An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat

Jing, Danlong; Chen, Weiwei; Hu, Ruoqian; Zhang, Yuchen; Xia, Yan; Wang, Shuming; He, Qiang; Guo, Qigao; Liang, Guolu

doi:10.3390/ijms21145107

Cited by 28 publications

(21 citation statements)

References 87 publications

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“…Herein, the flowering phenology of male and female flowers at a specific time ensures normal pollination and seed/fruit development. At present, studies on flowering are research hotspot for many model species and crucial horticultural plants [ 4 , 5 , 6 ]. In particular, for the model plant, Arabidopsis thaliana , several regulators involved in the flowering induction have been identified through studies on the ambient temperature, vernalization, photoperiod, gibberellin (GA), autonomous, age-dependent, circadian clock, and trehalose-6-phosphate (T6P) pathway [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Han

Cai

et al. 2022

IJMS

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Flowers are imperative reproductive organs and play a key role in the propagation of offspring, along with the generation of several metabolic products in flowering plants. In Juglans mandshurica, the number and development of flowers directly affect the fruit yield and subsequently its commercial value. However, owing to the lack of genetic information, there are few studies on the reproductive biology of Juglans mandshurica, and the molecular regulatory mechanisms underlying the development of female and male inflorescence remain unclear. In this study, phytohormones and transcriptomic sequencing analyses at the three stages of female and male inflorescence growth were performed to understand the regulatory functions underlying flower development. Gibberellin is the most dominant phytohormone that regulates flower development. In total, 14,579 and 7188 differentially expressed genes were identified after analyzing the development of male and female flowers, respectively, wherein, 3241 were commonly expressed. Enrichment analysis for significantly enriched pathways suggested the roles of MAPK signaling, phytohormone signal transduction, and sugar metabolism. Genes involved in floral organ transition and flowering were obtained and analyzed; these mainly belonged to the M-type MADS-box gene family. Three flowering-related genes (SOC1/AGL20, ANT, and SVP) strongly interacted with transcription factors in the co-expression network. Two key CO genes (CO3 and CO1) were identified in the photoperiod pathway. We also identified two GA20xs genes, one SVP gene, and five AGL genes (AGL8, AGL9, AGL15, AGL19, and AGL42) that contributed to flower development. The findings are expected to provide a genetic basis for the studies on the regulatory networks and reproductive biology in inflorescence development for J. mandshurica.

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Section: Introductionmentioning

confidence: 99%

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Han

Cai

et al. 2022

IJMS

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“…In EF vs. LF, “starch and sucrose metabolism” was the mainly enriched pathway. The two pathways were also reported in the integrative analysis of flower bud differentiation, flower bud elongation, and floral anthesis in Loquat ( Eriobotrya japonica ) (Jing et al, 2020 ). Based on these KEGG pathways, not only known flowering genes but also transcription factors, and plant hormone signal transduction, were selected as the flowering candidate genes of E. sibiricus .…”

Section: Discussionmentioning

confidence: 84%

Identification of Flowering Regulatory Networks and Hub Genes Expressed in the Leaves of Elymus sibiricus L. Using Comparative Transcriptome Analysis

et al. 2022

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Flowering is a significant stage from vegetative growth to reproductive growth in higher plants, which impacts the biomass and seed yield. To reveal the flowering time variations and identify the flowering regulatory networks and hub genes in Elymus sibiricus, we measured the booting, heading, and flowering times of 66 E. sibiricus accessions. The booting, heading, and flowering times varied from 136 to 188, 142 to 194, and 148 to 201 days, respectively. The difference in flowering time between the earliest- and the last-flowering accessions was 53 days. Furthermore, transcriptome analyses were performed at the three developmental stages of six accessions with contrasting flowering times. A total of 3,526 differentially expressed genes (DEGs) were predicted and 72 candidate genes were identified, including transcription factors, known flowering genes, and plant hormone-related genes. Among them, four candidate genes (LATE, GA2OX6, FAR3, and MFT1) were significantly upregulated in late-flowering accessions. LIMYB, PEX19, GWD3, BOR7, PMEI28, LRR, and AIRP2 were identified as hub genes in the turquoise and blue modules which were related to the development time of flowering by weighted gene co-expression network analysis (WGCNA). A single-nucleotide polymorphism (SNP) of LIMYB found by multiple sequence alignment may cause late flowering. The expression pattern of flowering candidate genes was verified in eight flowering promoters (CRY, COL, FPF1, Hd3, GID1, FLK, VIN3, and FPA) and four flowering suppressors (CCA1, ELF3, Ghd7, and COL4) under drought and salt stress by qRT-PCR. The results suggested that drought and salt stress activated the flowering regulation pathways to some extent. The findings of the present study lay a foundation for the functional verification of flowering genes and breeding of new varieties of early- and late-flowering E. sibiricus.

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“…However, ARF, SAUR, PYL, PLR, and other genes were significantly expressed in the signaling pathway of IAA and ABA in the male and female flower buds of J. mandshurica , indicating that these two plant hormones could regulate the differentiation of male and female flower buds. The endogenous GA3, ZT and ABA of loquat ( Eriobotrya japonica ) flower were determined during its development, and it was found that there was a high correlation between the change of endogenous hormone concentration and the expression level of genes related to hormone signal transduction pathway ( Jing et al, 2020 ). In addition, transcriptome analysis of Madhuca pasquieri showed that auxin, GA, ABA and cytokinin metabolism pathway were related to seed germination and post germination ( Kan et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim

BaiTing

Sun

et al. 2021

PeerJ

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Juglans mandshurica Maxim is a hermaphroditic plant belonging to the genus Juglans in the family Juglandaceae. The pollination period of female flowers is different from the loose powder period of male flowers on the same tree. In several trees, female flowers bloom first, whereas in others, male flowers bloom first. In this study, male and female flower buds of J. mandshurica at the physiological differentiation stage were used. Illumina-based transcriptome sequencing was performed, and the quality of the sequencing results was evaluated and analyzed. A total of 138,138 unigenes with an average length of 788 bp were obtained. There were 8,116 differentially expressed genes (DEGs); 2,840 genes were upregulated, and 5,276 genes were downregulated. The DEGs were classified by Gene Ontology and analyzed by Kyoto Encyclopedia of Genes and Genomes. The signal transduction factors involved in phytohormone synthesis were selected. The results displayed that ARF and SAUR were expressed differently in the auxin signaling pathway. Additionally, DELLA protein (a negative regulator of gibberellin), the cytokinin synthesis pathway, and A-ARR were downregulated. On April 2nd, the contents of IAA, GA, CTK, ETH and SA in male and female flower buds of two types of J. mandshurica were opposite, and there were obvious genes regulating gender differentiation. Overall, we found that the sex differentiation of J. mandshurica was related to various hormone signal transduction pathways, and hormone signal transduction plays a leading role in regulation.

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An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat

Cited by 28 publications

References 87 publications

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Characterization of Phytohormones and Transcriptomic Profiling of the Female and Male Inflorescence Development in Manchurian Walnut (Juglans mandshurica Maxim.)

Identification of Flowering Regulatory Networks and Hub Genes Expressed in the Leaves of Elymus sibiricus L. Using Comparative Transcriptome Analysis

Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim

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