International Journal of Molecular Sciences

Research

15 pages, 4175 KiB

Open AccessArticle

Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Seed-Shattering-Related Genes in Common Buckwheat

by Chuyi Chen, Yuke Zhang, Yang Liu, Jingbin Cui, Xingxing He, Yichao Wu, Linqing Yue, Jian Zhang, Mengqi Ding, Zelin Yi and Xiaomei Fang

Int. J. Mol. Sci. 2023, 24(12), 10013; https://doi.org/10.3390/ijms241210013 - 11 Jun 2023

Viewed by 1177

Abstract

Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the [...] Read more.

Common buckwheat (Fagopyrum esculentum M.) is an important traditional miscellaneous grain crop. However, seed-shattering is a significant problem in common buckwheat. To investigate the genetic architecture and genetic regulation of seed-shattering in common buckwheat, we constructed a genetic linkage map using the F₂ population of Gr (green-flower mutant and shattering resistance) and UD (white flower and susceptible to shattering), which included eight linkage groups with 174 loci, and detected seven QTLs of pedicel strength. RNA-seq analysis of pedicel in two parents revealed 214 differentially expressed genes DEGs that play roles in phenylpropanoid biosynthesis, vitamin B6 metabolism, and flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) was performed and screened out 19 core hub genes. Untargeted GC-MS analysis detected 138 different metabolites and conjoint analysis screened out 11 DEGs, which were significantly associated with differential metabolites. Furthermore, we identified 43 genes in the QTLs, of which six genes had high expression levels in the pedicel of common buckwheat. Finally, 21 candidate genes were screened out based on the above analysis and gene function. Our results provided additional knowledge for the identification and functions of causal candidate genes responsible for the variation in seed-shattering and would be an invaluable resource for the genetic dissection of common buckwheat resistance-shattering molecular breeding. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

19 pages, 5770 KiB

Open AccessArticle

Volatile Composition and Classification of Paeonia lactiflora Flower Aroma Types and Identification of the Fragrance-Related Genes

by Qian Zhao, Lina Gu, Yuqing Li, Hui Zhi, Jianrang Luo and Yanlong Zhang

Int. J. Mol. Sci. 2023, 24(11), 9410; https://doi.org/10.3390/ijms24119410 - 28 May 2023

Cited by 4 | Viewed by 2069

Abstract

Flower scent is one of the main ornamental characteristics of herbaceous peony, and the improvement of flower fragrance is a vital objective of herbaceous peony breeding. In this study, 87 herbaceous peony cultivars were divided into three groups (no/light fragrance, medium fragrance, and [...] Read more.

Flower scent is one of the main ornamental characteristics of herbaceous peony, and the improvement of flower fragrance is a vital objective of herbaceous peony breeding. In this study, 87 herbaceous peony cultivars were divided into three groups (no/light fragrance, medium fragrance, and strong fragrance) based on their sensory evaluation scores, and 16 strong fragrance cultivars and one no fragrance cultivar were selected for subsequent analysis. Sixty-eight volatile components were detected in these 17 cultivars based on solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS), and 26 types were identified as important scent components. They were composed of terpenoids, benzenoids/phenylpropanoids, and fatty acid derivatives. According to the content and odor threshold of these main aroma components, the characteristic aroma substances of herbaceous peony were identified, including linalool, geraniol, citronellol, and phenylethyl alcohol (2-PE). The cultivars of strong scented herbaceous peony were divided into three types: rose scent, lily scent, and mixed scent. We explored the possible key genes of characteristic aroma substances in herbaceous peony petals with different odors through the qRT-PCR. The key genes encoding monoterpene biosynthesis were found to be PlDXS2, PlDXR1, PlMDS1, PlHDR1, PlGPPS3, and PlGPPS4. In addition, the linalool synthase (LIS) gene and the geraniol synthase (GES) gene were also found. PlAADC1, PlPAR1, and PlMAO1, related to the biosynthesis of 2-PE were detected, and the synthetic pathway of 2-PE was speculated. In conclusion, these findings revealed that the difference in gene expression of monoterpene and 2-PE synthesis pathway was related to the difference in the fragrance of herbaceous peony. This study explored the releasing pathway of herbaceous peony characteristic aroma substances and provided key genetic resources for fragrance improvement. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

18 pages, 3711 KiB

Open AccessArticle

The Transcription Factors WRKY41 and WRKY53 Mediate Early Flowering Induced by the Novel Plant Growth Regulator Guvermectin in Arabidopsis thaliana

by Chenyu Yang, Chongxi Liu, Shanshan Li, Yanyan Zhang, Yi Zhang, Xiangjing Wang and Wensheng Xiang

Int. J. Mol. Sci. 2023, 24(9), 8424; https://doi.org/10.3390/ijms24098424 - 8 May 2023

Cited by 4 | Viewed by 1878

Abstract

Flowering is a crucial stage for plant reproductive success; therefore, the regulation of plant flowering has been widely researched. Although multiple well-defined endogenous and exogenous flowering regulators have been reported, new ones are constantly being discovered. Here, we confirm that a novel plant [...] Read more.

Flowering is a crucial stage for plant reproductive success; therefore, the regulation of plant flowering has been widely researched. Although multiple well-defined endogenous and exogenous flowering regulators have been reported, new ones are constantly being discovered. Here, we confirm that a novel plant growth regulator guvermectin (GV) induces early flowering in Arabidopsis. Interestingly, our genetic experiments newly demonstrated that WRKY41 and its homolog WRKY53 were involved in GV-accelerated flowering as positive flowering regulators. Overexpression of WRKY41 or WRKY53 resulted in an early flowering phenotype compared to the wild type (WT). In contrast, the w41/w53 double mutants showed a delay in GV-accelerated flowering. Gene expression analysis showed that flowering regulatory genes SOC1 and LFY were upregulated in GV-treated WT, 35S:WRKY41, and 35S:WRKY53 plants, but both declined in w41/w53 mutants with or without GV treatment. Meanwhile, biochemical assays confirmed that SOC1 and LFY were both direct targets of WRKY41 and WRKY53. Furthermore, the early flowering phenotype of 35S:WRKY41 lines was abolished in the soc1 or lfy background. Together, our results suggest that GV plays a function in promoting flowering, which was co-mediated by WRKY41 and WRKY53 acting as new flowering regulators by directly activating the transcription of SOC1 and LFY in Arabidopsis. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

19 pages, 3672 KiB

Open AccessArticle

Study on the Flower Induction Mechanism of Hydrangea macrophylla

by Yun Liu, Tong Lyu and Yingmin Lyu

Int. J. Mol. Sci. 2023, 24(9), 7691; https://doi.org/10.3390/ijms24097691 - 22 Apr 2023

Cited by 3 | Viewed by 2788

Abstract

The flower induction of Hydrangea macrophylla “Endless Summer” is regulated by a complex gene network that involves multiple signaling pathways to ensure continuous flowering throughout the growing season, but the molecular determinants of flower induction are not yet clear. In this study, genes [...] Read more.

The flower induction of Hydrangea macrophylla “Endless Summer” is regulated by a complex gene network that involves multiple signaling pathways to ensure continuous flowering throughout the growing season, but the molecular determinants of flower induction are not yet clear. In this study, genes potentially involved in signaling pathway mediating the regulatory mechanism of flower induction were identified through the transcriptomic profiles, and a hypothetical model for this regulatory mechanism was obtained by an analysis of the available transcriptomic data, suggesting that sugar-, hormone-, and flowering-related genes participated in the flower induction process of H. macrophylla “Endless Summer”. The expression profiles of the genes involved in the biosynthesis and metabolism of sugar showed that the beta-amylase gene BAM1 displayed a high expression level at the BS2 stage and implied the hydrolysis of starch. It may be a signaling molecule that promotes the transition from vegetative growth to reproductive growth in H. macrophylla “Endless Summer”. Complex hormone regulatory networks involved in abscisic acid (ABA), auxin (IAA), zeatin nucleoside (ZR), and gibberellin (GA) also induced flower formation in H. macrophylla. ABA participated in flower induction by regulating flowering genes. The high content of IAA and the high expression level of the auxin influx carrier gene LAX5 at the BS2 stage suggested that the flow of auxin between sources and sinks in H. macrophylla is involved in the regulation of floral induction as a signal. In addition, flowering-related genes were mainly involved in the photoperiodic pathway, the aging pathway, and the gibberellin pathway. As a result, multiple pathways, including the photoperiodic pathway, the aging pathway, and the gibberellin pathway, which were mainly mediated by crosstalk between sugar and hormone signals, regulated the molecular network involved in flower induction in H. macrophylla “Endless Summer”. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

14 pages, 2044 KiB

Open AccessArticle

Identification and Characterization of Transcription Factors Involved in Geraniol Biosynthesis in Rosa chinensis

by Jiayao Yu, Xiaoyu Liu, Yifang Peng, Qi Li and Yu Han

Int. J. Mol. Sci. 2022, 23(23), 14684; https://doi.org/10.3390/ijms232314684 - 24 Nov 2022

Cited by 4 | Viewed by 1801

Abstract

Fragrance is an important characteristic of rose flowers and is largely determined by the terpenes. Rose has a unique NUDX1 (NUDIX HYDROLASES 1)–dependent monoterpene geraniol biosynthesis pathway, but little is known about its transcriptional regulation. In this study, we characterized two China rose [...] Read more.

Fragrance is an important characteristic of rose flowers and is largely determined by the terpenes. Rose has a unique NUDX1 (NUDIX HYDROLASES 1)–dependent monoterpene geraniol biosynthesis pathway, but little is known about its transcriptional regulation. In this study, we characterized two China rose (Rosa chinensis) materials from the ‘Old Blush’ variety with contrasting aromas. We profiled the volatile metabolome of both materials, and the results revealed that geraniol was the main component that distinguishes the aroma of these two materials. We performed a comparative transcriptome analysis of the two rose materials, from which we identified the hydrolase RcNUDX1 as a key factor affecting geraniol content, as well as 17 transcription factor genes co-expressed with RcNUDX1. We also determined that the transcription factor RcWRKY70 binds to four W–box motifs in the promoter of RcNUDX1, repressing RcNUDX1 expression, based on yeast one-hybrid and transient dual-luciferase assays. These results provide important information concerning the transcriptional regulatory framework underlying the control of geraniol production in rose. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

12 pages, 2194 KiB

Open AccessArticle

FaesAP3_1 Regulates the FaesELF3 Gene Involved in Filament-Length Determination of Long-Homostyle Fagopyrum esculentum

by Zhiyuan Ma, Qingyu Yang, Lingtian Zeng, Jiayi Li, Xinyu Jiao and Zhixiong Liu

Int. J. Mol. Sci. 2022, 23(22), 14403; https://doi.org/10.3390/ijms232214403 - 19 Nov 2022

Viewed by 1320

Abstract

The identification downstream genes of floral organ identity regulators are critical to revealing the molecular mechanisms underlying floral morphogenesis. However, a general regulatory pathway between floral organ identity genes and their downstream targets is still unclear because of the lack of studies in [...] Read more.

The identification downstream genes of floral organ identity regulators are critical to revealing the molecular mechanisms underlying floral morphogenesis. However, a general regulatory pathway between floral organ identity genes and their downstream targets is still unclear because of the lack of studies in nonmodel species. Here, we screened a direct downstream target gene, FaesELF3, of a stamen identity transcription factor, FaesAP3_1, in long-homostyle (LH) Fagopyrum esculentum moench by using yeast one-hybrid (Y1H) and dual-luciferase reporter (DR) assays. Furthermore, FaesAP3_1-silenced LH plants that produced flowers with part stamens or anthers homeotically converted into a tepaloid structure, and FaesELF3-silenced plants that had flowers with part stamens consisting of a short filament and empty anther (male sterile anther). All these suggested that transcription factor (TF) FaesAP3_1 directly activates FaesELF3 in order to regulate filament elongation and pollen grain development in LH buckwheat. Our data also suggested that other stamen development pathways independent of FaesAP3_1 remain in F. esculentum. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

20 pages, 10758 KiB

Open AccessArticle

Exploring the Molecular Mechanism of Sepal Formation in the Decorative Flowers of Hydrangea macrophylla ′Endless Summer′ Based on the ABCDE Model

by Qi Wang, Tong Lyu and Yingmin Lyu

Int. J. Mol. Sci. 2022, 23(22), 14112; https://doi.org/10.3390/ijms232214112 - 15 Nov 2022

Cited by 2 | Viewed by 2398

Abstract

With its large inflorescences and colorful flowers, Hydrangea macrophylla has been one of the most popular ornamental plants in recent years. However, the formation mechanism of its major ornamental part, the decorative floret sepals, is still not clear. In this study, we compared [...] Read more.

With its large inflorescences and colorful flowers, Hydrangea macrophylla has been one of the most popular ornamental plants in recent years. However, the formation mechanism of its major ornamental part, the decorative floret sepals, is still not clear. In this study, we compared the transcriptome data of H. macrophylla ‘Endless Summer’ from the nutritional stage (BS1) to the blooming stage (BS5) and annotated them into the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. The 347 identified differentially expressed genes (DEGs) associated with flower development were subjected to a trend analysis and a protein–protein interaction analysis. The combined analysis of the two yielded 60 DEGs, including four MADS-box transcription factors (HmSVP-1, HmSOC1, HmAP1-2, and HmAGL24-3) and genes with strong connectivity (HmLFY and HmUFO). In addition, 17 transcription factors related to the ABCDE model were screened, and key candidate genes related to the development of decorative floret sepals in H. macrophylla were identified by phylogenetic and expression pattern analysis, including HmAP1-1, HmAP1-2, HmAP1-3, HmAP2-3, HmAP2-4, and HmAP2-5. On this basis, a gene regulatory network model of decorative sepal development was also postulated. Our results provide a theoretical basis for the study of the formation mechanism of decorative floret sepals and suggest a new direction for the molecular breeding of H. macrophylla. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

15 pages, 1984 KiB

Open AccessArticle

Genome-Wide Analysis of SQUAMOSA-Promoter-Binding Protein-like Family in Flowering Pleioblastus pygmaeus

by Wenjing Yao, Chuanzhe Li, Huajun Fu, Meng Yang, Hongyu Wu, Yulong Ding, Long Li and Shuyan Lin

Int. J. Mol. Sci. 2022, 23(22), 14035; https://doi.org/10.3390/ijms232214035 - 14 Nov 2022

Cited by 2 | Viewed by 1693

Abstract

SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL [...] Read more.

SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus. Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies. Homologous analysis shows that as many as 32 pairs of homologous genes were found between P. pygmaeus and rice, and 83 pairs were found between P. pygmaeus and Moso bamboo, whose Ka/Ks values are all <1. MiRNA target prediction reveals that 13 out of the 28 PpSPLs have recognition sites complementary to miRNA156. To screen the SPLs involved in the reproductive growth of bamboo plants, the mRNA abundance of the 28 PpSPLs was profiled in the different tissues of flowering P. pygmaeus and non-flowering plants by RNA-Seq. Moreover, the relative expression level of eight PpSPLs is significantly higher in flowering P. pygmaeus than that in non-flowering plants, which was also validated by RT-qPCR. Combined with phylogenetic analysis and homologous analysis, the eight significant, differentially expressed PpSPLs were identified to be associated with the reproductive process and flower organ development. Among them, there are four potential miRNA156-targeting PpSPLs involved in the flowering process. Of significant interest in the study is the identification of 28 SPLs and the exploration of four key flowering-related SPLs from P. pygmaeus, which provides a theoretic basis for revealing the underlying functions of SPLs in the reproductive growth of bamboo plants. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

19 pages, 6030 KiB

Open AccessArticle

The miR156-Targeted SQUAMOSA PROMOTER BINDING PROTEIN (PmSBP) Transcription Factor Regulates the Flowering Time by Binding to the Promoter of SUPPRESSOR OF OVEREXPRESSION OF CO1 (PmSOC1) in Prunus mume

by Xue Yong, Tangchun Zheng, Yu Han, Tianci Cong, Ping Li, Weichao Liu, Aiqing Ding, Tangren Cheng, Jia Wang and Qixiang Zhang

Int. J. Mol. Sci. 2022, 23(19), 11976; https://doi.org/10.3390/ijms231911976 - 9 Oct 2022

Cited by 2 | Viewed by 1553

Abstract

Prunus mume, a famous perennial ornamental plant and fruit tree in Asia, blooms in winter or early spring in the Yangtze River area. The flowering time directly determines its ornamental and economic value, so it is of great significance to study the [...] Read more.

Prunus mume, a famous perennial ornamental plant and fruit tree in Asia, blooms in winter or early spring in the Yangtze River area. The flowering time directly determines its ornamental and economic value, so it is of great significance to study the molecular mechanism of flowering time. SQUAMOSA PROMOTER BINDING PROTEIN (SBP), often regulated by miR156, is an important flowering regulator, although its function is unknown in P. mume. Here, 11 miR156 precursors were analyzed and located in five chromosomes of the P. mume genome. The expression pattern showed that PmSBP1/6 was negatively correlated with miR156. The promoters of PmSBP1/6 were specifically expressed in the apical meristem. Overexpression of PmSBP1/6 in tobacco promoted flowering and changed the length ratio of pistil and stamen. Moreover, PmSBP1 also affected the number and vitality of pollen and reduced the fertility of transgenic tobacco. Furthermore, ectopic expression of PmSBP1/6 caused up-regulated expression of endogenous SUPPRESSOR OF OVEREXPRESSION OF CO1 (NtSOC1). The yeast-one hybrid assay showed that PmSBP1 was bonded to the promoters of PmSOC1s. In conclusion, a miR156-PmSBP1-PmSOC1s pathway was formed to participate in the regulation of flowering time in P. mume, which provided references for the molecular mechanism of flowering time regulation and molecular breeding of P. mume. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

15 pages, 5668 KiB

Open AccessArticle

Identification and Characterization of Circular RNAs Involved in the Flower Development and Senescence of Rhododendron delavayi Franch

by Xiaorong Xu, Yufeng Xiao, Ximin Zhang, Ming Tang and Jing Tang

Int. J. Mol. Sci. 2022, 23(19), 11214; https://doi.org/10.3390/ijms231911214 - 23 Sep 2022

Cited by 1 | Viewed by 1324

Abstract

Floral development and senescence are a crucial determinant for economic and ornamental value. CircRNAs play an essential role in regulating plant growth and development; however, there is no systematic identification of circRNAs during the lifespan of flowers. This study aims to explore the [...] Read more.

Floral development and senescence are a crucial determinant for economic and ornamental value. CircRNAs play an essential role in regulating plant growth and development; however, there is no systematic identification of circRNAs during the lifespan of flowers. This study aims to explore the expression profile and functional role of circRNAs in the full flowering stages of Rhododendron delavayi Franch. We carried out transcriptome sequencing of the six stages of Rhododendron delavayi Franch flowers to identify the circular RNA expression profile. In addition, using bioinformatics methods, we explored the functions of circRNAs, including analysis of the circRNA-miRNA-mRNA network, short time-series expression miner (STEM), and so on. We identified 146 circRNAs, of which 79 were differentially expressed from the budding to fading stages. Furthermore, using STEM analysis, one of the 42 circRNA expression model profiles was significantly upregulated during the senescence stage, including 16 circRNAs. Additionally, 7 circRNA-miRNA-mRNA networks were constructed with 10 differentially expressed circRNAs, in which some target mRNA may regulate the development and senescence of the Rhododendron flowers. Finally, by analyzing the correlation between circRNAs and mRNA, combined with existing reports, we proposed that circRNAs play a regulatory role during flower development and senescence by mediating the jasmonate signaling pathway. Overall, these results provide new clues to the potential mechanism of circRNAs acting as novel post-transcriptional regulators in the development and senescence process of flowers. Full article

(This article belongs to the Special Issue Transcriptional Regulatory Networks in Flowers)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Transcriptional Regulatory Networks in Flowers

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (10 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI