with the same color

Fig. 5

Comparative physical mapping showing the degree of orthologous relationships of MAPK cascade genes with Brachypodium, Sorghum, Maize, Rice, Soybean and Grape

Fig. 6

Hierarchical clustering of expression profiles of barley MAPKKK cascade genes across different stages. CAR15: bracts removed grains at 15DPA; CAR5: bracts removed grains at 5DPA; EMB: embryos dissected from 4d-old germinating grains; EPI: epidermis with 4 weeks old; ETI: etiolated from 10-day old seedling; INF1: young inflorescences with 5 mm; INF2: young inflorescences with 1–1.5 cm; LEA: shoot with the size of 10 cm from the seedlings; LEM: lemma with 6 weeks after anthesis; LOD: lodicule with 6 weeks after anthesis; NOD: developing tillers at six-leaf stage; PAL: 6-week old palea; RAC: rachis with 5 weeks after anthesis; ROO2: root from 4-week old seedlings; ROO: Roots from the seedlings at 10 cm shoot stage; SEN: senescing leaf

Fig. 7

Hierarchical clustering of expression profiles of barley MAPKKK cascade genes under five stressed conditions. a: Drought stress; b: Heat stress; c: Salt stress; d: Zinc and Iron stress

Fig. 8

The co-expression regulatory network of MAPK cascade genes in barley. Box colour: blue, MAPK gene in barley; green, miRNA s found in barley