Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

Abstract

Background Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant growth and development. To date, although the nsLTP gene family of barley (Hordeum vulgare L.) has been preliminarily identified, it is still unclear in the recently completed genome database of barley and Qingke, and its transcriptional profiling under abiotic stress has not been elucidated as well. Results We identified 40 barley nsLTP (HvLTP) genes through a strict screening strategy based on the latest barley genome and 35 Qingke nsLTP (HtLTP) orthologues using blastp, and these LTP genes were divided into four types (1, 2, D and G). At the same time, a comprehensive analysis of the physical and chemical characteristics, homology alignment, conserved motifs, gene structure and evolution of HvLTPs and HtLTPs further supported their similar nsLTP characteristics and classification. The genomic location of HvLTPs and HtLTPs showed that these genes were unevenly distributed, and obvious HvLTP and HtLTP gene clusters were found on the 7 chromosomes including six pairs of tandem repeats and one pair of segment repeats in the barley genome, indicating that these genes may be co-evolutionary and co-regulated. A spatial expression analysis showed that most HvLTPs and HtLTPs had different tissue-specific expression patterns. Moreover, the upstream cis-element analysis of HvLTPs and HtLTPs showed that there were many different stress-related transcriptional regulatory elements, and the expression pattern of HvLTPs and HtLTPs under abiotic stress also indicated that numerous HvLTP and HtLTP genes were related to the abiotic stress response. Taken together, these results may be due to the differences in promoters rather than by genes themselves resulting in different expression patterns under abiotic stress. Conclusion Due to a stringent screening and comprehensive analysis of the nsLTP gene family in barley and Qingke and its expression profile under abiotic stress, this study can be considered a useful source for the future studies of nsLTP genes in either barley or Qingke or for comparisons of different plant species.

Genome-Wide Identification and Expression Analysis of nsLTP Gene Family in Rapeseed (Brassica napus) Reveals Their Critical Roles in Biotic and Abiotic Stress Responses

“…An increasing number of studies have shown that plant nsLTP genes play an important role in the response to biotic and abiotic stresses and in plant growth and development [ 11 , 18 , 21 , 23 , 25 , 28 , 29 , 31 ]. To date, with the availability and feasibility of plant reference genomes, the nsLTP gene family has been identified at the genome-wide level in various plant species, including Arabidopsis, Gossypium , sesame, cotton, wheat, potato, tomato, tobacco, barley, maize, cabbage and Chinese cabbage [ 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 58 , 59 , 60 , 61 ]. In this study, 283, 127, 151 and 106 nsLTP genes were identified in B. napus , B. rapa , B. oleracea and A. thaliana genomes, respectively.…”

The Influence of Biomolecule Composition on Colloidal Beer Structure

“…Studies have shown the uniqueness of the set of genes responsible for the reproduction of LTP protein in cereals [ 45 , 46 ].…”

“…Table 2 shows the total number of nsLTP gene families in the main cereal crops used in the brewing process [ 45 ]. The researchers noted differences between grain crops in the types of genes and the uniqueness of type E for dicotyledons, while barley LTPs are also deficient for types C and X.…”

“…The theoretical isoelectric point (PI) and molecular weight (MW) were analyzed for all the putative LTPs of barley: the average length is 132 aa (91–200 aa), with a molecular weight ranging from 9206.81 to 19,981.15 Da. The average MW LTPs of barley is 13,344 Da with an average theoretical indicator of the isoelectric point pI LTPs of 8.07, which shows the main properties of this protein sequence [ 45 ].…”

BGFD: an integrated multi-omics database of barley gene families

“…The role of the bZIP TF family as related to starch synthesis has been reported [ 26 ]. Many other gene families have been well-documented in barley, such as xyloglucan endotransglucosylase/hydrolases ( XTH s) [ 27 ], non-specific lipid transfer proteins ( nsLTP s) [ 28 ], SQUAMOSA - promoter binding like ( SPL ) [ 29 ], and GRAS (named after the first three identified proteins within this family, GAI, RGA, and SCR) [ 30 ] gene families. However, there is no integrated database with large-scale multi-omics data for barley gene families.…”