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Article ; Online: The Genetic and Hormonal Inducers of Continuous Flowering in Orchids

Sagheer Ahmad / Donghui Peng / Yuzhen Zhou / Kai Zhao

Cells, Vol 11, Iss 657, p

An Emerging View

2022 Volume 657

Abstract: Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time ... ...

Abstract	Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.
Keywords	continuous flowering ; orchids ; key regulators ; hormones ; miRNAs ; transcription factors ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Research Progress on Anthocyanin-Mediated Regulation of ‘Black’ Phenotypes of Plant Organs

Fei Wang / Jinliao Chen / Ruonan Tang / Ruixin Wang / Sagheer Ahmad / Zhongjian Liu / Donghui Peng

Current Issues in Molecular Biology, Vol 45, Iss 458, Pp 7242-

2023 Volume 7256

Abstract: The color pattern is one of the most important characteristics of plants. Black stands out among the vibrant colors due to its rare and distinctive nature. While some plant organs appear black, they are, in fact, dark purple. Anthocyanins are the key ... ...

Abstract	The color pattern is one of the most important characteristics of plants. Black stands out among the vibrant colors due to its rare and distinctive nature. While some plant organs appear black, they are, in fact, dark purple. Anthocyanins are the key compounds responsible for the diverse hues in plant organs. Cyanidin plays an important role in the deposition of black pigments in various plant organs, such as flower, leaf, and fruit. A number of structural genes and transcription factors are involved in the metabolism of anthocyanins in black organs. It has been shown that the high expression of R2R3-MYB transcription factors, such as PeMYB7 , PeMYB11 , and CsMYB90 , regulates black pigmentation in plants. This review provides a comprehensive overview of the anthocyanin pathways that are involved in the regulation of black pigments in plant organs, including flower, leaf, and fruit. It is a great starting point for further investigation into the molecular regulation mechanism of plant color and the development of novel cultivars with black plant organs.
Keywords	color patterns ; plant organs ; anthocyanins ; structural genes ; transcription factors ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Decapitation Experiments Combined with the Transcriptome Analysis Reveal the Mechanism of High Temperature on Chrysanthemum Axillary Bud Formation

Yujie Yang / Sagheer Ahmad / Qingqing Yang / Cunquan Yuan / Qixiang Zhang

International Journal of Molecular Sciences, Vol 22, Iss 9704, p

2021 Volume 9704

Abstract: Temperature is an important factor that largely affects the patterns of shoot branching in plants. However, the effect and mechanism of temperature on axillary bud development in chrysanthemum remains poorly defined. The purpose of the present study is ... ...

Abstract	Temperature is an important factor that largely affects the patterns of shoot branching in plants. However, the effect and mechanism of temperature on axillary bud development in chrysanthemum remains poorly defined. The purpose of the present study is to investigate the effect of high temperature on the axillary bud growth and the mechanism of axillary bud formation in chrysanthemum. Decapitation experiments combined with the transcriptome analysis were designed. Results showed that the axillary bud length was significantly inhibited by high temperature. Decapitation of primary shoot (primary decapitation) resulted in slower growth of axillary buds (secondary buds) under 35 °C. However, secondary decapitation resulted in complete arrest of tertiary buds at high temperature. These results demonstrated that high temperature not only inhibited axillary bud formation but also retarded bud outgrowth in chrysanthemum. Comparative transcriptome suggested differentially expressed gene sets and identified important modules associated with bud formation. This research helped to elucidate the regulatory mechanism of high temperature on axillary bud growth, especially bud formation in chrysanthemum. Meanwhile, in-depth studies of this imperative temperature signaling can offer the likelihood of vital future applications in chrysanthemum breeding and branching control.
Keywords	chrysanthemum ; high temperature ; WGCNA ; double decapitation ; hormonal regulation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	669
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Three Orchids

Xuewei Zhao / Mengmeng Zhang / Xin He / Qinyao Zheng / Ye Huang / Yuanyuan Li / Sagheer Ahmad / Dingkun Liu / Siren Lan / Zhongjian Liu

International Journal of Molecular Sciences, Vol 24, Iss 10039, p

2023 Volume 10039

Abstract: SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and ... ...

Abstract	SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and functions of the SPL s in the Orchidaceae. In this study, Cymbidium goeringii Rchb. f., Dendrobium chrysotoxum Lindl., and Gastrodia elata BI. were used as research objects. The SPL gene family of these orchids was analyzed on a genome-wide scale, and their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns were studied. Transcriptome and qRT-PCR methods were combined to investigate the regulatory effect of SPL s on the development of flower organs during the flowering process (bud, initial bloom, and full bloom). This study identifies a total of 43 SPL s from C. goeringii (16), D. chrysotoxum (17), and G. elata (10) and divides them into eight subfamilies according to the phylogenetic tree. Most SPL proteins contained conserved SBP domains and complex gene structures; half of the genes had introns longer than 10 kb. The largest number and variety of cis-acting elements associated with light reactions were enriched, accounting for about 45% of the total (444/985); 13/43 SPL s contain response elements of miRNA156 . GO enrichment analysis showed that the functions of most SPL s were mainly enriched in the development of plant flower organs and stems. In addition, expression patterns and qRT-PCR analysis suggested the involvement of SPL genes in the regulation of flower organ development in orchids. There was little change in the expression of the CgoSPL in C. goeringii , but DchSPL9 and GelSPL2 showed significant expression during the flowering process of D. chrysotoxum and G. elata , respectively. In summary, this paper provides a reference for exploring the regulation of the SPL gene family in orchids.
Keywords	SPL genes ; Orchidaceae ; phylogenetic analysis ; flower development ; expression analysis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Genome-Level Survey of the WOX Gene Family in Melastoma dodecandrum Lour.

Ruiyue Zheng / Yukun Peng / Jiemin Chen / Xuanyi Zhu / Kai Xie / Sagheer Ahmad / Kai Zhao / Donghui Peng / Zhong-Jian Liu / Yuzhen Zhou

International Journal of Molecular Sciences, Vol 24, Iss 24, p

2023 Volume 17349

Abstract: Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Melastoma dodecandrum Lour., which shows pioneer position in land ecosystem formation and produces nutritional fruits. Identifying the ... ...

Abstract	Though conserved in higher plants, the WOX transcription factors play crucial roles in plant growth and development of Melastoma dodecandrum Lour., which shows pioneer position in land ecosystem formation and produces nutritional fruits. Identifying the WOX family genes in M. dodecandrum is imperative for elucidating its growth and development mechanisms. However, the WOX genes in M. dodecandrum have not yet been characterized. In this study, by identification 22 WOX genes in M. dodecandrum based on current genome data, we classified family genes into three clades and nine types with homeodomains. We highlighted gene duplications of MedWOX4 , which offered evidences of whole-genome duplication events. Promoter analysis illustrated that cis-regulatory elements related to light and stress responses and plant growth were enriched. Expression pattern and RT-qPCR results demonstrated that the majority of WOX genes exhibited expression in the stem. MedWOX13s displayed highest expression across various tissues. MedWOX4s displayed a specific expression in the stem. Collectively, our study provided foundations for elucidating WOX gene functions and further molecular design breeding in M. dodecandrum .
Keywords	WOX transcription factors ; physicochemical properties ; expression analysis ; plant growth ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-Wide Identification of the YABBY Gene Family in Dendrobium Orchids and Its Expression Patterns in Dendrobium chrysotoxum

Qinyao Zheng / Xuewei Zhao / Ye Huang / Meng-Meng Zhang / Xin He / Shijie Ke / Yuanyuan Li / Cuili Zhang / Sagheer Ahmad / Siren Lan / Minghe Li / Zhong-Jian Liu

International Journal of Molecular Sciences, Vol 24, Iss 10165, p

2023 Volume 10165

Abstract: The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. Dendrobium chrysotoxum , D. huoshanense , and D. nobile are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. ... ...

Abstract	The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. Dendrobium chrysotoxum , D. huoshanense , and D. nobile are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. However, the relationships and specific functions of the YABBY genes in the Dendrobium species remain unknown. In this study, six DchYABBY s, nine DhuYABBY s, and nine DnoYABBY s were identified from the genome databases of the three Dendrobium species, which were unevenly distributed on five, eight, and nine chromosomes, respectively. The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. A sequence analysis showed that most of the YABBY proteins contained conserved C2C2 zinc-finger and YABBY domains, while a gene structure analysis revealed that 46% of the total YABBY genes contained seven exons and six introns. All the YABBY genes harbored a large number of Methyl Jasmonate responsive elements, as well as anaerobic induction cis -acting elements in the promoter regions. Through a collinearity analysis, one, two, and two segmental duplicated gene pairs were identified in the D. chrysotoxum , D. huoshanense , and D. nobile genomes, respectively. The Ka/Ks values of these five gene pairs were lower than 0.5, indicating that the Dendrobium YABBY genes underwent negative selection. In addition, an expression analysis revealed that DchYABBY2 plays a role in ovary and early-stage petal development, while DchYABBY5 is essential for lip development and DchYABBY6 is crucial for early sepal formation. DchYABBY1 primarily regulates sepals during blooming. Furthermore, there is the potential involvement of DchYABBY2 and DchYABBY5 in gynostemium development. The results of a comprehensive genome-wide study would provide significant clues for future functional investigations and pattern analyses of YABBY genes in different flower parts during flower development in the Dendrobium species.
Keywords	YABBY transcription factor ; Dendrobium orchid ; expression pattern ; D. chrysotoxum ; D. huoshanense ; D. nobile ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The bZIP Transcription Factors in Current Jasmine Genomes

Kai Zhao / Xianmei Luo / Mingli Shen / Wen Lei / Siqing Lin / Yingxuan Lin / Hongyan Sun / Sagheer Ahmad / Guohong Wang / Zhong-Jian Liu

International Journal of Molecular Sciences, Vol 25, Iss 1, p

Identification, Characterization, Evolution and Expressions

2023 Volume 488

Abstract: Jasmine, a recently domesticated shrub, is renowned for its use as a key ingredient in floral tea and its captivating fragrance, showcasing significant ornamental and economic value. When cultivated to subtropical zone, a significant abiotic stress ... ...

Abstract	Jasmine, a recently domesticated shrub, is renowned for its use as a key ingredient in floral tea and its captivating fragrance, showcasing significant ornamental and economic value. When cultivated to subtropical zone, a significant abiotic stress adaptability occurs among different jasmine varieties, leading to huge flower production changes and plantlet survival. The bZIP transcription factors (TFs) are reported to play indispensable roles in abiotic stress tolerance. Here, we performed a genome-level comparison of bZIP s using three-type jasmine genomes. Based on their physicochemical properties, conserved motif analysis and phylogenetic analysis, about 63 bZIP genes were identified and clustered in jasmine genomes, noting a difference of one member compared to the other two types of jasmines. The HTbZIP genes were categorized into 12 subfamilies compared with A. thaliana . In cis-acting element analysis, all genes contained light-responsive elements. The abscisic acid response element (ABRE) was the most abundant in HTbZIP62 promoter, followed by HTbZIP33 . Tissue-specific genes of the bZIPs may play a crucial role in regulating the development of jasmine organs and tissues, with HTbZIP36 showing the most significant expressions in roots. Combined with complicated protein interactions, HTbZIP62 and HTbZIP33 might play a crucial role in the ABA signaling pathway and stress tolerance. Combined with RT-qPCR analysis, SJbZIP37/57/62 were more sensitive to ABA response genes compared with other bZIPs in DJ amd HT genomes. Our findings provide a useful resource for further research on the regulation of key genes to improve abiotic stress tolerance in jasmine.
Keywords	jasmine cultivars ; stress response ; individual genomic differences ; evolution ; functional differentiation ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Stage Specificity, the Dynamic Regulators and the Unique Orchid Arundina graminifolia

Sagheer Ahmad / Chuqiao Lu / Yonglu Wei / Jie Gao / Jianpeng Jin / Chuanyuan Zheng / Genfa Zhu / Fengxi Yang

International Journal of Molecular Sciences, Vol 22, Iss 10935, p

2021 Volume 10935

Abstract: Orchids take years to reach flowering, but the unique bamboo orchid ( Arundina graminifolia ) achieves reproductive maturity in six months and then keeps on year round flowering. Therefore, studying different aspects of its growth, development and ... ...

Abstract	Orchids take years to reach flowering, but the unique bamboo orchid ( Arundina graminifolia ) achieves reproductive maturity in six months and then keeps on year round flowering. Therefore, studying different aspects of its growth, development and flowering is key to boost breeding programs for orchids. This study uses transcriptome tools to discuss genetic regulation in five stages of flower development and four tissue types. Stage specificity was focused to distinguish genes specifically expressed in different stages of flower development and tissue types. The top 10 highly expressed genes suggested unique regulatory patterns for each stage or tissue. The A. graminifolia sequences were blasted in Arabidopsis genome to validate stage specific genes and to predict important hormonal and cell regulators. Moreover, weighted gene co-expression network analysis (WGCNA) modules were ascertained to suggest highly influential hubs for early and late stages of flower development, leaf and root. Hormonal regulators were abundant in all data sets, such as auxin (LAX2, GH3.1 and SAUR41), cytokinin (LOG1), gibberellin (GASA3 and YAB4), abscisic acid (DPBF3) and sucrose (SWEET4 and SWEET13). Findings of this study, thus, give a fine sketch of genetic variability in Orchidaceae and broaden our understanding of orchid flower development and the involvement of multiple pathways.
Keywords	bamboo orchid ; stage specificity ; flowering ; hormonal regulation ; transcriptome ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

Xue Yong / Tangchun Zheng / Xiaokang Zhuo / Sagheer Ahmad / Lulu Li / Ping Li / Jiayao Yu / Jia Wang / Tangren Cheng / Qixiang Zhang

PeerJ, Vol 9, p e

2021 Volume 10785

Abstract: Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely ... ...

Abstract	Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely unknown in Rosaceae. Abscisic acid (ABA) is a stress hormone involving abiotic stress response pathways. The ABRE-binding factor/ABA-responsive element-binding protein (ABF/AREB) is a subfamily of the basic domain/leucine zipper (bZIP) transcription factor family. It plays an important role in the ABA-mediated signaling pathway. Here, we analyzed the ABF/AREB subfamily genes in nine Rosaceae species. A total of 64 ABF/AREB genes were identified, including 18, 28, and 18 genes in the Rosoideae, Amygdaloideae, and Maloideae traditional subfamilies, respectively. The evolutionary relationship of the ABF/AREB subfamily genes was studied through the phylogenetic analysis, the gene structure and conserved motif composition, Ka/Ks values, and interspecies colinearity. These gene sets were clustered into four groups. In the Prunus ABF/AREB (PmABF) promoters, several cis-elements related to light, hormone, and abiotic stress response were predicted. PmABFs expressed in five different tissues, except PmABF5, which expressed only in buds. In the dormancy stages, PmABF1, 2, 5 and 7 showed differential expression. The expression of PmABF3, 4 and 6 was positively correlated with the ABA concentration. Except for PmABF5, all the PmABFs were sensitive to ABA. Several ABRE elements were contained in the promoters of PmABF1, 3, 6, 7. Based on the findings of our study, we speculate that PmABFs may play a role in flower bud dormancy in P. mume.
Keywords	Rosaceae ; ABF/AREB ; ABRE ; Evolution ; Expression ; Prunus mume ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Maize productivity and soil nutrients variations by the application of vermicompost and biochar

Khadim Dawar / Ahtesham Khan / Ishaq Ahmad Mian / Bushra Khan / Shamsher Ali / Sagheer Ahmad / Piotr Szulc / Shah Fahad / Rahul Datta / Ashraf Atef Hatamleh / Munirah Abdullah Al-Dosary / Subhan Danish

PLoS ONE, Vol 17, Iss

2022 Volume 5

Abstract: Poor soil organic matter is one of the major causes of the deterioration of soil health. Most soils fertility is also decreased when enough organic carbon is not present in the soil. Maize is most susceptible to this poor soil fertility status. A ... ...

Abstract	Poor soil organic matter is one of the major causes of the deterioration of soil health. Most soils fertility is also decreased when enough organic carbon is not present in the soil. Maize is most susceptible to this poor soil fertility status. A significant amount of maize growth and yield is lost when it is cultivated in low organic matter and poor fertility soil. To overcome this issue organic amendments can play an imperative role. Biochar and vermicompost are organic amendments that can not only improve organic residues but also increase soil nutrient concentration. The current experiment was conducted to explore the sole and combined application of both organic amendments with recommended NPK fertilizer. Four treatments were tested i.e., control, biochar (BC1), vermicompost (VC1) and VC1+BC1 with and without nitrogen (N), phosphorus (P) and potassium (K) in the experiment. Results showed that VC1+BC1+NPK performed significantly best for improvement in maize plant height (6.25 and 3.00%), 1000 grains weight (30.48 and 29.40%), biological yield (18.86 and 43.12%) and grains yield (30.58 and 39.59%) compared to BC0+VC0+NPK and control respectively. A significant improvement in soil N, P and K also validated the efficacious role of VC1+BC1+NPK over BC0+VC0+NPK and control. Treatment VC1+BC1+NPK is recommended for the achievement of better maize growth and yield in poor organic matter soils. More investigations are suggested in variable climatic conditions to declare VC1+BC1+NPK as the best amendment compared to control for enhancing soil N, P and K status as well as maize productivity.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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