Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds

Abstract

BackgroundRamet propagation in strawberry (Fragaria × ananassa) is the most effective way in production. However, the lack of systematically phenotypic observations and high-throughput methods limits our ability to analyze the key factors regulating the heterogeneity in strawberry stolon buds.ResultsFrom observation, we found that the axillary bud located in the first node quickly stepped into dormancy (DSB), after several bract and leaf buds were differentiated. The stolon apical meristem (SAM) degenerated as the new ramet leaf buds (RLB), and the new active axillary stolon buds (ASB) differentiated continually after the differentiation of the first leaf. Using the tandem mass tags (TMT) labeling method, a total of 7271 strawberry proteins were identified. Between ASB and DSB, the spliceosome DEPs, such as Ser/Arg-rich (SR) and heterogeneous nuclear ribonucleoprotein particle (hnRNP), showed the highest enrichment and high PPI connectivity. This indicated that the differences in DEPs (e.g., SF-3A and PK) at the transcriptional level may be causing the differences between the physiological statuses of ASB and DSB. As expected, the photosynthetic pre-form RLB mainly differentiated from ASB and DSB judging by the DEP enrichment of photosynthesis. However, there are still other specialized features of DEPs between RLB and DSB and between ASB and DSB. The DEPs relative to DNA duplication [e.g., minichromosome maintenance protein (MCM 2, 3, 4, 7)], provide a strong hint of functional gene duplication leading the bud heterogeneity between RLB and DSB. In addition, the top fold change DEP of LSH 10-like might be involved in the degeneration of SAM into RLBs, based on its significant function in modulating the plant shoot initiation. As for RLB/ASB, the phenylpropanoid biosynthesis pathway probably regulates the ramet axillary bud specialization, and further promotes the differentiation of xylem when ASB develops into a new stolon [e.g., cinnamyl alcohol dehydrogenase 1 (CAD1) and phenylalanine ammonia-lyase 1 (PAL1)].ConclusionsBy using phenotypic observation combined with proteomic networks with different types of strawberry stolon buds, the definite dormancy phase of DSB was identified, and the biological pathways and gene networks that might be responsible for heterogeneity among different stolon buds in strawberry were also revealed.

The Short Inflorescence Mutation in Diploid Strawberry Fragaria vesca Affects Inflorescence Architecture and Runner Elongation

“…An early proteomics study (Fang et al 2011) described the major proteomic differences between the proximal internode (I-1) and the distal internode (I-2); however, the technique used would not have identified regulatory factors directing the different developmental outcomes. A more recent proteomics analysis of runner nodes identified 7271 proteins and revealed distinct protein differences among the tissues examined: the dormant axillary bud at node 1; the runner apical meristem; the runner producing axillary bud at node 2; and the developing leaves at node 2 (Guan et al 2019). However, no mechanism(s) for the developmental differences at node 1 and node 2 were obvious from the data that would account for the phenotype of the sin runners.…”

“…Strawberry runner growth from the meristem requires both cell division and cell elongation, which first result in a usually nonproductive node, although the node occasionally produces a thin, weak runner (Darrow 1929(Darrow , 1966Guan et al 2019). Following further extension, a clonal daughter plant capable of forming its own runners is produced at the tip.…”

Exogenous GR24 Inhibits Strawberry Tillering by Affecting the Phytohormone Signaling and Sugar Metabolism Pathways

“…However, in China, during mid-October every year, favorable external environmental conditions lead to a significant sprouting of stolons. This excessive growth can disrupt the balance between the reproductive and nutritional growth processes of strawberries, resulting in yield reduction and loss of fruit quality [2]. Therefore, it is critical to effectively control the formation of stolons during the cultivation process of strawberries.…”

KRAS, YWHAE, SP1 and MSRA as biomarkers in endometrial cancer

“…In our previous research ( 14 ), the consumption of hydrogen-enriched drinking water was shown to reduce endometrial tumor volume, density and weight in a xenograft mice model ( Figure S1 ), suggesting that drinking hydrogen-rich water (HRW) might be served as an effective treatment or adjuvant therapy for EC, while the mechanism of how they function remain unknow. To characterize the effect of hydrogen water on signal transduction, substrate specificity, and peptidase functional efficiencies, a new approach called quantitative multiplex substrate profiling by mass spectrometry (qMSP-MS) ( 15 ) which utilizes isobaric tandem mass tags (TMTs) was utilized herein. TMTs are available with different reactive groups, which enables deep proteome coverage for multiple samples in a reasonable amount of time ( 16 , 17 ).…”