Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis

Abstract

Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.

Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly

“…The corresponding transcript was homologous to an ABC transporter G family member-39 protein of Glycine soja and to ATP-BINDING CASSETTE G40 ( AT1G15520 ) in Arabidopsis . Earlier, we detected increased expression of the same transcript in early flowering guar plants grown under long day conditions compared with delayed flowering plants [ 28 ]. Importantly, the early-flowering guar genotypes were also proven to be early maturing, showing the highest percentage of matured seeds by harvesting (‘maturity index’) [ 3 ].…”

“…Using the genome-guided guar transcriptome assembly, that was based on RNA-Seq data from 15 plants included in the present analysis [ 28 ], we were able to investigate whether the associated SNPs directly correspond to the coding sequence or regulatory regions. Among the six SNPs associated with the percentage of pods matured to the harvest date, just one (contig_182:841660, Table 1 ) was found inside the putative transcript sequence.…”

“…The latter presumes the sequential reversible phosphorylation of the 6-carbon cyclic alcohol myo -inositol ring (Ins) resulting in the synthesis of a series of soluble Ins phosphates, as follows: Ins → Ins(3)P1→ Ins(3,4)P2 → Ins(3,4,6)P3 → Ins(1,3,4,6)P4 → Ins(1,3,4,5,6)P5 → Ins(1,2,3,4,5,6)P6 [ 30 ]. It is noteworthy, that perturbations in the IPs metabolic pathways, leading to the increased concentration of myo -inositol in its free dephosphorylated form, was previously suggested as a biomarker of early flowering (and presumably early maturing) of guar plants [ 28 ]. In maize, the ABC transporter-like gene (orthologous to AT1G15520 in Arabidopsis ) was co-expressed with the purple acid phosphatase (PAP)-like gene [ 29 ], whose ortholog in Arabidopsis ( AtPAP15 ) encodes phytase that hydrolyzes myo -inositol hexakisphosphate (Ins(1,2,3,4,5,6)P6, also known as phytic acid) to yield free myo -inositol and free phosphate [ 31 ].…”

“…Phospholipase C is involved in Ca 2+ signal transduction [ 32 ] and IP metabolism by releasing IP3 from phosphatidylinositol [ 33 ]. We recently found that the phosphatidylinositol signaling pathway is initiated in early-flowering guar genotypes through the activation of the phospholipase C ( PLC ) gene, resulting in an exponential increase in the amount of myo -inositol in its free form [ 28 ]. Thus, function annotation of the contig_188 sequence may reveal genes playing key roles in earliness of guar varieties.…”

Characterization of metabolic changes associated with floral transition in Arabidopsis: RAFFINOSE SYNTHASE 5 contributes to determine the timing of floral transition

“…The analytical power of metabolomic approaches has greatly improved in the last decade (Patti et al, 2012). Moreover, the application of multi-omic approaches, including metabolomics together with transcriptomics and/or proteomics, or even with high-throughput phenotyping, has shown to be useful for the elucidation of relevant pathways (Clark et al, 2021; Grigoreva et al, 2021; Z. Li et al, 2022; Peng et al, 2022).…”