Synergy of arbuscular mycorrhizal symbiosis and exogenous Ca²⁺ benefits peanut (Arachis hypogaea L.) growth through the shared hormone and flavonoid pathway

Abstract

Peanut yield is severely affected by exchangeable calcium ion (Ca²⁺) deficiency in the soil. Arbuscular mycorrhizal (AM) symbiosis increases the absorption of Ca²⁺ for host plants. Here, we analyzed the physiological and transcriptional changes in the roots of Arachis hypogaea L. colonized by Funneliformis mosseae under Ca²⁺-deficient and -sufficient conditions. The results showed that exogenous Ca²⁺ application increased arbuscular mycorrhizal fungi (AMF) colonization, plant dry weight, and Ca content of AM plants. Simultaneously, transcriptome analysis showed that Ca²⁺ application further induced 74.5% of differentially expressed gene transcripts in roots of AM peanut seedlings. These genes are involved in AM symbiosis development, hormone biosynthesis and signal transduction, and carotenoid and flavonoid biosynthesis. The transcripts of AM-specific marker genes in AM plants with Ca²⁺ deprivation were further up-regulated by Ca²⁺ application. Gibberellic acid (GA₃) and flavonoid contents were higher in roots of AM- and Ca²⁺-treated plants, but salicylic acid (SA) and carotenoid contents specifically increased in roots of the AM plants. Thus, these results suggest that the synergy of AM symbiosis and Ca²⁺ improves plant growth due to the shared GA- and flavonoid-mediated pathway, whereas SA and carotenoid biosynthesis in peanut roots are specific to AM symbiosis.

Introduction

Peanut (Arachis hypogaea L.) is an important oil crop and protein source for humans that contributes 20% to oil production and 11% of the human protein supply per year. The yield is often limited by exchangeable Ca²⁺ deficiency in soil, which causes early embryo abortion in peanut^1,2. Therefore, Ca²⁺ plays a crucial role in the growth and development of peanut. Calcium is an important macronutrient required for plant growth and development and represents 0.1 to 5% of all plant dry biomass³. Additionally, as a second messenger, Ca²⁺ has been shown to mediate various aspects of cell and plant development, such as cell division, cell polarity, cell elongation, photomorphogenesis, and biotic and abiotic stress responses^4–6.

In peanut, Ca²⁺ partly regulates turnover of the PSII reaction center components to reduce the stress of photoinhibition to PSII⁷, and is involved in hormone-induced peanut pod formation by increasing gibberellic acid (GA) and auxin contents¹. However, Ca²⁺ is largely confined to uptake via the young root tips and can only be taken up by the young root system from the soil and delivered to the shoot via the xylem, and it is not remobilized from old to young tissues⁸. Thus, Ca²⁺ deficiency commonly affects plant growth and development if the soil cannot be supplemented with exogenous Ca²⁺. Fortunately, most plants have coped with limited Ca²⁺ availability via the establishment of symbiotic associations with microbes, more specifically known as AM association. The fungi forming AM symbiosis belong to the subphylum Glomeromycotina⁹.

This symbiosis plays a significant role in the uptake of nutrients and the carbon cycle, and consequently impacts ecosystem sustainability¹⁰. To establish the symbiosis, plant roots recognize chemical signals from AMF, e.g. lipochitooligosaccharides and chitooligosaccharides, which trigger coordinated differentiation and form the symbiotic state¹¹. In turn, AMF require signal communication from the plants that produce strigolactones (which are derived from the carotenoid synthesis pathway), flavonoids, and other diffusible signals exuded by plant roots that induce the germination of AMF spores and branched fungal hyphae¹². Then, the AM symbiosis is established by the common symbiosis signaling pathway induced by calcium oscillation after perception of diffusible signals from the symbionts¹³. In the process of establishing the AM symbiosis, many AM-specific marker genes must be initiated by Ca²⁺ concentration change¹⁴, such as RAM1 (REDUCED ARBUSCULAR MYCORRHIZA 1), RAM2 (glycerol-3-phosphate acetyltransferase), CCD1 (carotenoid cleavage dioxygenase), PT1 (phosphate transporter), and DELLA^15–17. These findings suggest that Ca²⁺ plays an important role in AM development.

From recognition of the fungi to establishment of the symbiosis, complicated transcriptional reprogramming occurs in plant roots, and many specifically expressed genes involved in development of the symbiosis have been identified in legumes^18–20. Some of the changes associated with plant hormones were considered to play important roles in this symbiosis²¹, such as auxin, cytokinins (CKs), gibberellins (GAs), and strigolactones, and were also altered in the roots of AM plants^16,22. In addition, increases in flavonoid and anthocyanin were considered to be indispensable in regulating the establishment of AM symbiosis^22,23.

Even though the molecular basis of the improvement of plant nutrient acquisitions have been well characterized for phosphorus, nitrogen, sulfur, and potassium^18,24,25, the role of plant uptake of Ca²⁺ needs further study. Several reports showed that a moderate level of Ca²⁺ supply enhanced the colonization of AMF^26,27, and Ca²⁺ benefited the maintenance of a functioning mycorrhiza²⁸. However, the transcriptional changes in plant roots colonized by an AMF accompanied with sufficient Ca²⁺ are still unknown.

Cui et al. (2019) demonstrated that AM symbiosis increased the Ca²⁺ content in peanut seedlings, and Ca²⁺ application can also promote the development of AM symbiosis²⁹. However, the molecular mechanism of how AMF and Ca²⁺ application synergistically promote the growth of peanut seedlings is unclear. In this study, we investigated a combination of transcriptional changes, hormone and metabolomic analyses in roots of peanut seedlings inoculated by AMF and Ca²⁺ application and compared the observed changes with those in AM plants or Ca²⁺-treated plants. We observed that changes in secondary metabolites in roots of AM and Ca²⁺-treated plants coincide with the transcriptional regulation of related biosynthesis pathways. These alternations, such as the increases in GA₃ and flavonoid content, were considered to be involved in the growth enhancement of peanut seedlings by the synergy of AMF with Ca²⁺ application.

Results

AM symbiosis improves the dry biomass of peanut

The quantification of AMF colonization showed that 60.33% and 80.67% of plant roots were inoculated by F. mosseae under both Ca²⁺-deficient and Ca²⁺-sufficient conditions, respectively (Fig. 1A), indicating that Ca²⁺ application could significantly improve the number of fungal colonizers.

Figure 1.

Impact of AM symbiosis on plant growth under Ca²⁺ deficient and sufficient conditions. (A) The rate of AMF colonization in peanut roots was assayed under Ca²⁺ deprivation and sufficiency. Shoot (B) and root (C) dry weight were determined in AM and NM plants under different Ca²⁺ treatments. (D) Ca²⁺ content was measured in roots of AM and NM plants under Ca²⁺ deficient and Ca²⁺ sufficient conditions. Letters represent significant differences between treatments and the control (one-way ANOVA, P < 0.05). Bars indicate means ± SD from six plants. DW, dry weight.

Shoot dry weight significantly increased in the AM plants compared with the nonmycorrhized (NM) plants and Ca²⁺ application further increased the shoot dry weight (Fig. 1B). Moreover, root dry weight was significantly increased in AM plants under Ca₀ conditions and Ca²⁺ further improved the root dry weight; AM symbiosis did not increase the root dry weight (Fig. 1C). Additionally, the Ca²⁺ content was significantly higher in Ca²⁺-sufficient seedlings compared with Ca²⁺-deficient ones, and AM association improved Ca²⁺ level in roots (Fig. 1D).

Comparative analysis of differentially expressed genes (DEGs) in the AM and Ca²⁺-treated plants

Using Ca₀-AM as the control, there were 510, 1483, and 1795 significantly differentially expressed genes (DEGs) from roots of the Ca₀ + AM, Ca₆ − AM, and Ca₆ + AM plants, respectively (Fig. 2A). In all, 304 DEGs were shared by Ca₀ + AM, Ca₆ − AM, and Ca₆ + AM plants and the number of DEGs gradually increased in the plants (Fig. 2B), indicating that AM symbiosis combined with exogenous Ca²⁺ induced more transcriptional changes. In total, 421 DEGs were shared by Ca₀ + AM and Ca₆ + AM treatments, representing 82.55% and 23.45% of total DEGs in Ca₀ + AM plants (510) and Ca₆ + AM plants (1795), respectively. The expression levels of 380 DEGs in Ca₀ + AM plants could be further regulated by Ca²⁺ application (Supplementary Fig. S1); only 40 DEGs were conversely regulated (Supplementary Table S1). This result implied that Ca²⁺ application could further strengthen the effects of AM on plant growth. In addition, 22 categories involved in molecular functions of GO enrichment analyses were identified, and the number of DEGs involved in transferase activity was the highest, followed by metal ion binding and oxidoreductase activity. Four categories, including calcium ion binding, signaling receptor activity, zinc ion binding, and antioxidant activity were the highest in Ca₆ − AM plants; among the other 18 categories, the number of DEGs involved in each molecular function of GO was the highest in the Ca₆ + AM plants, followed by the Ca₆ − AM plants, and the Ca₀ + AM plants (Fig. 2C).

Figure 2.

Transcriptional profiling of peanut roots with or without colonization by AMF under Ca²⁺ deficient and sufficient conditions. (A) The number of DEGs up-regulated and down-regulated in roots of Ca₀ − AM, Ca₆ − AM, and Ca₆ + AM plants compared with Ca₀-AM plants (the control). (B) Venn diagram showing the number of DEGs shared and specifically up- or down-regulated in roots of Ca₀ − AM, Ca₆ − AM, and Ca₆ + AM plants. (C) Significantly enriched GO molecular function terms for the number of DEGs analyzed in different treatments.

To confirm RNA-Seq results, 15 genes were selected randomly from various functional categories and qRT-PCR analysis was conducted using RNA samples from the RNA-Seq experiments. The results were consistent with the expression levels of genes from RNA-Seq data (Fig. 3).

Figure 3.

qRT-PCR verification of selected genes. Comparison of gene expression level from transcriptome analyses and qRT-PCR experiments.

Effects of Ca²⁺ combined with AM symbiosis on the transcripts of AM-specific markers and Ca-related genes

We analyzed the roles of Ca²⁺ application on the establishment of AM symbiosis. In total, 25 AM-specific marker genes were identified in Ca₆ + AM plants, with 12 GRAS family transcription factors (TFs) ten of which were up-regulated and two down-regulated. However, only 12 AM-specific marker genes were induced in Ca₀ + AM plants and the transcripts of ten up-regulated genes were further increased by Ca²⁺ application (Table 1), including MYB, AP2, CCD, DELLA1, RAM1, RAM2, and DELLA. In addition, some AM-specific marker genes were specifically expressed in AM plants by Ca²⁺ application, e.g. DXS2, DIM2, SbtM1, and PUB1.

Table 1.

Differentially expressed genes of AM-specific markers in roots of Ca₀ + AM and Ca₆ + AM treated plants compared with controls.

Gene Name	Gene ID	Annotation	Ca0 + AM/CK	Ca6 + AM/CK
DXS2	Araip.581AC	1-Deoxy-D-xylulose-5-phosphate synthase	—	−1.37
DIM2	Araip.7E8G5	receptor-like kinase	—	4.14
SbtM1	Araip.2Y3EX	subtilisin-like protease	—	2.23
IPD3	Araip.02MA2	cyclops protein	—	1.51
PUB1	Araip.658mf	E3 ubiquitin ligase	—	2.24
MYB	Araip.62YF9	MYB transcription factor	2.87	4.39
AP2	BGI_novel_G002001	AP2 transcription factor	1.93	2.98
CCD1	Araip.S2QC7	carotenoid cleavage dioxygenase	2.99	5.63
CCD7	Araip.RJ87T	carotenoid cleavage dioxygenase 7	1.13	2.65
CCD8	Araip.MNC08	carotenoid cleavage dioxygenase 8	2.86	4.03
PT1	Araip.QVW26	phosphate transporter	—	4.23
PT4	Araip.WR1Z1	inorganic phosphate transporter	5.33	5.22
RAM2	Araip.1QC5L	glycerol-3-phosphate acyltransferase	3.43	5.32
RAM1	Araip.N9QES	GRAS family transcription factor	4.15	6.30
DELLA1	BGI_novel_G000145	GRAS family transcription factor	2.89	5.05
DELLA	Araip.LT9MF	GRAS family transcription factor	1.80	2.47
DELLA	BGI_novel_G000391	GRAS family transcription factor	1.81	2.84
DELLA	Araip.DNQ5K	GRAS family transcription factor	−2.49	−3.62
DELLA	Araip.RWP2N	GRAS family transcription factor	—	4.47
DELLA	Araip.TD6FV	GRAS family transcription factor	—	3.40
DELLA	BGI_novel_G001778	GRAS family transcription factor	—	1.15
DELLA	Araip.W23GC	GRAS family transcription factor	—	−1.51
DELLA	Araip.KB0T7	GRAS family transcription factor	—	1.46
DELLA	Araip.KK7TK	GRAS family transcription factor	—	1.18
DELLA	BGI_novel_G001435	GRAS family transcription factor	—	1.08

Values represent significant changes in roots of AM plants under Ca²⁺ deficient and sufficient conditions compared with the control (NM-Ca). Positive and negative ratios indicate up- and down-regulated genes. − Represents no significant alterations at log₂FoldChange ≥ 1 and P value ≤ 0.05 level.

We further investigated the effects of AM symbiosis on Ca and Ca²⁺ signal-related genes. The number of DEGs involved in Ca signals in the Ca₆ − AM and Ca₆ + AM plants was 29 and 32, respectively (Supplementary Table S2). However, there were 14 DEGs shared by Ca₆ − AM and Ca₆ + AM plants and the transcript levels of nine of these DEGs were further regulated by AM symbiosis. Additionally, AM symbiosis specifically up-regulated the transcripts of Araip.IZ5U3 and Araip.R6YEY genes, which code the potassium channel KAT3 and AKT2/3, respectively. These results suggest that the Ca²⁺ signal pathway induced by exogenous Ca²⁺ is partially different from AM symbiosis.

Effects of AM symbiosis and Ca²⁺ on genes involved in hormone biosynthesis

DEGs involved in plant hormone biosynthesis were screened, including auxin, CKs, GA, and SA (Table 2). One gene encoding auxin responsive protein indoleacetic acid (IAA) was specifically up-regulated in AM plants without Ca²⁺ application. Two genes belonging to the auxin responsive GH3 family were down-regulated in AM plants, and Ca²⁺ application further down-regulated its transcripts. The genes encoding cytokinin dehydrogenase, which catalyze the irreversible degradation of CK, were either up- or down-regulated. In addition, we observed an increase in transcripts of genes involved in the biosynthesis of GA. Compared with the control, all DEGs encoding gibberellin 20-oxidase were up-regulated in AM plants, and more transcripts were observed in Ca₆ + AM plants. Two selected DEGs, namely, gibberellins 2-oxidase and gibberellin receptor GID1, were only up-regulated in Ca₆ + AM plants. Meanwhile, one  TF TGA (Araip.FKG2G) involved in the biosynthesis of SA was specifically up-regulated by Ca²⁺ application, and was further up-regulated by AM symbiosis.

Table 2.

List of selected altered genes involved in hormone signal transduction in roots of Ca₀+AM, Ca₆—AM, and Ca₆+AMtreated plants compared with controls.

GeneID	Gene Description	Ca0 + AM/CK	Ca6 − AM/CK	Ca6 + AM/CK
Auxin
Araip.I2M0Y	auxin responsive protein IAA	1.54	—	—
Araip.PP5S8	auxin responsive GH3 gene family	−2.20	−2.60	−3.42
Araip.V8NJN	auxin responsive GH3 gene family	−2.31	−5.41	−5.42
Cytokinin
Araip.DKI8Z	cytokinin dehydrogenase	—	2.00	2.22
Araip.ZXC56	cytokinin dehydrogenase	−1.44	−1.97	−2.48
Araip.2I0VZ	histidine-containing phosphotransfer protein	—	−2.32	−3.17
Araip.W2KBF	cytokinin dehydrogenase	—	—	−2.05
Gibberellin
Araip.9GU4E	gibberellin 20-oxidase	2.39	1.88	3.03
Araip.UXP0Y	gibberellin 20-oxidase	2.03	1.62	2.48
Araip.X2IEW	gibberellin 20-oxidase	1.84	1.39	2.73
Araip.B4LS2	gibberellin-regulated protein	—	1.85	2.07
Araip.HQ99N	gibberellin 20-oxidase	—	1.26	1.57
Araip.L4RII	gibberellin 20-oxidase	—	1.45	1.60
Araip.E8TE0	gibberellin 20-oxidase	—	—	4.62
Araip.4FI3B	gibberellin 20-oxidase	—	—	1.77
Araip.78FT4	gibberellin 20-oxidase	—	—	2.15
Araip.50IUR	gibberellin 20-oxidase	—	—	1.73
Araip.6PA6C	gibberellin 2-oxidase	—	—	1.87
Araip.99KY6	gibberellin receptor GID1	—	—	1.58
Salicylic acid
Araip.FKG2G	transcription factor TGA	—	2.80	4.08

Values represent significant alterations in AM or Ca²⁺-treated plants compared with the control. Positive and negative ratios indicate up- and down-regulated genes. − Represents no significant alterations at log₂FoldChange ≥ 1 and P ≤ 0.05 level.

In order to verify whether the hormone level is consistent with the transcriptional changes in DEGs, we tested the content of IAA, trans-zeatin riboside (tZR), GA₃, and SA. IAA content significantly increased in AM plants with Ca₀ treatment, but decreased in Ca₆ treatment (Fig. 4A). Changes in tZR content were consistent with the transcript changes of cytokinin dehydrogenase genes: it significantly decreased in Ca₀ + AM and Ca₆ − AM plants, and further decreased in Ca₆ + AM plants (Fig. 4B). Additionally, the GA₃ content only significantly increased in Ca₆ treatment (Fig. 4C), which was consistent with the transcriptional changes of GAs biosynthesis. SA content significantly increased only in the roots of AM plants (Fig. 4D).

Figure 4.

Determination of hormone levels in peanut roots. The IAA (A), tZR (B), GA₃ (C), and SA (D) content were quantified in roots of the AM plants and NM plants under Ca²⁺ deficient and sufficient conditions. Bars indicate means ± SD from six plants. Letters represent significant differences between treatments and the control (one-way ANOVA, P < 0.05). FW: fresh weight.

Effects of AM symbiosis and Ca²⁺ on genes involved in carotenoid and flavonoid biosynthesis

We found an increase in transcripts of DEGs involved in carotenoid biosynthesis. The genes encoding 3-oxoacyl-[acyl-carrier protein] reductase (BGI_novel_G000088), 15-cis-phytoene/all-trans-phytoene synthase (Araip.40 × 13), and 9-cis-beta-carotene 9′,10′-cleaving dioxygenase (CCD7, Araip.RJ87T) involved in carotenoid biosynthesis were only up-regulated in AM plants, and were further up-regulated by Ca₆ treatment (Table 3). In addition, the genes encoding unknown protein (BGI_novel_G003217), capsanthin/capsorubin synthase (Araip.3B5FU), and beta-carotene isomerase (Araip.FA949, DWARF27) were specifically up-regulated in Ca₆ + AM plants.

Table 3.

Differentially expressed genes involved in carotenoid biosynthesis in roots of AMF and Ca²⁺ treated plants compared with controls.

Gene ID	Annotation	Ca0 + AM/CK	Ca6 + AM/CK	Ca6 − AM/CK
BGI_novel_G000088	3-oxoacyl-[acyl-carrier protein] reductase	2.49	3.80	—
Araip.Y8SSF	abscisate beta-glucosyltransferase	−1.45	−2.31	−2.58
BGI_novel_G001960	momilactone-A synthase	2.46	4.22	2.10
Araip.40X13	15-cis-phytoene/all-trans-phytoene synthase	2.23	5.38	—
Araip.MNC08	carotenoid cleavage dioxygenase 8	2.86	4.03	1.20
Araip.D2DUM	xanthoxin dehydrogenase	−1.83	−1.97	−2.15
Araip.RJ87T	9-cis-beta-carotene 9′,10′-cleaving dioxygenase	1.13	2.65	—
Araip.AB0RD	prolycopene isomerase	—	−1.46	−1.18
Araip.D5CVZ	momilactone-A synthase	—	—	−1.45
BGI_novel_G003217	unknown protein	—	2.96	—
Araip.3B5FU	capsanthin/capsorubin synthase	—	2.18	—
Araip.FA949	beta-carotene isomerase	—	2.79	—

Values represent significant alterations in AM or Ca²⁺-treated plants compared with the control. Positive and negative ratios indicate up- and down-regulated genes. − Represents no significant alterations at log₂FoldChange ≥ 1 and P ≤ 0.05 level.

Transcriptional changes involved in flavonoid biosynthesis were also observed. The genes encoding chalcone synthase involved in early steps of flavonoid biosynthesis were all down-regulated in Ca₀ and Ca₆ treatments. In contrast, one gene (BGI_novel_G001027) encoding shikimate O-hydroxycinnamoyltransferase was up-regulated in the Ca₀ and Ca₆ treatments, and the expression level was the highest in AM plants treated with Ca₆. However, the other gene encoding shikimate O-hydroxycinnamoyltransferase was specifically up-regulated in Ca₆ + AM plants. In addition, the gene (Araip.6PA6C) encoding flavonol synthase responsible for the biosynthesis of flavanol, was specifically up-regulated in AM plants with Ca₆ treatment (Supplementary Table S3).

Next, we verified whether transcriptional changes of carotenoid- and flavonoid-related genes impacted their respective content. As expected, total carotenoid content was higher in Ca₀ + AM plants than the control and was the highest in Ca₆ + AM plants, but was unchanged in Ca₆ − AM plants (Fig. 5A). However, total flavonoid content was the highest in Ca₆ treatments, and was higher than the control in Ca₀ treatment (Fig. 5B); both increases were significant.

Figure 5.

Quantification of carotenoids and flavonoids in roots of peanut seedlings. Carotenoids content (A) and total flavonoids content (B) were determined in roots of the AM plants and NM plants under Ca²⁺ deficient and sufficient conditions. Bars indicate means ± SD from six plants. Letters represent significant differences between treatments and the control (one-way ANOVA, P < 0.05). DW, dry weight.

Discussion

Calcium is an essential macronutrient for plant growth and development, and also plays various important roles as a secondary messenger. Prolonged Ca²⁺ deficiency limits root development³⁰. In this study, AM symbiosis increased the Ca²⁺ content in peanut seedlings (Fig. 1D), because AMF increased the root surface and root projections, which promote plant uptake of nutrients³¹. Conversely, the increase in Ca²⁺ content enhanced potassium level in plants by enhancing the transcripts of genes encoding the potassium channel³², and together with AM symbiosis improved plant nutrient uptake⁹, thus increasing the shoot and root dry weight. This indicated that the interaction between AM symbiosis and exogenous Ca²⁺ benefited the growth of peanut seedlings.

Our previous study reported that AM symbiosis combined with exogenous Ca²⁺ was better than AM symbiosis or Ca²⁺ application alone at improving the growth of peanut seedlings²⁹. This, together with our observations on plant dry weight, could explain why Ca²⁺ application strengthens the role of AM symbiosis in plant growth by further regulating a major overlap of transcriptional changes in roots of AM plants (380 out of 510 genes, approximately 74%). In addition, the establishment of AM symbiosis requires the expression of AM-specific marker genes³³. In this study, Ca²⁺ further up-regulated and specifically induced the transcripts of AM-specific marker genes in AM plants. It is possible that the Ca²⁺-calmodulin association with CCaMK induces the phosphorylation of CYCLOPS and forms a complex in the presence of calcium, which acts in concert with GRAS  TFs such as DELLA proteins to initiate the expression of AM-specific marker genes that are necessary to establish the AM symbiosis¹⁴. These results suggest that Ca²⁺ plays a vital role in the formation of AM symbiosis.

GRAS family TF encoding DELLA protein is a positive regulator in the formation of AM associations^17,34, and is also involved in GA biosynthesis as a negative regulator of GA signaling³⁵. AM symbiosis up-regulation of GA-related genes and GA content in roots has been reported in M. truncatula and tomato^36,37. Hence, the observed increase of GA₃ content may be the factor involved in Ca²⁺ further up-regulating the transcripts of DELLAs and the genes encoding gibberellins 20-oxidase, which is a key enzyme that catalyzes the penultimate steps in GA biosynthesis. This result implied that AM symbiosis positively regulated the transcriptional changes involved in GA biosynthesis, and that Ca²⁺ strengthens this effect.

tZR is the major transport form of CKs from root to shoot in plants^22,38. However, it has been reported that CKs act as a negative regulator in lateral root initiation, because overproduction of CKs inhibited lateral root initiation^39,40. In this study, the lower tZR in roots of AM plants suggested that the genes encoding cytokinin dehydrogenase, which catalyze the irreversible degradation of cytokinin, were down-regulated by Ca²⁺ application. Reduced tZR content may be beneficial to the initiation of AM symbiotic roots. This result supports the finding in some studies that CKs might not be involved in the regulation of AM symbiosis development¹⁶. In addition, SA and carotenoid have been demonstrated to be activated by AM colonization^16,41, and these activations were specific to AM symbiosis but not Ca²⁺ (Fig. 4), suggesting that increases in SA and carotenoid content can serve as AM-specific marker metabolites.

Flavonoid is involved in hyphal growth and branching²³, and in turn, AMF benefit flavonoid biosynthesis and accumulation in roots of M. truncatula^42,43. This is in line with our observation that more flavonoids were accumulated in roots of AM plants treated by Ca²⁺ application, which is attributed to Ca²⁺ inducing more transcripts of DELLA genes. DELLA-mediated signaling participates in regulating the accumulation of anthocyanin, one of the derivatives of flavonoids⁴⁴. Additionally, the accumulation of SA can increase the flavonoid content in AM plants⁴⁵. Thus, more flavonoids were observed in AM plants treated by Ca²⁺. These results suggested that Ca²⁺ and AM symbiosis might share the flavonoid biosynthetic pathway for improving plant growth.

Based on our data, we propose a model of interactive pathways that modulate hormone levels, secondary metabolism, and ultimately the growth of AM and Ca²⁺ plants (Fig. 6). In this model, AM symbiosis promotes the growth of peanut seedlings by increasing contents of GAs, IAA, SA, carotenoids, and flavonoids. However, exogenous Ca²⁺ application only enhances the GA level and flavonoid content for improving plant growth. The increase in flavonoid content in AM symbiosis or Ca²⁺-treated plants may be a reason for the regulated DELLA that may enhance flavonoid accumulation. The proposed model reveals that synergy of AM symbiosis with Ca²⁺ promotes peanut growth by regulating GAs and flavonoid biosynthesis, but carotenoid and SA biosynthesis are specifically regulated by AM symbiosis. These findings should be validated in future research.

Figure 6.

Proposed model of AM- and Ca²⁺- regulated pathways in peanut roots. AM symbiosis increases the content of IAA, GAs, SA, carotenoids, and flavonoids. Total flavonoids were also accumulated by regulating the transcripts of DELLA genes and the increase of SA in AM plants. Ca²⁺ application only increases the GA and flavonoid contents.

Methods

Plant material and growth conditions

Peanut cultivar ‘Huayu 22’ seeds were surface sterilized with 70% alcohol for 3 min and rinsed six times with sterile water. They were then germinated in the dark at 25 °C for 3 days. The germinated seeds were transferred to pots filled with quartz sand which was rinsed with deionized water 10 times to remove as much Ca²⁺ as possible, and then seeds were sterilized at 121 °C for 30 min. Half of the young seedlings were inoculated with about 300 F. mosseae spores (BEG HEB02); the other half were not colonized by F. mosseae. The peanut seedlings were grown in a greenhouse at 24 °C/18 °C with a 16/8 h photoperiod, at a photosynthetic photo flux density of 700 µmol·m⁻²·s⁻¹, and 60% relative humidity. Each seedling was watered regularly with 80 ml of modified Hoagland’s solution (5 mM KNO₃, 2 mM MgSO₄·7H₂O, 1 mM KH₂PO₄, 0.1 mM EDTA-Na₂, 0.1 mM FeSO₄·7H₂O, 46 µM H₃BO₄, 0.32 µM CuSO₄·5H₂O, 0.77 µM ZnSO₄·7H₂O and 0.11 µM H₂MoO₄) supplemented with 6 mM Ca(NO₃)₂·4H₂O (Ca²⁺ sufficient) or 6 mM NH₄·NO₃ (Ca²⁺ deficient, used for balancing nitrogen in Ca(NO₃)₂). There were four treatments: Ca₀-AM, Ca₀ + AM, Ca₆ − AM, and Ca₆ + AM, where 0 and 6 represent the Ca²⁺ concentrations (mM), + and − represent with or without inoculation of F. mosseae spores. In this study, 6 mM of Ca(NO₃)₂ was chosen according to our previous report⁶. Six weeks later, the shoots and roots of AM and NM plants were harvested and further analyzed.

Mycorrhizal quantification and determination of dry weight and Ca²⁺ content

After six weeks, shoots and roots of the AM and NM plants under Ca²⁺-deficient or Ca²⁺-sufficient conditions were harvested separately. Young roots of AM plants were examined by light microscopy (OLYMPUS, CX41, Japan) to estimate the extent to which the roots had been colonized by hyphae and arbuscules⁴⁶. The fresh shoots and roots were dried at 105 °C for 30 min, and then dried at 80 °C until a constant weight. The Ca²⁺ contents in the roots from the different treatments were determined according to Yang et al.⁶.

RNA extraction and sequencing

Total RNA was isolated from roots of AM and NM plants, and then enrichment of mRNA and synthesis of cDNA were conducted¹. The cDNA from three biological replicates composed of four plants in each treatment were sequenced using an Illumina HiSeq. 2000 Platform. After filtering, high quality clean reads were aligned with a reference genome (https://peanutbase.org/organism/Arachis/ipaensis) using HISAT⁴⁷; on average 70.61% reads were mapped, indicating that the samples were comparable.

RNA-Seq analysis and data deposition

After genome mapping, we used StringTie software to reconstruct transcripts with genome annotation information⁴⁷, then identified novel transcripts using Cuffcompare and predicted the coding ability of those new transcripts using CPC software^48,49. After novel transcript detection, the gene expression level was calculated for each sample with RSEM⁵⁰. Based on the gene expression level, we used DEseq. 2 algorithms to detect differentially expressed genes (DEGs). A threshold of 1 for transcript ratio (log₂FoldChange) in treatments versus control (Ca₀-AM), and Padj (statistic of adjusted P value) ≤0.05 were set as criteria for the selection of DEGs in NM plants and AM plants under Ca²⁺-deficient and Ca²⁺-sufficient conditions. With DEGs, Gene Ontology (GO) classification and functional enrichment were performed using WEGO software⁵¹, and the pathway analyses were obtained using the KEGG database (https://www.genome.jp/kegg/pathway.html).

Quantitative real-time PCR

To verify the RNA-Seq results, the expression levels of 15 selected genes were determined by quantitative RT-PCR. mRNA was isolated from the same samples sequenced by RNA-Seq, and the first-strand cDNAs were synthesized for qRT-PCR analyses using SYBR Premix Ex Taq polymerase (Takara) according to the manufacturer’s protocol. The designed primers are shown in Supplementary Table S4. The control reactions were conducted using primers Tua5-F and Tua5-R⁵². At least three replicates were tested per sample. Relative mRNA (fold) differences were assessed with the 2^{− ΔΔCt} formula⁵³, the values were subsequently transformed to the log₂ scale.

Determination of plant hormones

The roots (fresh weight) were ground into a powder in liquid nitrogen, and 1.0 g of powder was used to determine the concentration of endogenous hormones by high performance liquid chromatography (HPLC)⁵⁴, including IAA, tZR, and GA₃. The SA content was measured according to a previous method⁵⁵. Three independent replicates per sample were statistically analyzed.

Carotenoid and flavonoid content analyses

Carotenoids were extracted from the roots of AM and NM plants⁵⁶. Total carotenoid content in roots was calculated using absorbance at 450 nm. Flavonoids in roots were measured by chloride colorimetric assay⁵⁷, and total flavonoid content was determined according to the standard curve of quercetin at an absorbance of 510 nm.

Statistical analysis

Analysis of variance was performed using SSPS software version 16.0 for Windows. One-way analysis of variance (ANOVA) was used, followed by Duncan's test for multiple comparisons. The values obtained are the mean ± SE for the three replicates in each treatment. A P value ≤ 0.05 was considered to be significant.

Author contributions

S.W. and X.L. designed the experiment and drafted the manuscript. L.C. and F.G. carried out most of the experiments and analyzed the transcriptome data. J.Z. and S.Y. determined the hormone levels. J.M. and Y.G. performed the validation of qRT-PCR experiment. All authors read and approved the final manuscript.

Competing interests

The authors declare no competing interests.

Supplementary information

is available for this paper at 10.1038/s41598-019-52630-7.