Genome‐Wide Analysis of Soybean LATERAL ORGAN BOUNDARIES Domain‐Containing Genes: A Functional Investigation of GmLBD12

Abstract

Plant-specific LBD (LATERAL ORGAN BOUNDARIES Domain) genes play critical roles in various plant growth and development processes. However, the number and characteristics of LBD genes in soybean [Glycine max (L.) Merr.] remain unknown. Here, we identified 90 LBD homologous genes in the soybean genome that phylogenetically clustered into two classes (I and II). The majority of the GmLBD genes were evenly distributed across all 20 soybean chromosomes, and 77 (81.11%) of them were detected in segmental duplicated regions. Furthermore, the exon-intron organization and motif composition for each GmLBD were analyzed. A close phylogenetic relationship was identified between the soybean LBD genes and 41 previously reported genes of different plants in the same group, providing insights into their putative functions. Expression analysis indicated that more than half of the LBD genes were expressed, with the two gene classes showing differential tissue expression characteristics; in addition, they were differentially induced by biotic and abiotic stresses. To further explore the functions of LBD genes in soybean, GmLBD12 was selected for functional characterization. GmLBD12 was mainly localized to the nucleus and showed high expression in root and seed tissues. Overexpressing GmLBD12 in Arabidopsis thaliana (L.) Heynh resulted in increases in lateral root (LR) number and plant height. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis demonstrated that GmLBD12 was induced by drought, salt, cold, indole acetic acid (IAA), abscisic acid (ABA), and salicylic acid SA treatments. This study provides the first comprehensive analysis of the soybean LBD gene family and a valuable foundation for future functional studies of GmLBD genes.

Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus

“…In this study, we identified 126 BnLBD genes in B. napus. These BnLBD genes were divided into two groups and ten subgroups based on the evolutionary relationships, which is highly consistent with the reports in Arabidopsis, G. max, and Z. mays [1,6,12]. The variations in the structure of BnLBDs might be because of the gain or loss of introns/exons in the long-term evolutionary process.…”

“…WGD/segmental duplication is very common in plant genomes, as most plants have undergone polyploidy events during evolution, and thus retain many duplicated chromosome segments in their genomes [50,51]. Compared with other plant species such as Arabidopsis, O. sativa, Z. mays, G. max, and Populus, which contain 43,35,44,80, and 57 LBD genes [1,6,12,13], respectively, we found B. napus with the largest number of LBD genes, indicating the genome duplication during evolution of B. napus greatly contributed to the diversification of BnLBDs. Further, all 126 BnLBD genes were identified as the result of gene duplication, 93 of them were identified with WGD or segmental duplications history, and the rest resulted from dispersed duplications.…”

“…Following the identification of LBD genes in Arabidopsis, LBDs have been found in other plant species, such as Oryza sativa, Malus domestica, Zea mays, Vitis vinifera, Morus notabilis, Lotus japonicas, Medicago truncatula, Brachypodium distachyon, Glycine max, and Eucalyptus grandis. The number of LBD members ranged from 28 to 90 in different plants [4][5][6][7][8][9][10][11][12][13]. However, LBDs have never been identified in any species other than plants, indicating that LBD is a plant-specific gene family [1].…”

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.…”