The barley DIR gene family: An expanded gene family that is involved in stress responses

Abstract

Gene family expansion plays a central role in adaptive divergence and, ultimately, speciation is influenced by phenotypic diversity in different environments. Barley (Hordeum vulgare) is the fourth most important cereal crop in the world and is used for brewing purposes, animal feed, and human food. Systematic characterization of expanded gene families is instrumental in the research of the evolutionary history of barley and understanding of the molecular function of their gene products. A total of 31,750 conserved orthologous groups (OGs) were identified using eight genomes/subgenomes, of which 1,113 and 6,739 were rapidly expanded and contracted OGs in barley, respectively. Five expanded OGs containing 20 barley dirigent genes (HvDIRs) were identified. HvDIRs from the same OG were phylogenetically clustered with similar gene structure and domain organization. In particular, 7 and 5 HvDIRs from OG0000960 and OG0001516, respectively, contributed greatly to the expansion of the DIR-c subfamily. Tandem duplication was the driving force for the expansion of the barley DIR gene family. Nucleotide diversity and haplotype network analysis revealed that the expanded HvDIRs experienced severe bottleneck events during barley domestication, and can thus be considered as potential domestication-related candidate genes. The expression profile and co-expression network analysis revealed the critical roles of the expanded HvDIRs in various biological processes, especially in stress responses. HvDIR18, HvDIR19, and HvDIR63 could serve as excellent candidates for further functional genomics studies to improve the production of barley products. Our study revealed that the HvDIR family was significantly expanded in barley and might be involved in different developmental processes and stress responses. Thus, besides providing a framework for future functional genomics and metabolomics studies, this study also identified HvDIRs as candidates for use in improving barley crop resistance to biotic and abiotic stresses.

Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.

“…DIR gene family members are widely distributed in various plant species. Advances in genome sequencing technology have facilitated the identification of DIR genes in several plant genomes, including Arabidopsis [ 3 ], Capsicum annuum [ 15 ], Solanum lycopersicum [ 1 ], Solanum melongena [ 16 ], Oryza sativa [ 11 , 17 ], Hordeum vulgare [ 18 ] and Glycine max [ 14 ]. In this study, a total of 57 NtDIRs in tobacco and 33 StDIRs in potato were identified.…”

“…A study on tomato ( Solanum lycopersicum ) identified 31 DIR genes [ 1 ], while 24 DIR genes were found in eggplant ( Solanum melongena L.) [ 16 ]. Additionally, a total of 54 rice DIR genes were found in rice ( Oryza sativa ) [ 11 , 17 ], 64 DIR genes in barley ( Hordeum vulgare ) [ 18 ], and 54 DIR genes in soybean ( Glycine max ) [ 14 ].…”

Cytokinin-inducibleDIRIGENT13involved in lignan synthesis and ROS accumulation promotes root growth and abiotic stress tolerance inArabidopsis

“…Our results clearly show that DIR13 plays an important role in salt and drought stress tolerance for different assays including seed germination, root growth and progressive stress to soil-grown plants. This is in agreement with previous findings based on expression analyses, suggesting the role of dirigent genes in various stress responses (Paniagua et al ., 2017; Luo et al ., 2022). For instance, recent studies have shown that silencing of pepper CaDIR7 weakened plant defense and increased susceptibility to biotic and salt stresses (Khan et al ., 2018).…”

Lignin Biosynthesis and Its Diversified Roles in Disease Resistance

“…Dirigent proteins have been shown to act in initiating lignan synthesis [ 44 ]. Both dirigent and lignan are proposed to have vital roles in defense responses [ 67 , 68 , 69 ]. Particularly, some dirigent proteins boost disease resistance by directly promoting lignan accumulation [ 70 ].…”