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Kumar A, Mushtaq M, Kumar P, Sharma DP, Gahlaut V. Insights into flowering mechanisms in apple (Malus × domestica Borkh.) amidst climate change: An exploration of genetic and epigenetic factors. Biochim Biophys Acta Gen Subj 2024; 1868:130593. [PMID: 38408683 DOI: 10.1016/j.bbagen.2024.130593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/05/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
Apple (Malus × domestica Borkh.) holds a prominent position among global temperate fruit crops, with flowering playing a crucial role in both production and breeding. This review delves into the intricate mechanisms governing apple flowering amidst the backdrop of climate change, acknowledging the profound influence of external and internal factors on biennial bearing, flower bud quality, and ultimately, fruit quality. Notably, the challenge faced in major apple production regions is not an inadequacy of flowers but an excess, leading to compromised fruit quality necessitating thinning practices. Climate change exacerbates these challenges, rendering apple trees more susceptible to crop failure due to unusual weather events, such as reduced winter snowfall, early spring cold weather, and hailstorms during flowering and fruit setting. Altered climatic conditions, exemplified by increased spring warming coupled with sub-freezing temperatures, negatively impact developing flower buds and decrease overall crop production. Furthermore, changing winter conditions affect chilling accumulation, disrupting flower development and synchronicity. Although the physiological perception of apple flowering has been reviewed in the past, the genetic, epigenetic, and multi-omics regulatory mechanisms governing floral induction and flowering are still rarely discussed in the case of apple flowering. This article comprehensively reviews the latest literature encompassing all aspects of apple flowering, aiming to broaden our understanding and address flowering challenges while also laying a solid foundation for future research in developing cultivars that are ideally adapted to climate change.
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Affiliation(s)
- Anshul Kumar
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University, Bhajol, Solan, Himachal Pradesh 173229, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India.
| | - Dharam Paul Sharma
- Department of Fruit Science, Dr. YS Parmar University of Horticulture and Forestry Nauni Solan, Himachal Pradesh 173230, India
| | - Vijay Gahlaut
- University Centre for Research & Development, Chandigarh University, Punjab 140413, India.
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Feng X, Yu Q, Zeng J, He X, Ma W, Ge L, Liu W. Comprehensive Analysis of the INDETERMINATE DOMAIN (IDD) Gene Family and Their Response to Abiotic Stress in Zea mays. Int J Mol Sci 2023; 24:ijms24076185. [PMID: 37047154 PMCID: PMC10094743 DOI: 10.3390/ijms24076185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.
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Guo X, Zhou M, Chen J, Shao M, Zou L, Ying Y, Liu S. Genome-Wide Identification of the Highly Conserved INDETERMINATE DOMAIN ( IDD) Zinc Finger Gene Family in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2022; 23:ijms232213952. [PMID: 36430436 PMCID: PMC9695771 DOI: 10.3390/ijms232213952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins, a family of transcription factors unique to plants, function in multiple developmental processes. Although the IDD gene family has been identified in many plants, little is known about it in moso bamboo. In this present study, we identified 32 PheIDD family genes in moso bamboo and randomly sequenced the full-length open reading frames (ORFs) of ten PheIDDs. All PheIDDs shared a highly conserved IDD domain that contained two canonical C2H2-ZFs, two C2HC-ZFs, and a nuclear localization signal. Collinearity analysis showed that segmental duplication events played an important role in expansion of the PheIDD gene family. Synteny analysis indicated that 30 PheIDD genes were orthologous to those of rice (Oryza sativa). Thirty PheIDDs were expressed at low levels, and most PheIDDs exhibited characteristic organ-specific expression patterns. Despite their diverse expression patterns in response to exogenous plant hormones, 8 and 22 PheIDDs responded rapidly to IAA and 6-BA treatments, respectively. The expression levels of 23 PheIDDs were closely related to the outgrowth of aboveground branches and 20 PheIDDs were closely related to the awakening of underground dormant buds. In addition, we found that the PheIDD21 gene generated two products by alternative splicing. Both isoforms interacted with PheDELLA and PheSCL3. Furthermore, both isoforms could bind to the cis-elements of three genes (PH02Gene17121, PH02Gene35441, PH02Gene11386). Taken together, our work provides valuable information for studying the molecular breeding mechanism of lateral organ development in moso bamboo.
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Song P, Li G, Xu J, Ma Q, Qi B, Zhang Y. Genome-Wide Analysis of Genes Involved in the GA Signal Transduction Pathway in ' duli' Pear ( Pyrus betulifolia Bunge). Int J Mol Sci 2022; 23:6570. [PMID: 35743013 PMCID: PMC9224306 DOI: 10.3390/ijms23126570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
Gibberellic acid (GA) is an important phytohormone that regulates every aspect of plant growth and development. While elements involved in GA signaling have been identified and, hence, their functions have been well studied in model plants, such as Arabidopsis and rice, very little is known in pear. We, therefore, analyzed the genes related to GA signaling from the recently sequenced genome of the wildtype 'duli' pear (Pyrus betulifolia Bunge), a widely used rootstock for grafting in pear cultivation in China due to its vigorous growth and resistance to abiotic and biotic stress. In total, 15 genes were identified, including five GA receptors PbGID1s (GA-INSENSTIVE DWARF 1), six GA negative regulators, PbDELLAs, and four GA positive regulators, PbSLYs. Exogenous application of GA could promote the expression of PbGID1s but inhibit that of PbDELLAs and PbSLYs in tissue culture 'duli' pear seedlings. The expression profiles of these genes in field-grown trees under normal growth conditions, as well as in tissue-cultured seedlings treated with auxin (IAA), GA, paclobutrazol (PAC), abscisic acid (ABA), and sodium chloride (NaCl), were also studied, providing further evidence of the involvement of these genes in GA signaling in 'duli' pear plants. The preliminary results obtained in this report lay a good foundation for future research into GA signaling pathways in pear. Importantly, the identification and preliminary functional verification of these genes could guide molecular breeding in order to obtain the highly desired dwarf pear rootstocks for high-density plantation to aid easy orchard management and high yielding of pear fruits.
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Affiliation(s)
- Pingli Song
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (P.S.); (G.L.); (J.X.); (Q.M.)
| | - Gang Li
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (P.S.); (G.L.); (J.X.); (Q.M.)
| | - Jianfeng Xu
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (P.S.); (G.L.); (J.X.); (Q.M.)
| | - Qingcui Ma
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (P.S.); (G.L.); (J.X.); (Q.M.)
| | - Baoxiu Qi
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (P.S.); (G.L.); (J.X.); (Q.M.)
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Yuxing Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (P.S.); (G.L.); (J.X.); (Q.M.)
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Jiang Y, Chen J, Zheng X, Tan B, Ye X, Wang W, Zhang L, Li J, Li Z, Cheng J, Feng J. Multiple indeterminate domain (IDD)-DELLA1 complexes participate in gibberellin feedback regulation in peach. PLANT MOLECULAR BIOLOGY 2022; 109:147-157. [PMID: 35362935 DOI: 10.1007/s11103-022-01263-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Peach encodes 14 INDETERMINATE DOMAIN (IDD) transcription factors. PpIDD4, -12 and -13 mediated PpDELLA1 binding to the PpGA20ox1 promoter. Each of these three PpIDD-DELLA1 complexes activated transcription of PpGA20ox1. PpTPR1 and -4 interrupted the interaction of PpIDDs with PpDELLA1. The plant growth regulator gibberellin (GA) plays an important role in the rapid growth of annual shoots in peach. Our previous study showed that the peach cultivar 'FenHuaShouXingTao' (FHSXT), a gibberellic acid receptor (gid1) mutant, accumulates active GAs in annual shoot tips. This mutant enhances GA feedback regulation in peach. The results of this study suggested that the PpIDD-DELLA1 complex is the underlying mechanism of GA feedback regulation in peach. Fourteen IDD genes were identified in peach, and three PpIDDs (PpIDD4, -12 and -13, all from group IV) interacted with PpDELLA1, an important component in GA signaling pathway. Truncation, segmentation and site mutation of the promoter of PpGA20ox1 (a GA biosynthesis gene) showed that all three PpIDD proteins recognized the core motif TTGTC. PpIDD4 and -13 mainly bind to site 3, while PpIDD12 binds to site 5 of the PpGA20ox1 promoter. All three PpIDD-DELLA1 complexes activated the PpGA20ox1 promoter-LUC fusion. These data suggested that PpIDDs bridge PpDELLA1 and the promoter of PpGA20ox1, which then activated the transcription of PpGA20ox1. In addition, PpTPR1 and -4 disrupted the interaction of PpIDDs with PpDELLA1. Our research will be helpful for understanding and possibly modifying the regulation of annual shoot growth and GA biosynthesis.
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Affiliation(s)
- Yajun Jiang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Jiajia Chen
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Bin Tan
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Langlang Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Jidong Li
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Zhiqian Li
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China.
| | - Jiancan Feng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, Henan Province, China.
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Ma X, Su J, Wang B, Jin X. Identification of Characteristic Genes in Whole Blood of Intervertebral Disc Degeneration Patients by Weighted Gene Coexpression Network Analysis (WGCNA). COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:6609901. [PMID: 35069789 PMCID: PMC8776439 DOI: 10.1155/2022/6609901] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022]
Abstract
Intervertebral disc degeneration (IDD) is a major cause of lower back pain. However, to date, the molecular mechanism of the IDD remains unclear. Gene expression profiles and clinical traits were downloaded from the Gene Expression Omnibus (GEO) database. Firstly, weighted gene coexpression network analysis (WGCNA) was used to screen IDD-related genes. Moreover, least absolute shrinkage and selection operator (LASSO) logistic regression and support vector machine (SVM) algorithms were used to identify characteristic genes. Furthermore, we further investigated the immune landscape by the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm and the correlations between key characteristic genes and infiltrating immune cells. Finally, a competing endogenous RNA (ceRNA) network was established to show the regulatory mechanisms of characteristic genes. A total of 2458 genes were identified by WGCNA, and 48 of them were disordered. After overlapping the genes obtained by LASSO and SVM-RFE algorithms, genes including LINC01347, ASAP1-IT1, lnc-SEPT7L-1, B3GNT8, CHRNB3, CLEC4F, LOC102724000, SERINC2, and LOC102723649 were identified as characteristic genes of IDD. Moreover, differential analysis further identified ASAP1-IT1 and SERINC2 as key characteristic genes. Furthermore, we found that the expression of both ASAP1-IT1 and SERINC2 was related to the proportions of T cells gamma delta and Neutrophils. Finally, a ceRNA network was established to show the regulatory mechanisms of ASAP1-IT1 and SERINC2. In conclusion, the present study identified ASAP1-IT1 and SERINC2 as the key characteristic genes of IDD through integrative bioinformatic analyses, which may contribute to the diagnosis and treatment of IDD.
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Affiliation(s)
- Xiaobo Ma
- Department of Orthopaedics, Yuncheng Central Hospital, Shanxi University, Yuncheng, China 044000
| | - Junqiang Su
- Department of Orthopaedics, Yuncheng Central Hospital, Shanxi University, Yuncheng, China 044000
| | - Bo Wang
- Department of Orthopaedics, Yuncheng Central Hospital, Shanxi University, Yuncheng, China 044000
| | - Xiasheng Jin
- Department of Orthopaedics, Yuncheng Central Hospital, Shanxi University, Yuncheng, China 044000
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Li K, Wei YH, Wang RH, Mao JP, Tian HY, Chen SY, Li SH, Tahir MM, Zhang D. Mdm-MIR393b-mediated adventitious root formation by targeted regulation of MdTIR1A expression and weakened sensitivity to auxin in apple rootstock. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110909. [PMID: 34034866 DOI: 10.1016/j.plantsci.2021.110909] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Adventitious root (AR) formation is of great significance for apple rootstock breeding. It is widely accepted that miR393 influences AR formation in many plant species; however, the molecular mechanism by which factors regulate AR formation remains insufficient. In this study, the evolutionary relationship of mdm-miR393 and candidate target genes MdTIR1/AFB was systematically identified, and the expression patterns were analysed. Multisequence alignment analysis of miR393 family members suggests that miR393 conservatively evolved between different species. The evolutionary relationship of the TIR1/AFBs can be divided into G1, G2 and G3 subgroups. During AR formation, the expression level of mdm-miR393a/b/c was significantly upregulated at 1 d and 7 d by exogenous auxin treatment. Furthermore, the expression levels of MdTIR1A, MdTIR1D, MdAFB1, MdAFB2, MdAFB3, MdAFB4 and MdAFB8 also appeared to be significantly changed by exogenous auxin induction. Subsequently, tissue-specific expression analysis showed that the expression levels of mdm-miR393 and MdTIR1/AFBs in different tissues exhibited significant differences. The promoter of mdm-miR393 contains multiple elements that respond to ABA, adversity and light signals; auxin treatment can activate the mdm-MIR393b promoter but is obviously inhibited by NPA treatment. The targeting relationship between mdm-MIR393b and MdTIR1A was verified by expression patterns, degradation group data, transient tobacco conversion results, and genes functions experiments. Heterologous overexpression of mdm-MIR393b (35S::mdm-MIR393b) decreased the number of ARs in the phenotype and reduced the expression level of the target gene NtTIR1 in tobacco. Compared to the wild type, the 35S::mdm-MIR393b transgenic plants demonstrated insensitivity to auxin. Furthermore, tir1 mutant exhibited reduced root system structure relative to the control. The above results illustrated that mdm-MIR393b is involved in mediating AR formation by targeted regulation of MdTIR1A expression in apple rootstock.
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Affiliation(s)
- Ke Li
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Yan-Hong Wei
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Rong-Hua Wang
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Jiang-Ping Mao
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Hui-Yue Tian
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Shi-Yue Chen
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Shao-Huan Li
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Muhammad-Mobeen Tahir
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
| | - Dong Zhang
- College of Horticulture, Yangling Subsidiary Center Project of the National Apple Improvement Center, Northwest Agriculture & Forestry University, Yangling, 712100, China.
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Zhang C, An N, Jia P, Zhang W, Liang J, Zhang X, Zhou H, Ma W, Han M, Xing L, Ren X. Genomic identification and expression analysis of nuclear pore proteins in Malus domestica. Sci Rep 2020; 10:17426. [PMID: 33060661 PMCID: PMC7566457 DOI: 10.1038/s41598-020-74171-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022] Open
Abstract
The nuclear pore complex (NPC), comprised of individual nucleoporin (Nup) proteins, controls nucleo-cytoplasmic transport of RNA and protein, and is important for regulating plant growth and development. However, there are no reports on this complex in fruit tree species. In this study, we identified 38 apple Nups and named them based on the known Arabidopsis thaliana homologs. We also completed bioinformatics analyses of the intron and exon structural data for apple Nups. The proteins encoded by the apple Nups lacked a universally conserved domain. Moreover, a phylogenetic analysis separated the apple and A. thaliana Nups into three groups. The phylogenetic tree indicated that MdNup54 and MdNup62 are most closely related to genes in other Rosaceae species. To characterize the 38 candidate Malus domestica Nups, we measured their stage-specific expression levels. Our tests revealed these proteins were differentially expressed among diverse tissues. We analyzed the expression levels of seven apple Nups in response to an indole-3-acetic acid (IAA) treatment. The phytohormone treatment significantly inhibited apple flowering. A qRT-PCR analysis proved that an IAA treatment significantly inhibited the expression of these seven genes. A preliminary study regarding two members of the Nup62 subcomplex, MdNup54 and MdNup62, confirmed these two proteins can interact with each other. A yeast two-hybrid assay verified that MdNup54 can interact with MdKNAT4 and MdKNAT6. On the basis of the study results, we identified apple NPC and predicted its structure and function. The data generated in this investigation provide important reference material for follow-up research.
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Affiliation(s)
- Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Peng Jia
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Wei Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Xu Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Hua Zhou
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, China.
| | - Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, China.
| | - Xiaolin Ren
- College of Horticulture, Northwest A&F University, Yangling, China.
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9
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Prochetto S, Reinheimer R. Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms. ANNALS OF BOTANY 2020; 126:85-101. [PMID: 32206771 PMCID: PMC7304464 DOI: 10.1093/aob/mcaa052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
INTRODUCTION The Indeterminate Domain (IDD) proteins are a plant-specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, but the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail. METHODS In this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes. KEY RESULTS We identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, but all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns. CONCLUSIONS IDDs were present in the last common ancestor of Streptophyta. On land, IDDs duplicated extensively, leading to ten lineages. Later, IDDs were recruited by angiosperms where they diversified greatly in number, C-terminal and expression patterns. Interestingly, such diversification occurred during the evolution of novel traits of the plant body. This study provides a solid framework of the orthology relationships of green land plant IDD transcription factors, thus increasing the accuracy of orthologue identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.
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Affiliation(s)
- Santiago Prochetto
- Fellow of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), FBCB, Santa Fe, Argentina
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
| | - Renata Reinheimer
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), FBCB, Santa Fe, Argentinaand
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
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10
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Jia P, Zhang C, Xing L, Li Y, Shah K, Zuo X, Zhang D, An N, Han M, Ren X. Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica. FRONTIERS IN PLANT SCIENCE 2020; 11:128. [PMID: 32153621 PMCID: PMC7047289 DOI: 10.3389/fpls.2020.00128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/28/2020] [Indexed: 05/11/2023]
Abstract
Knotted1-like Homeobox (KNOX) proteins play important roles in regulating plant growth, development, and other biological processes. However, little information is available on the KNOX gene family in apple (Malus domestica Borkh.). In this study, 22 KNOX genes were identified in the apple genome. The gene structure, protein characteristics, and promoter region were characterized. The MdKNOX family members were divided into three classes based on their phylogenetic relationships. Quantitative real-time PCR analysis revealed that the majority of MdKNOX genes exhibited strongly preferential expression in buds and were significantly up-regulated during the flower induction period. The transcript levels of MdKNOX genes were responsive to treatments with flowering- and stress-related hormones. The putative upstream regulation factor MdGRF could directly bind to the promoter of MdKNOX15 and MdKNOX19, and inhibit their transcriptional activities, which were confirmed by yeast one-hybrid and dual-luciferase assays. The results provide an important foundation for future analysis of the regulation and functions of the MdKNOX gene family.
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Affiliation(s)
- Peng Jia
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Chenguang Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Libo Xing
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Youmei Li
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Kamran Shah
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Xiya Zuo
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Dong Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Na An
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Mingyu Han
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- *Correspondence: Mingyu Han, ; Xiaolin Ren,
| | - Xiaolin Ren
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- *Correspondence: Mingyu Han, ; Xiaolin Ren,
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11
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Chen Z, Han Y, Deng C, Chen W, Jin L, Chen H, Wang K, Shen H, Qian L. Inflammation‐dependent downregulation of miR‐194‐5p contributes to human intervertebral disc degeneration by targeting CUL4A and CUL4B. J Cell Physiol 2019; 234:19977-19989. [PMID: 30945295 DOI: 10.1002/jcp.28595] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/07/2019] [Accepted: 03/19/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Zhi Chen
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Yingchao Han
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Chao Deng
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Wei Chen
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Linyu Jin
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Hao Chen
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Kun Wang
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Hongxing Shen
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
| | - Lie Qian
- Department of Spine Surgery Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai China
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12
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Su X, Meng T, Zhao Y, Li G, Cheng X, Abdullah M, Sun X, Cai Y, Lin Y. Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear ( Pyrus bretschneideri). PeerJ 2019; 7:e6628. [PMID: 30941270 PMCID: PMC6440465 DOI: 10.7717/peerj.6628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 12/12/2022] Open
Abstract
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Tiankai Meng
- School of Life Sciences and Technology, TongJi University, Shanghai, China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Xu Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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13
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Fan S, Zhang D, Gao C, Wan S, Lei C, Wang J, Zuo X, Dong F, Li Y, Shah K, Han M. Mediation of Flower Induction by Gibberellin and its Inhibitor Paclobutrazol: mRNA and miRNA Integration Comprises Complex Regulatory Cross-Talk in Apple. PLANT & CELL PHYSIOLOGY 2018; 59:2288-2307. [PMID: 30137602 DOI: 10.1093/pcp/pcy154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/27/2018] [Indexed: 05/14/2023]
Abstract
Guaranteeing successful flowering is very important in economic plant species, especially apple (Malus domestica Borkh.), which is difficult to induce to flower. However, the gene expression and networks involved in flowering have not been totally characterized. Here, we employed mRNA and microRNA (miRNA) sequencing to understand the different responses to gibberellin- and its inhibitor paclobutrazol- (PAC) mediated flower induction. Significant opposite cytological and morphological changes were observed in treated terminal buds, which led to a reduced flowering rate under gibberellin and an increased flowering rate under PAC. We also found that the differentially expressed mRNAs, miRNAs and miRNA target genes participated in different biological networks including hormones, photosynthesis, redox state and other metabolic processes, which provided important clues to understand the complex networks involved in apple flower induction. Additionally, we subsequently focused on one important candidate, MdSPL3, which is one of 31 apple SPL gene family members and whose transcription was inhibited by gibberellin but promoted by PAC. Functional investigation showed that MdSPL3 was located in the nucleus, and ectopic MdSPL3 activated floral meristem identity genes, promoted the formation of floral primordia and led to an earlier flowering phenotype in Arabidopsis. Our research identified critical mRNA and miRNA responsive to gibberellin or PAC, and provided a candidate framework for flower induction. This carefully orchestrated regulatory cross-talk highlighted potential targets for developing regulatory techniques and genetic improvement of flower induction in apple.
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Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuyuan Wan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Chao Lei
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jue Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Feng Dong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
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14
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Fan S, Wang J, Lei C, Gao C, Yang Y, Li Y, An N, Zhang D, Han M. Identification and characterization of histone modification gene family reveal their critical responses to flower induction in apple. BMC PLANT BIOLOGY 2018; 18:173. [PMID: 30126363 DOI: 10.1186/s12870-018-1388-1380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/14/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Histone methylation and acetylation regulate biological processes in plants through various histone modifications (HMs) gene families. However, knowledge of HMs genes is limited in horticultural deciduous trees, including apple (Malus domestica). RESULTS Here, a comprehensive study of identifying and investigating HMs genes was performed using the recently published apple genome. In total, 198 MdHMs were identified, including 71 histone methyltransferases, 44 histone demethylases, 57 histone acetylases, and 26 histone deacetylases. Detailed analysis of the MdHMs, including chromosomes locations, gene structures, protein motif and protein-protein interactions were performed, and their orthologous genes were also predicted against nine plant species. Meanwhile, a syntenic analysis revealed that tandem, segmental, and whole genome duplications were involved in the evolution and expansion of the MdHMs gene family. Most MdHMs underwent purifying selection. The expression profiles of 198 MdHMs were investigated in response to 6-BA treatment and different flowering varieties (easy-flowering 'Yanfu No.6' and difficult-flowering 'Nagafu No.2') using transcriptome sequencing data, and most MdHMs were involved in flower induction processes. Subsequent quantitative real-time PCR was then performed to confirm the expression levels of candidate MdHMs under different flowering-related circumstances. CONCLUSION MdHMs were involved in, and responsive to, flower induction in apple. This study established an MdHMs platform that provided valuable information and presented enriched biological theories on flower induction in apple. The data could also be used to study the evolutionary history and functional prospects of MdHMs genes, as well as other trees.
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Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jue Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chao Lei
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yang Yang
- Innovation Experimental College, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Fan S, Wang J, Lei C, Gao C, Yang Y, Li Y, An N, Zhang D, Han M. Identification and characterization of histone modification gene family reveal their critical responses to flower induction in apple. BMC PLANT BIOLOGY 2018; 18:173. [PMID: 30126363 PMCID: PMC6102887 DOI: 10.1186/s12870-018-1388-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/14/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Histone methylation and acetylation regulate biological processes in plants through various histone modifications (HMs) gene families. However, knowledge of HMs genes is limited in horticultural deciduous trees, including apple (Malus domestica). RESULTS Here, a comprehensive study of identifying and investigating HMs genes was performed using the recently published apple genome. In total, 198 MdHMs were identified, including 71 histone methyltransferases, 44 histone demethylases, 57 histone acetylases, and 26 histone deacetylases. Detailed analysis of the MdHMs, including chromosomes locations, gene structures, protein motif and protein-protein interactions were performed, and their orthologous genes were also predicted against nine plant species. Meanwhile, a syntenic analysis revealed that tandem, segmental, and whole genome duplications were involved in the evolution and expansion of the MdHMs gene family. Most MdHMs underwent purifying selection. The expression profiles of 198 MdHMs were investigated in response to 6-BA treatment and different flowering varieties (easy-flowering 'Yanfu No.6' and difficult-flowering 'Nagafu No.2') using transcriptome sequencing data, and most MdHMs were involved in flower induction processes. Subsequent quantitative real-time PCR was then performed to confirm the expression levels of candidate MdHMs under different flowering-related circumstances. CONCLUSION MdHMs were involved in, and responsive to, flower induction in apple. This study established an MdHMs platform that provided valuable information and presented enriched biological theories on flower induction in apple. The data could also be used to study the evolutionary history and functional prospects of MdHMs genes, as well as other trees.
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Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jue Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chao Lei
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yang Yang
- Innovation Experimental College, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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16
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Shalmani A, Fan S, Jia P, Li G, Muhammad I, Li Y, Sharif R, Dong F, Zuo X, Li K, Chen KM, Han M. Genome Identification of B-BOX Gene Family Members in Seven Rosaceae Species and Their Expression Analysis in Response to Flower Induction in Malus domestica. Molecules 2018; 23:molecules23071763. [PMID: 30021984 PMCID: PMC6100437 DOI: 10.3390/molecules23071763] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 11/22/2022] Open
Abstract
BBX proteins play important roles in regulating plant growth and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses. At present, the genomes of seven Rosaceae fruit species have been fully sequenced. However, little is known about the BBX gene family and their evolutionary history in these Rosaceae species. Therefore, in this study total, 212 BBX genes were investigated from seven Rosaceae species (67 from Malus × domestica, 40 from Pyruscommunis, 22 from Rosa Chinesis, 20 from Prunuspersica, 21 from Fragariavesca, 22 from Prunusavium, and 20 from Rubusoccidentalis). The chemical properties, gene structures, and evolutionary relationships of the BBX genes were also studied. All the BBX genes were grouped into six subfamilies on the basis of their phylogenetic relationships and structural features. Analysis of gene structure, segmental and tandem duplication, gene phylogeny, and tissue-specific expression with the ArrayExpress database showed their diversification in function, quantity, and structure. The expression profiles of 19 MdBBX genes in different tissues were evaluated through qRT-PCR. These genes showed distinct transcription level among the tested tissues (bud, flower, fruit, stem, and leaf). Moreover, expression patterns of 19 MdBBX genes were examined during flowering induction time under flowering-related hormones and treatments (GA3, 6-BA, and sucrose). The expressions of the candidates BBX genes were affected and showed diverse expression profile. Furthermore, changes in response to these flowering-related hormones and treatment specifying their potential involvement in flowering induction. Based on these findings, BBX genes could be used as potential genetic markers for the growth and development of plants particularly in the area of functional analysis, and their involvement in flower induction in fruit plants.
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Affiliation(s)
- Abdullah Shalmani
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Peng Jia
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Guofang Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Izhar Muhammad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Feng Dong
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Ke Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China.
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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17
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Fan S, Zhang D, Zhang L, Gao C, Xin M, Tahir MM, Li Y, Ma J, Han M. Comprehensive analysis of GASA family members in the Malus domestica genome: identification, characterization, and their expressions in response to apple flower induction. BMC Genomics 2017; 18:827. [PMID: 29078754 PMCID: PMC5658915 DOI: 10.1186/s12864-017-4213-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The plant-specific gibberellic acid stimulated Arabidopsis (GASA) gene family is critical for plant development. However, little is known about these genes, particularly in fruit tree species. RESULTS We identified 15 putative Arabidopsis thaliana GASA (AtGASA) and 26 apple GASA (MdGASA) genes. The identified genes were then characterized (e.g., chromosomal location, structure, and evolutionary relationships). All of the identified A. thaliana and apple GASA proteins included a conserved GASA domain and exhibited similar characteristics. Specifically, the MdGASA expression levels in various tissues and organs were analyzed based on an online gene expression profile and by qRT-PCR. These genes were more highly expressed in the leaves, buds, and fruits compared with the seeds, roots, and seedlings. MdGASA genes were also responsive to gibberellic acid (GA3) and abscisic acid treatments. Additionally, transcriptome sequencing results revealed seven potential flowering-related MdGASA genes. We analyzed the expression levels of these genes in response to flowering-related treatments (GA3, 6-benzylaminopurine, and sugar) and in apple varieties that differed in terms of flowering ('Nagafu No. 2' and 'Yanfu No. 6') during the flower induction period. These candidate MdGASA genes exhibited diverse expression patterns. The expression levels of six MdGASA genes were inhibited by GA3, while the expression of one gene was up-regulated. Additionally, there were expression-level differences induced by the 6-benzylaminopurine and sugar treatments during the flower induction stage, as well as in the different flowering varieties. CONCLUSION This study represents the first comprehensive investigation of the A. thaliana and apple GASA gene families. Our data may provide useful clues for future studies and may support the hypotheses regarding the role of GASA proteins during the flower induction stage in fruit tree species.
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Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lizhi Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Mingzhi Xin
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Muhammad Mobeen Tahir
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Juanjuan Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Fan S, Zhang D, Gao C, Zhao M, Wu H, Li Y, Shen Y, Han M. Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica. Front Physiol 2017; 8:253. [PMID: 28503152 PMCID: PMC5408086 DOI: 10.3389/fphys.2017.00253] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/10/2017] [Indexed: 12/02/2022] Open
Abstract
GRAS genes encode plant-specific transcription factors that play important roles in plant growth and development. However, little is known about the GRAS gene family in apple. In this study, 127 GRAS genes were identified in the apple (Malus domestica Borkh.) genome and named MdGRAS1 to MdGRAS127 according to their chromosomal locations. The chemical characteristics, gene structures and evolutionary relationships of the MdGRAS genes were investigated. The 127 MdGRAS genes could be grouped into eight subfamilies based on their structural features and phylogenetic relationships. Further analysis of gene structures, segmental and tandem duplication, gene phylogeny and tissue-specific expression with ArrayExpress database indicated their diversification in quantity, structure and function. We further examined the expression pattern of MdGRAS genes during apple flower induction with transcriptome sequencing. Eight higher MdGRAS (MdGRAS6, 26, 28, 44, 53, 64, 107, and 122) genes were surfaced. Further quantitative reverse transcription PCR indicated that the candidate eight genes showed distinct expression patterns among different tissues (leaves, stems, flowers, buds, and fruits). The transcription levels of eight genes were also investigated with various flowering related treatments (GA3, 6-BA, and sucrose) and different flowering varieties (Yanfu No. 6 and Nagafu No. 2). They all were affected by flowering-related circumstance and showed different expression level. Changes in response to these hormone or sugar related treatments indicated their potential involvement during apple flower induction. Taken together, our results provide rich resources for studying GRAS genes and their potential clues in genetic improvement of apple flowering, which enriches biological theories of GRAS genes in apple and their involvement in flower induction of fruit trees.
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Affiliation(s)
- Sheng Fan
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Dong Zhang
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Cai Gao
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Ming Zhao
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Haiqin Wu
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Youmei Li
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Yawen Shen
- College of Horticulture, Northwest A&F UniversityYangling, China
| | - Mingyu Han
- College of Horticulture, Northwest A&F UniversityYangling, China
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