Genome-wide Analysis of LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family in Brassica rapa

Abstract

LOB (lateral organ boundaries)-domain proteins define a family of plant-specific transcription factors involved in developmental process from embryogenesis to seed production. They play a crucial role in shaping the plant architecture through coordinating cell fate at meristem to organ boundaries. Identification of LBD genes from Brassica rapa genome, and analysis of phylogeny，gene structure, chromosome location, phylogenetic and tissue expression pattern analysis of LBD family genes in Chinese cabbage will be useful to the functions identification of plant LBD genes. Based on Brassica rapa genome database and bioinformatic method, Chinese cabbage LBD family genes were identified and the genes were sequenced. A phylogenetic tree was created using the MEGA5 program. Gene structure and chromosomes location were done by MapDraw, GSDS and Clustal X. Expression pattern of LBD genes at different development stages was analyzed based on RNA-seq. A total of 62 LBD genes were identified and could be classified into two classes and four subclasses according to the gene structure and conserved domain phylogeny relationship. Distribution mapping showed that the predicted LBDs were unevenly localized on all the 10 chromosomes, suggesting that they have an extensive distribution on the Brassica rapa chromosomes. Most of the LBD genes had differential expression pattern and showed highly diverse tissue-specific expression and functional diversity. To our knowledge, this is the first report of a genome wide analysis of the Brassica rapa LBD gene family, which would provide valuable information for understanding the classification and putative functions of the gene family.

Comprehensive characterization and gene expression patterns of LBD gene family in Gossypium

“…LBD genes comprise a plant-specific transcription factor family, which had been proven to have essential roles in the regulation of lateral organ development and metabolic processes, such as anthocyanin and nitrogen metabolism in higher plants (Iwakawa et al 2002;Shuai et al 2002;Majer and Hochholdinger 2011). Comprehensive analyses of this gene family had been conducted in many species such as Arabidopsis (Liu et al 2005), Eucalyptus grandis (Lu et al 2018), Brassica rapa (Huang et al 2018), grapevine (Grimplet et al 2017), soybean (Yang et al 2017), and Camellia sinensis (Teng et al 2018). However, no systematic study of LBD genes has been conducted in allotetraploid cotton.…”

“…Additionally, the MdLBD13 protein can inhibit anthocyanin synthesis and nitrogen uptake in apple (Li et al 2017). Genome-wide analysis of LBD gene family have been studied in plants like Camellia sinensis (Zhang et al 2019), Solanum tuberosum (Liu et al 2019), Eucalyptus grandis (Lu et al 2018), Brassica rapa (Huang et al 2018), grapevine (Grimplet et al 2017), and soybean (Yang et al 2017). However, the function of the LBD genes in Gossypium remains largely unexplored.…”

Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Sweet Potato (Ipomoea batatas)

“…In Gossypium, expression and functional characterization indicated the involvement of GhLBDs in abiotic stresses responses, especially in drought conditions [29]. In Brassica rapa, the LBD gene is mainly expressed in roots, and most genes of Class II were expressed in each tissue with a high expression level [30]. According to latest reports, overexpressing ZmLBD5 increased drought sensitivity by increasing the stomatal number and apertures in Arabidopsis under drought conditions [31].…”

RNAi of a Putative Grapevine Susceptibility Gene as a Possible Downy Mildew Control Strategy

“…The S-gene VvLBDp1 [from here on called VviLBDIf7 based on Grimplet et al (2017) nomenclature], encoding for an LOB (LATERAL ORGAN BOUNDARIES) domain-containing (LBD) protein, belongs to plant LOB family of transcription factors. This family has been comprehensively analyzed in many species, such as Arabidopsis thaliana ( Liu et al, 2005 ), Malus domestica ( Wang et al, 2013 ), Glycine max ( Yang et al, 2017 ), Eucalyptus grandis ( Lu et al, 2018 ), Brassica rapa ( Huang et al, 2018 ), Camellia sinensis ( Teng et al, 2018 ), Gossypium spp. ( Yu et al, 2020 ), and Pyrus bretschneideri ( Song et al, 2020 ).…”