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Article ; Online: Genome-wide identification of the bHLH transcription factor family in Rosa persica and response to low-temperature stress

Yueying Zhuang / Lijun Zhou / Lifang Geng / Lv Jiang / Yunji Sui / Le Luo / Huitang Pan / Qixiang Zhang / Chao Yu

PeerJ, Vol 12, p e

2024 Volume 16568

Abstract: Background Basic helix-loop-helix (bHLH) transcription factors are involved in plant growth and development, secondary metabolism, and abiotic stress responses have been studied in a variety of plants. Despite their importance in plant biology, the roles ...

Abstract	Background Basic helix-loop-helix (bHLH) transcription factors are involved in plant growth and development, secondary metabolism, and abiotic stress responses have been studied in a variety of plants. Despite their importance in plant biology, the roles and expression patterns of bHLH family genes in Rosa persica have not been determined. Methods In this study, the RbebHLH family genes were systematically analyzed using bioinformatics methods, and their expression patterns under low-temperature stress were analyzed by transcriptome and related physiological index measurements. Results In total, 142 RbebHLHs were identified in the genome of R. persica, distributed on seven chromosomes. Phylogenetic analysis including orthologous genes in Arabidopsis divided RbebHLHs into 21 subfamilies, with similar structures and motifs within a subfamily. A collinearity analysis revealed seven tandem duplications and 118 segmental duplications in R. persica and 127, 150, 151, 172, and 164 segmental duplications between R. persica and Arabidopsis thaliana, Prunus mume, Fragaria vesca, Rosa chinensis, and Prunus persica, respectively. A number of cis-regulatory elements associated with abiotic stress response and hormone response were identified in RbebHLHs, and 21 RbebHLHs have potential interactions with the CBF family. In addition, the expression results showed that part of bHLH may regulate the tolerance of R. persica to low-temperature stress through the jasmonic acid and pathway. Transcriptomic data showed that the expression levels of different RbebHLHs varied during overwintering, and the expression of some RbebHLHs was significantly correlated with relative conductivity and MDA content, implying that RbebHLHs play important regulatory roles in R. persica response to low-temperature stress. Overall, this study provides valuable insights into the study of RbebHLHs associated with low-temperature stress.
Keywords	Rosa persica ; Basic helix-loop-helix transcription factor ; Gene expression ; Transcription factor ; Low-temperature stress ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Functional Analysis of Aux/IAA s and SAUR s on Shoot Growth of Lagerstroemia indica through Virus-Induced Gene Silencing (VIGS)

Lu Feng / Xiaohan Liang / Yang Zhou / Ye Zhang / Jieru Liu / Ming Cai / Jia Wang / Tangren Cheng / Qixiang Zhang / Huitang Pan

Forests, Vol 11, Iss 1288, p

2020 Volume 1288

Abstract: The plant hormone auxin plays an important role in cell division and the elongation of shoots to affect the plant architecture, which has a great impact on the plant yield, fruit quality and ornamental value; however, the regulatory mechanism of auxin ... ...

Abstract	The plant hormone auxin plays an important role in cell division and the elongation of shoots to affect the plant architecture, which has a great impact on the plant yield, fruit quality and ornamental value; however, the regulatory mechanism of auxin controlling shoot growth is unclear in crape myrtle. In this study, two auxin/indole-3-acetic acid ( Aux/IAA) genes and four small auxin upregulated RNA ( SAUR) genes of auxin response gene families were isolated from dwarf and non-dwarf progenies of Lagerstroemia indica and then functionally characterized. Sequence alignment revealed that the six genes contain typical conserved domains. Different expression patterns of the six genes at three different tissue stages of two types of progenies showed that the regulation mechanism of these genes may be different. Functional verification of the six genes upon shoot growth of crape myrtle was performed via virus-induced gene silencing. When the LfiAUX22 gene was silenced, a short shoot phenotype was observed in non-dwarf progenies, accompanied by decreased auxin content. Therefore, we preliminarily speculated that LfiAUX22 plays an important role in the shoot growth of crape myrtle, which regulates the accumulation of indole-3-acetic acid (IAA) and the elongation of cells to eventually control shoot length.
Keywords	Lagerstroemia indica ; branch growth ; auxin ; Aux/IAA ; SAUR ; VIGS ; Plant ecology ; QK900-989
Subject code	580
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Reference gene selection for qRT-PCR analysis of flower development in Lagerstroemia indica and L. speciosa.

Tangchun Zheng / Zhilin Chen / Yiqian Ju / Han Zhang / Ming Cai / Huitang Pan / Qixiang Zhang

PLoS ONE, Vol 13, Iss 3, p e

2018 Volume 0195004

Abstract: Quantitative real-time polymerase chain reaction (qRT-PCR) is a prevalent method for gene expression analysis, depending on the stability of the reference genes for data normalization. Lagerstroemia indica and L. speciosa are popular ornamental plants ... ...

Abstract	Quantitative real-time polymerase chain reaction (qRT-PCR) is a prevalent method for gene expression analysis, depending on the stability of the reference genes for data normalization. Lagerstroemia indica and L. speciosa are popular ornamental plants which are famous for the long flowering period. However, no systematic studies on reference genes in Lagerstroemia have yet been conducted. In the present study, we selected nine candidate reference genes (GAPDH, TUA, TUB, 18S, RPII, EF-1α, ATC, EIF5A and CYP) and evaluated their expression stability in different tissues during floral development of L. indica and L. speciosa using four algorithms (geNorm, NormFinder, BestKeeper and, RefFinder). Results showed that RPII and EF-1α were the most stably expressed and suitable reference genes for both of Lagerstroemia species. Moreover, ACT exhibited high expression stability in L. indica and GAPDH was a suitable reference gene for L. speciosa in different flower development stages. TUB was an unsuitable reference gene for gene expression normalization due to significant variations in expression across all samples. Finally, we verified the reliability of the selected candidate reference genes by amplifying an AGAMOUS homolog (LsAG1) of Arabidopsis thaliana. This study provides a list of suitable reference genes, thereby broadening the genetic basis of the gene expression patterns in Lagerstroemia species.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Red to Far-Red Light Ratio Modulates Hormonal and Genetic Control of Axillary bud Outgrowth in Chrysanthemum (Dendranthema grandiflorum ‘Jinba’)

Cunquan Yuan / Sagheer Ahmad / Tangren Cheng / Jia Wang / Huitang Pan / Liangjun Zhao / Qixiang Zhang

International Journal of Molecular Sciences, Vol 19, Iss 6, p

2018 Volume 1590

Abstract: Single-flower cut Chrysanthemum (Dendranthema grandiflorum ‘Jinba’) holds a unique status in global floriculture industry. However, the extensive axillary bud outgrowth presents a major drawback. Shade is an environment cue that inhibits shoot branching. ...

Abstract	Single-flower cut Chrysanthemum (Dendranthema grandiflorum ‘Jinba’) holds a unique status in global floriculture industry. However, the extensive axillary bud outgrowth presents a major drawback. Shade is an environment cue that inhibits shoot branching. Present study was aimed at investigating the effect of ratio of red to far-red light (R:FR) in regulating the lateral bud outgrowth of Chrysanthemum and the detailed mechanism. Results showed that the fate of axillary buds at specific positions in stem exhibited difference in response to R:FR. Decreasing R:FR resulted in elevation of abscisic acid (ABA) accumulation in axillary buds. Expression of ABA, indole-3-acetic acid (IAA) and strigolactones (SL) -related metabolism and signal transduction genes was significantly changed in response to low R:FR. In addition, low R:FR caused the re-distribution of sucrose across the whole plant, driving more sucrose towards bottom buds. Our results indicate that low R:FR not always inhibits bud outgrowth, rather its influence depends on the bud position in the stem. ABA, SL and auxin pathways were involved in the process. Interestingly, sucrose also appears to be involved in the process which is necessary to pay attention in the further studies. The present study also lays the foundation for developing methods to regulate axillary bud outgrowth in Chrysanthemum.
Keywords	chrysanthemum ; R:FR ; bud outgrowth ; hormone ; sucrose ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2018-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Screening of Applicable SSR Molecular Markers Linked to Creeping Trait in Crape Myrtle

Tangchun Zheng / Bo Qin / Suzhen Li / Ming Cai / Huitang Pan / Jia Wang / Tangren Cheng / Qixiang Zhang

Forests, Vol 10, Iss 5, p

2019 Volume 429

Abstract: Creeping plants have unique ornamental value because they have more branches and flowers and the creeping trait is rare in crape myrtle ( Lagerstroemia indica L.). In this study, the first filial generation (F 1 ) population was derived from ... ...

Abstract	Creeping plants have unique ornamental value because they have more branches and flowers and the creeping trait is rare in crape myrtle ( Lagerstroemia indica L.). In this study, the first filial generation (F 1 ) population was derived from Lagerstroemia fauriei Koehne (standard) and L. indica “Creole” (creeping) and the backcross1 (BC 1 ) population was derived from the backcross of F 1 individual S82 (creeping) and L. fauriei . The segregation of the creeping trait was analyzed for 174 seedlings of the BC 1 population to examine the linkage relationship between simple sequence repeat (SSR) molecular markers and the creeping trait. Creeping genes were screened using bulked segregant analysis combined with 322 SSR primers, which were detected with good polymorphism. The results show that two SSR markers (S364 and LYS12) were detected, with genetic distances of 23.49 centimorgan (cM) and 25.86 cM from the loci controlling the plant opening angle trait and the branching angle trait, respectively. The accuracy rate for phenotypic verification using S364 and LYS12 was 76.51% and 74.14%, respectively. Our results provide basic information for the molecular marker-assisted selective breeding and cloning of the creeping gene to improve architecture diversity in the breeding of crape myrtle.
Keywords	Lagerstroemia species ; simple sequence repeat markers ; bulked segregant analysis ; creeping trait ; plant architecture ; Plant ecology ; QK900-989
Subject code	580
Language	English
Publishing date	2019-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Genetic Linkage Map of BC 2 Population Reveals QTL Associated with Plant Architecture Traits in Lagerstroemia

Yang Zhou / Yuanjun Ye / Lu Feng / Ye Zhang / Qifang Lin / Jieru Liu / Ming Cai / Jia Wang / Tangren Cheng / Qixiang Zhang / Huitang Pan

Forests, Vol 12, Iss 322, p

2021 Volume 322

Abstract: Plant architecture improvement is of great significance in influencing crop yield, harvesting efficiency and ornamental value, by changing the spatial structure of the canopy. However, the mechanism on plant architecture in woody plants is still unclear. ...

Abstract	Plant architecture improvement is of great significance in influencing crop yield, harvesting efficiency and ornamental value, by changing the spatial structure of the canopy. However, the mechanism on plant architecture in woody plants is still unclear. In order to study the genetic control of plant architecture traits and promote marker-assisted selection (MAS), a genetic linkage map was constructed, and QTL mapping was performed. In this study, using 188 BC 2 progenies as materials, a genetic map of Lagerstroemia was constructed using amplification fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers, and the QTLs of four key plant architecture traits (plant height, crown width, primary lateral branch height and internode length) were analyzed. The genetic map contains 22 linkage groups, including 198 AFLP markers and 36 SSR markers. The total length of the genome covered by the map is 1272 cM, and the average distance between markers is 6.8 cM. Three QTLs related to plant height were located in LG1, LG4 and LG17 linkage groups, and the phenotypic variation rates were 32.36, 16.18 and 12.73%, respectively. A QTL related to crown width was located in LG1 linkage group, and the phenotypic variation rate was 18.07%. Two QTLs related to primary lateral branch height were located in the LG1 and LG7 linkage groups, and the phenotypic variation rates were 20.59 and 15.34%, respectively. Two QTLs related to internode length were located in the LG1 and LG20 linkage groups, and the phenotypic variation rates were 14.86 and 9.87%. The results provide a scientific basis for finely mapping genes of plant architecture traits and marker-assisted breeding in Lagerstroemia .
Keywords	Lagerstroemia ; genetic map ; QTL ; plant height ; branching ; internode length ; Plant ecology ; QK900-989
Subject code	580
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: RcAP1 , a Homolog of APETALA1 , is Associated with Flower Bud Differentiation and Floral Organ Morphogenesis in Rosa chinensis

Yu Han / Aoying Tang / Jiayao Yu / Tangren Cheng / Jia Wang / Weiru Yang / Huitang Pan / Qixiang Zhang

International Journal of Molecular Sciences, Vol 20, Iss 14, p

2019 Volume 3557

Abstract: Rosa chinensis is one of the most popular flower plants worldwide. The recurrent flowering trait greatly enhances the ornamental value of roses, and is the result of the constant formation of new flower buds. Flower bud differentiation has always been a ... ...

Abstract	Rosa chinensis is one of the most popular flower plants worldwide. The recurrent flowering trait greatly enhances the ornamental value of roses, and is the result of the constant formation of new flower buds. Flower bud differentiation has always been a major topic of interest among researchers. The APETALA1 ( AP1 ) MADS-box (Mcm1, Agamous, Deficiens and SRF) transcription factor-encoding gene is important for the formation of the floral meristem and floral organs. However, research on the rose AP1 gene has been limited. Thus, we isolated AP1 from Rosa chinensis ‘Old Blush’. An expression analysis revealed that RcAP1 was not expressed before the floral primordia formation stage in flower buds. The overexpression of RcAP1 in Arabidopsis thaliana resulted in an early-flowering phenotype. Additionally, the virus-induced down-regulation of RcAP1 expression delayed flowering in ‘Old Blush’. Moreover, RcAP1 was specifically expressed in the sepals of floral organs, while its expression was down-regulated in abnormal sepals and leaf-like organs. These observations suggest that RcAP1 may contribute to rose bud differentiation as well as floral organ morphogenesis, especially the sepals. These results may help for further characterization of the regulatory mechanisms of the recurrent flowering trait in rose.
Keywords	APETALA1 ; Rosa chinensis ; sepal ; flower bud differentiation ; floral organ morphogenesis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcriptome analysis of the genes regulating phytohormone and cellular patterning in Lagerstroemia plant architecture

Yiqian Ju / Lu Feng / Jiyang Wu / Yuanjun Ye / Tangchun Zheng / Ming Cai / Tangren Cheng / Jia Wang / Qixiang Zhang / Huitang Pan

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 14

Abstract: Abstract Plant architecture is a popular research topic because plants with different growth habits that may generate economic or ornamental value are in great demand by orchards and nurseries. However, the molecular basis of the architecture of woody ... ...

Abstract	Abstract Plant architecture is a popular research topic because plants with different growth habits that may generate economic or ornamental value are in great demand by orchards and nurseries. However, the molecular basis of the architecture of woody perennial plants is poorly understood due to the complexity of the phenotypic and regulatory relationships. Here, transcriptional profiling of dwarf and non-dwarf crapemyrtles was performed, and potential target genes were identified based on the phenotype, histology and phytohormone metabolite levels. An integrated analysis demonstrated that the internode length was explained mainly by cell number and secondarily by cell length and revealed important hormones in regulatory pathway of Lagerstroemia architecture. Differentially expressed genes (DEGs) involved in phytohormone pathways and cellular patterning regulation were analysed, and the regulatory relationships between these parameters were evaluated at the transcriptional level. Exogenous indole-3-acetic acid (IAA) and gibberellin A4 (GA4) treatments further indicated the pivotal role of auxin in cell division within the shoot apical meristem (SAM) and suggested an interaction between auxin and GA4 in regulating the internode length of Lagerstroemia. These results provide insights for further functional genomic studies on the regulatory mechanisms underlying Lagerstroemia plant architecture and may improve the efficiency of woody plant molecular breeding.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2018-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whole-Transcriptome Analysis of Differentially Expressed Genes in the Vegetative Buds, Floral Buds and Buds of Chrysanthemum morifolium.

Hua Liu / Ming Sun / Dongliang Du / Huitang Pan / Tangren Cheng / Jia Wang / Qixiang Zhang

PLoS ONE, Vol 10, Iss 5, p e

2015 Volume 0128009

Abstract: Chrysanthemum morifolium is an important floral crop that is cultivated worldwide. However, due to a lack of genomic resources, very little information is available concerning the molecular mechanisms of flower development in chrysanthemum.The ... ...

Abstract	Chrysanthemum morifolium is an important floral crop that is cultivated worldwide. However, due to a lack of genomic resources, very little information is available concerning the molecular mechanisms of flower development in chrysanthemum.The transcriptomes of chrysanthemum vegetative buds, floral buds and buds were sequenced using Illumina paired-end sequencing technology. A total of 15.4 Gb of reads were assembled into 91,367 unigenes with an average length of 739 bp. A total of 43,137 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 25,424, 24,321 and 13,704 unigenes were assigned to 56 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1,876 differentially expressed genes (DEGs) (1,516 up-regulated, 360 down-regulated) were identified between vegetative buds and floral buds, and 3,300 DEGs (1,277 up-regulated, 1,706 down-regulated) were identified between floral buds and buds. Many genes encoding important transcription factors (e.g., AP2, MYB, MYC, WRKY, NAC and CRT) as well as proteins involved in carbohydrate metabolism, protein kinase activity, plant hormone signal transduction, and the defense responses, among others, were considerably up-regulated in floral buds. Genes involved in the photoperiod pathway and flower organ determination were also identified. These genes represent important candidate genes for molecular cloning and functional analysis to study flowering regulation in chrysanthemum.This comparative transcriptome analysis revealed significant differences in gene expression and signaling pathway components between the vegetative buds, floral buds and buds of Chrysanthemum morifolium. A wide range of genes was implicated in regulating the phase transition from vegetative to reproductive growth. These results should aid researchers in the study of flower-time regulation, breeding and molecular biology in ...
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genetic relationships and evolution of old Chinese garden roses based on SSRs and chromosome diversity

Jiongrui Tan / Jing Wang / Le Luo / Chao Yu / Tingliang Xu / Yuying Wu / Tangren Cheng / Jia Wang / Huitang Pan / Qixiang Zhang

Scientific Reports, Vol 7, Iss 1, Pp 1-

2017 Volume 10

Abstract: Abstract Old Chinese garden roses are the foundation of the modern rose, which is one of the best-selling ornamental plants. However, the horticultural grouping and evolution of old Chinese garden roses are unclear. Simple sequence repeat (SSR) markers ... ...

Abstract	Abstract Old Chinese garden roses are the foundation of the modern rose, which is one of the best-selling ornamental plants. However, the horticultural grouping and evolution of old Chinese garden roses are unclear. Simple sequence repeat (SSR) markers were employed to survey genetic diversity in old Chinese garden roses and genetic differentiation was estimated among different rose groups. Fluorescence in situ hybridization was used to study the physical localization of 5 S rDNA genes and a karyotype analysis was performed. The SSR data suggest that old Chinese garden roses could be divided into Old Blush group, Odorata group and Ancient hybrid China group. The Old Blush group had the most primitive karyotype. The Ancient hybrid China group and modern rose had the most evolved karyotypes and the highest genetic diversity. During the evolution of rose cultivars, 5 S rDNA increased in number, partially weakened in signal intensity and exhibited variation in distance from the centromere. In conclusion, rose cultivars evolved from the Old Blush Group to the Odorata group, the Ancient Hybrid China group and the modern rose. This work provides a basis for the collection, identification, conservation and innovation of rose germplasm resources.
Keywords	Medicine ; R ; Science ; Q
Subject code	950
Language	English
Publishing date	2017-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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