Thaumatin-Like Protein (TLP) Gene Family in Barley: Genome-Wide Exploration and Expression Analysis during Germination

Abstract

Thaumatin-like Proteins (TLPs) are known to play a vital role in plant defense, developmental processes and seed germination. We identified 19 TLP genes from the reference genome of barley and 37, 28 and 35 TLP genes from rice, Brachypodium and sorghum genomes, respectively. Comparative phylogenetic analysis classified the TLP family into nine groups. Localized gene duplications with diverse exon/intron structures contributed to the expansion of the TLP gene family in cereals. Most of the barley TLPs were localized on chromosome 5H. The spatiotemporal expression pattern of HvTLP genes indicated their predominant expression in the embryo, developing grains, root and shoot tissues. Differential expression of HvTLP14, HvTLP17 and HvTLP18 in the malting variety (Morex) over 16-96 h of grain germination revealed their possible role in malting. This study provides a description of the TLP gene family in barley and their possible involvement in seed germination and the malting process.

Keywords: barley; cereals; expression analysis; phylogenetics; thaumatin like-proteins.

Figure 1

(A) Number of thaumatin-like protein (TLP) genes in rice, barley, Brachypodium and sorghum. (B) Pipeline for the bioinformatics analysis. MLOC ID: barley gene ID/ transcript; CDD: Conserved Domain Database; BLASTP: protein blasting; TLPs: Thaumatin-like Proteins.

Figure 2

(A) Phylogenetic analysis of TLP protein family among cereals. The TLP domain was identified and the phylogenetic tree was constructed using a neighbor-joining method with 1000 bootstraps. Terminal tree markers are indicative of species (barley, bright green; rice, blue; sorghum, red; Brachypodium, pink). (B) Group wise distribution of cereal TLPs in the phylogenetic tree.

Figure 3

Structural features of barley TLP genes. From left to right is the 5′ to 3′ region containing untranslated region (UTR) in black, with maroon representing exons, blue triangles representing the start codons, red triangles for the stop codons, black narrow lines with slits symbolizing an intron and yellow triangles representing the thaumatin signature.

Figure 4

Spatiotemporal expression of HvTLPs genes in different barley tissues. The color scale bar at the top of heat map represents FPKM (Fragments per kilobase of exon model per million reads mapped) normalized log2-transformed values based on “Morex” RNA-seq data, representing high and low expression, respectively. Embry (EMB), shoot (LEA), inflorescences (INF1, INF2), root (ROO), tillers (NOD) and developing grains (CAR5 and CAR15) tissues were used for expression profiling. Details regarding these tissues are explained in Section 2.

Figure 5

Transcript abundance of HvTLP genes at different stages of seed germination. Gel representation of the expression profiles of HvTLPs (1, 2, 4, 5, 6, 7, 9, 13, 14, 16, 17 and 18) and the housekeeping genes β-actin and GAPDH at 16 h, 48 h and 96 h of germination in malting (MX = Morex) and feed (ST = Steptoe) varieties of barley using RT-PCR. 1.2% agarose gel was used to resolve the amplified bands.

Figure 6

Map locations of HvTLP genes in barley genomes. Exact positions are shown in Table 1.