In-Depth Genomic and Transcriptomic Analysis of Five K+ Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation

Abstract

Plants have evolved a sophisticated network of K+ transport systems to regulate growth and development. Limited K+ resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K+ transporters in plants. Here, we have identified 70 putative K+ transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K+ channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes. To clarify the molecular evolution of each family in soybean, we analyzed their phylogeny, mode of duplication, exon structures and splice sites, and paralogs. Additionally, ortholog clustering and syntenic analysis across five other dicots further explored the evolution of these gene families and indicated that the soybean data is suitable as a model for all other legumes. Available microarray data sets from Genevestigator about nodulation was evaluated and further confirmed with the RNA sequencing data available by a web server. For each family, expression models were designed based on Transcripts Per Kilobase Million (TPM) values; the outcomes indicated differential expression linked to nodulation and confirmed the genes' putative roles. In-depth studies such as ours provides the basis for understanding K+ inventories in all other plants.

Phylogenetic Diversity and Physiological Roles of Plant Monovalent Cation/H+ Antiporters

“…Some studies suggested that some GmKEAs could be localized to the plasma membrane (PM)—e.g. GmKEA2 (Glyma09g39770) and GmKEA5 (Glyma16g32821) ( Chen et al., 2015 ; Rehman et al., 2017 ) ( Table 1 ), although in the former case this unusual PM localization was only predicted ( Rehman et al., 2017 ). For GmKEA5, the localization pattern was based on GFP-tagged GmKEA5 distribution in the transformed onion cells ( Chen et al., 2015 ).…”

“…The main difference between SOS1A and SOS1B is likely to be in the presence of the cyclic nucleotide-binding domain (PF00027), located in the middle of the C-terminus tail ( Figure 1B ). Such cyclic nucleotide-binding domains are known to bind to the wide range of protein targets, in order to regulate multiple cellular processes ( Shabb and Corbin, 1992 ; LaFranzo et al., 2010 ; Rehmann et al., 2017 ; VanSchouwen et al., 2017 ). SOS1A and SOS1B are both localized to the plasma membrane ( Shi et al., 2000 ; An et al., 2007 ) ( Figure 2 ).…”

“…Based on the analysis of amino acid sequence, 12 GmKEA genes were identified in soybean, located in three branches in the phylogenetic tree, most of which expression were responsive to nodulation and abiotic stresses, such as K + deficiency and salinity ( Chen et al., 2015 ; Rehman et al., 2017 ). Some studies suggested that some GmKEAs could be localized to the plasma membrane (PM)—e.g.…”

Identification of Loci Controlling Mineral Element Concentration in Soybean Seeds

“…In rice, [22] demonstrated that HAK5 plays important roles in controlling both the in ux of K + into roots and its transport to the aerial parts of the plant. Two paralogs of our candidate gene (Glyma.02g154100 and Glyma.07g042500) were functionally characterized as being involved in the root uptake of K + in soybean [23,24]. Interestingly, in the work of Dhanapal et al [16], QTLs for K content do overlap with the genomic positions of these HAK5 paralogs.…”

Identification of Loci Controlling Mineral Element Concentration In Soybean Seeds

“…In rice, [22] demonstrated that HAK5 plays important roles in controlling both the influx of K + into roots and its transport to the aerial parts of the plant. Two paralogs of our candidate gene (Glyma.02g154100 and Glyma.07g042500) were functionally characterized as being involved in the root uptake of K + in soybean [23,24]. Interestingly, in the work of [16], QTLs for K content do overlap with the genomic positions of these HAK5 paralogs.…”