Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species.

Puwen Song,Yuanyuan Guan,Jun Xu,Huanting Gao,Ping Hu,Ye Tao

doi:10.7717/peerj.11811

Puwen Song, Yuanyuan Guan + Show 4 more

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https://doi.org/10.7717/peerj.11811

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Journal: PeerJ	Publication Date: Aug 11, 2021
Citations: 11	License type: CC BY 4.0

Affiliation: Henan Institute of Science and Technology

Abstract

BackgroundWheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species.MethodsUsing a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b).ResultsThe gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.

Highlights

Triticum aestivum is a global staple crop of the Poaceae family, providing large amounts of energy and protein for human diets (Shiferaw et al, 2013; Veraverbeke & Delcour, 2002).How to cite this article Xu J, Hu P, Tao Y, Song P, Gao H, Guan Y. 2021
According to a phylogenetic tree and branch lengths, these Lateral Organ Boundaries Domain (LBD) genes were divided into two major classes, classes I and II; class I was further assigned to five subgroups, classes I a–e; and class II was further assigned to two subgroups, classes II a and II b (Fig. 1)
When TaLBD4B-1 was used as a query gene, the results showed that its neighboring genes were relatively conserved across investigated genomes, and homologs of TaLBD4B-1 were found in the collinearity regions of T. urartu, Ae. tauschii and subgenomes A and B of T. dicoccoides (Fig. S2A )

Summary

Introduction

Triticum aestivum is a global staple crop of the Poaceae family, providing large amounts of energy and protein for human diets (Shiferaw et al, 2013; Veraverbeke & Delcour, 2002).How to cite this article Xu J, Hu P, Tao Y, Song P, Gao H, Guan Y. 2021. Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species. Large-scale RNA-seq analyses of wheat genes at different developmental stages and under a variety of stresses have provided convenient conditions for more detailed analyses (Ramirez-Gonzalez et al, 2018). Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. QRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat

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