Plants are continuously exposed to various biotic and abiotic factors that may trigger cascade reactions aimed at maintaining homeostasis. One of the most important components of plant protection from biotic factors is the synthesis of antimicrobial peptides (AMPs). AMPs are a large group of peptides present in insects, animals and plants. Plant innate immunity is provided by AMPs from different families that are categorized according to sequence similarity, the number and order of amino acid residues, and the tertiary structure of the mature peptide. AMPs may also participate in plant response to abiotic stresses such as high salinity, drought, high or low temperature, and heavy metals. In nitrogen-fixing nodules of some members of the Fabaceae family, AMP-like molecules named NCR peptides promote the differentiation of the symbiotic bacteria into bacteroids. Thus, AMPs are used by plants for fine tuning their responses to biotic and abiotic factors alike.

Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (Pisum sativum L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.

In garden pea (Pisum sativum L.), several symbiotic genes are known to control the development of mutualistic symbioses with nodule bacteria (NB) and arbuscular mycorrhizal fungi (AMF). Here, we studied whether the allelic state of the symbiotic genes was associated with the growth parameters of pea plants under single inoculation with NB and under double inoculation with NB + AMF. Using different statistical methods, we analyzed the dataset obtained from a pot experiment that involved 99 pea cultivars, 10 of which were characterized as having shortened internodes due to the presence of the natural mutation p.A229T in the developmental gene Le. The plant’s habitus strongly influenced most of the studied growth and yield parameters and the effectiveness of the symbiotic interactions under NB and NB + AMF inoculation. Double inoculation had different effects on Le⁺ (normal) and le⁻ (dwarf) plants with regard to nitrogen and phosphorus content in seeds. Regardless of the Le-status of plants, allelic states of the symbiotic gene LykX encoding the putative receptor of Nod factors (bacterial signal molecules) were shown to be associated with seed number, thousand-seed weight, and pod number at the level of FDR < 0.001, whereas associations of allelic states of the other studied symbiotic genes were less significant.

Pea (Pisum sativum L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype; thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown. Here, we compare the symbiotically responsive breeding line ‘Triumph’ of grain pea with its parental cultivars ‘Vendevil’ (a donor of high symbiotic responsivity) and ‘Classic’ (a donor of agriculturally valuable traits) using genome and transcriptome sequencing. We show that ‘Triumph’ inherited one-fourth of its genome from ‘Vendevil’, including the genes related to AM and nodule formation, and reveal that under combined inoculation with nodule bacteria and AM fungi, ‘Triumph’ and ‘Vendevil’, in contrast to ‘Classic’, demonstrate similar up-regulation of the genes related to solute transport, hormonal regulation and flavonoid biosynthesis in their roots. We also identify the gene PsGLP2, whose expression pattern distinguishing ‘Triumph’ and ‘Vendevil’ from ‘Classic’ correlates with difference within the promoter region sequence, making it a promising marker for the symbiotic responsivity trait. The results of this study may be helpful for future molecular breeding programs aimed at creation of symbiotically responsive cultivars of pea.

The C-TERMINALLY ENCODED PEPTIDE(CEP) peptides play crucial roles in plant growth and response to environmental factors. These peptides were characterized as positive regulators of symbiotic nodule development in legume plants. However, little is known about the CEP peptide family in pea. Here, we discovered in pea genome 21 CEP genes (PsCEPs), among which three genes contained additional conserved motifs corresponding to the PIP (PAMP-induced secreted peptides) consensus sequences. We characterized the expression patterns of pea PsCEP genes based on transcriptomic data, and for six PsCEP genes with high expression levels in the root and symbiotic nodules the detailed expression analysis at different stages of symbiosis and in response to nitrate treatment was performed. We suggest that at least three PsCEP genes, PsCEP1, PsCEP7 and PsCEP2, could play a role in symbiotic nodule development, whereas the PsCEP1 and PsCEP13 genes, downregulated by nitrate addition, could be involved in regulation of nitrate-dependent processes in pea. Further functional studies are required to elucidate the functions of these PsCEP genes.

In order to localize the mutation cdt, leading to increased cadmium tolerance in pea and increased cadmium accumulation in its biomass, the analysis of F₂ and F₃ progenies from crosses between mutant line SGECd^t and line JI281 was performed. The joint inheritance of 89 SSAP (sequence specific amplified polymorphism) markers, which differed between the parents, and the mutant trait of cadmium tolerance was performed. Linkage between the trait of cadmium tolerence and 4 SSAP markers: Tps1/146+, Tps1/167+, Tps1/44+ and Tps1/58+, localized in pea linkage group VI, was observed. Thus, the use of SSAP-analysis for primary localization of a mutation in the linkage group was demonstrated.