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Wang R, Luo Y, Lan Z, Qiu D. Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae). Sci Rep 2024; 14:13940. [PMID: 38886463 DOI: 10.1038/s41598-024-64509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks < 1 for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.
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Affiliation(s)
- Ru Wang
- Hubei Minzu University, School of Forestry and Horticulture, Enshi, 445000, China
| | - Yongjian Luo
- Hubei Minzu University, School of Forestry and Horticulture, Enshi, 445000, China
| | - Zheng Lan
- Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Daoshou Qiu
- Key Laboratory of Crops Genetics and Improvement of Guangdong Province, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Singh S, Singh R, Priyadarsini S, Ola AL. Genomics empowering conservation action and improvement of celery in the face of climate change. PLANTA 2024; 259:42. [PMID: 38270699 DOI: 10.1007/s00425-023-04321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/23/2023] [Indexed: 01/26/2024]
Abstract
MAIN CONCLUSION Integration of genomic approaches like whole genome sequencing, functional genomics, evolutionary genomics, and CRISPR/Cas9-based genome editing has accelerated the improvement of crop plants including leafy vegetables like celery in the face of climate change. The anthropogenic climate change is a real peril to the existence of life forms on our planet, including human and plant life. Climate change is predicted to be a significant threat to biodiversity and food security in the coming decades and is rapidly transforming global farming systems. To avoid the ghastly future in the face of climate change, the elucidation of shifts in the geographical range of plant species, species adaptation, and evolution is necessary for plant scientists to develop climate-resilient strategies. In the post-genomics era, the increasing availability of genomic resources and integration of multifaceted genomics elements is empowering biodiversity conservation action, restoration efforts, and identification of genomic regions adaptive to climate change. Genomics has accelerated the true characterization of crop wild relatives, genomic variations, and the development of climate-resilient varieties to ensure food security for 10 billion people by 2050. In this review, we have summarized the applications of multifaceted genomic tools, like conservation genomics, whole genome sequencing, functional genomics, genome editing, pangenomics, in the conservation and adaptation of plant species with a focus on celery, an aromatic and medicinal Apiaceae vegetable. We focus on how conservation scientists can utilize genomics and genomic data in conservation and improvement.
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Affiliation(s)
- Saurabh Singh
- Department of Vegetable Science, Rani Lakshmi Bai Central Agricultural University, Jhansi, UP, 284003, India.
| | - Rajender Singh
- Division of Crop Improvement and Seed Technology, ICAR-Central Potato Research Institute (CPRI), Shimla, India
| | - Srija Priyadarsini
- Institute of Agricultural Sciences, SOA (Deemed to be University), Bhubaneswar, 751029, India
| | - Arjun Lal Ola
- Department of Vegetable Science, Rani Lakshmi Bai Central Agricultural University, Jhansi, UP, 284003, India
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3
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Bishnoi R, Solanki R, Singla D, Mittal A, Chhuneja P, Meena OP, Dhatt AS. Comparative mitochondrial genome analysis reveals a candidate ORF for cytoplasmic male sterility in tropical onion. 3 Biotech 2024; 14:6. [PMID: 38074291 PMCID: PMC10700285 DOI: 10.1007/s13205-023-03850-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/08/2023] [Indexed: 01/19/2024] Open
Abstract
Cytoplasmic male sterility (CMS) has been widely exploited for hybrid seed production in onions (Allium cepa L.). In contrast to long-day onion cultivars, short-day onion has not yet been investigated for mitochondrial genome structure and DNA rearrangements associated with CMS activity. Here, we report the 3,16,321 bp complete circular mitochondrial genome of tropical onion CMS line (97A). Due to the substantial number of repetitive regions, the assembled mitochondrial genome of maintainer line (97B) remained linear with 15 scaffolds. Additionally, 13 and 20 chloroplast-derived fragments with a size ranging from 143 to 13,984 bp and 153-17,725 bp were identified in the 97A and 97B genomes, respectively. Genome annotation revealed 24 core protein-coding genes along with 24 and 28 tRNA genes in the mitochondrial genomes of 97A and 97B, respectively. Furthermore, comparative genome analysis of the 97A and 97B mitochondrial genomes showed that gene content was almost similar except for the chimeric ORF725 gene which is the extended form of the COX1 gene. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03850-2.
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Affiliation(s)
- Ritika Bishnoi
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Ravindra Solanki
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Om Prakash Meena
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004 India
| | - Ajmer Singh Dhatt
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, 141004 India
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Park S, Park S. Intrageneric structural variation in organelle genomes from the genus Dystaenia (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer. FRONTIERS IN PLANT SCIENCE 2023; 14:1283292. [PMID: 38116150 PMCID: PMC10728875 DOI: 10.3389/fpls.2023.1283292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Introduction During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed. Methods In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome). Results and Discussion We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Republic of Korea
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Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Chen G, Kang R, Wang Z, Jiang Y, Zhou H, Abuduaini A, Suo F, Huang L. The complete mitochondrial genome of Cuminum cyminum (Apiales: Apiaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:760-765. [PMID: 37521907 PMCID: PMC10375935 DOI: 10.1080/23802359.2023.2238357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
Cumin (Cuminum cyminum L). belongs to the family Apiaceae and the order Apiales, which is a widely grown spice and medicinal plant in Xinjiang province, China. In the current study, whole genome sequencing of C. cyminum was performed using the Illumina HiSeq 4000 platform, and the complete mitogenome sequence was assembled and annotated. We found that the single circular mitogenome of C. cyminum was 246,721 bp in length, and has about 45.5% GC content. It comprised 73 genes in the coding region (35 protein-coding genes, 18 tRNA genes, 3 rRNA genes, and 15 open-reading frames) and a non-coding region. Phylogenetic analysis indicated that C. cyminum is closely related to Daucus carota and the subtribes Daucinae. The mitogenome of C. cyminum revealed its phylogenetic relationships with other species in the Apiaceae family, which would further help in understanding its evolution.
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Affiliation(s)
- Ge Chen
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ruiping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Zihao Wang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huiying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Feiya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, Xinjiang, China
| | - Luodong Huang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Liu Q, Yuan H, Xu J, Cui D, Xiong G, Schwarzacher T, Heslop-Harrison JS. The mitochondrial genome of the diploid oat Avena longiglumis. BMC PLANT BIOLOGY 2023; 23:218. [PMID: 37098475 PMCID: PMC10131481 DOI: 10.1186/s12870-023-04217-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Avena longiglumis Durieu (2n = 2x = 14) is a wild relative of cultivated oat (Avena sativa, 2n = 6x = 42) with good agronomic and nutritional traits. The plant mitochondrial genome has a complex organization and carries genetic traits of value in exploiting genetic resources, not least male sterility alleles used to generate F1 hybrid seeds. Therefore, we aim to complement the chromosomal-level nuclear and chloroplast genome assemblies of A. longiglumis with the complete assembly of the mitochondrial genome (mitogenome) based on Illumina and ONT long reads, comparing its structure with Poaceae species. RESULTS The complete mitochondrial genome of A. longiglumis can be represented by one master circular genome being 548,445 bp long with a GC content of 44.05%. It can be represented by linear or circular DNA molecules (isoforms or contigs), with multiple alternative configurations mediated by long (4,100-31,235 bp) and medium (144-792 bp) size repeats. Thirty-five unique protein-coding genes, three unique rRNA genes, and 11 unique tRNA genes are identified. The mitogenome is rich in duplications (up to 233 kb long) and multiple tandem or simple sequence repeats, together accounting for more than 42.5% of the total length. We identify homologous sequences between the mitochondrial, plastid and nuclear genomes, including the exchange of eight plastid-derived tRNA genes, and nuclear-derived retroelement fragments. At least 85% of the mitogenome is duplicated in the A. longiglumis nuclear genome. We identify 269 RNA editing sites in mitochondrial protein-coding genes including stop codons truncating ccmFC transcripts. CONCLUSIONS Comparative analysis with Poaceae species reveals the dynamic and ongoing evolutionary changes in mitochondrial genome structure and gene content. The complete mitochondrial genome of A. longiglumis completes the last link of the oat reference genome and lays the foundation for oat breeding and exploiting the biodiversity in the genus.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Hongyu Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiaxin Xu
- College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gui Xiong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, LE1 7RH, UK.
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Ranaware AS, Kunchge NS, Lele SS, Ochatt SJ. Protoplast Technology and Somatic Hybridisation in the Family Apiaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1060. [PMID: 36903923 PMCID: PMC10005591 DOI: 10.3390/plants12051060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Species of the family Apiaceae occupy a major market share but are hitherto dependent on open pollinated cultivars. This results in a lack of production uniformity and reduced quality that has fostered hybrid seed production. The difficulty in flower emasculation led breeders to use biotechnology approaches including somatic hybridization. We discuss the use of protoplast technology for the development of somatic hybrids, cybrids and in-vitro breeding of commercial traits such as CMS (cytoplasmic male sterility), GMS (genetic male sterility) and EGMS (environment-sensitive genic male sterility). The molecular mechanism(s) underlying CMS and its candidate genes are also discussed. Cybridization strategies based on enucleation (Gamma rays, X-rays and UV rays) and metabolically arresting protoplasts with chemicals such as iodoacetamide or iodoacetate are reviewed. Differential fluorescence staining of fused protoplast as routinely used can be replaced by new tagging approaches using non-toxic proteins. Here, we focused on the initial plant materials and tissue sources for protoplast isolation, the various digestion enzyme mixtures tested, and on the understanding of cell wall re-generation, all of which intervene in somatic hybrids regeneration. Although there are no alternatives to somatic hybridization, various approaches also discussed are emerging, viz., robotic platforms, artificial intelligence, in recent breeding programs for trait identification and selection.
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Affiliation(s)
- Ankush S. Ranaware
- Institute of Chemical Technology, Marathwada Campus, Jalna 431203, Maharashtra, India
| | - Nandkumar S. Kunchge
- Research and Development Division, Kalash Seeds Pvt. Ltd., Jalna 431203, Maharashtra, India
| | - Smita S. Lele
- Institute of Chemical Technology, Marathwada Campus, Jalna 431203, Maharashtra, India
| | - Sergio J. Ochatt
- Agroécologie, InstitutAgro Dijon, INRAE, Université Bourgogne Franche-Comté, 21000 Dijon, France
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9
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Wang H, Cheng Q, Zhai Z, Cui X, Li M, Ye R, Sun L, Shen H. Transcriptomic and Proteomic Analyses of Celery Cytoplasmic Male Sterile Line and Its Maintainer Line. Int J Mol Sci 2023; 24:ijms24044194. [PMID: 36835607 PMCID: PMC9967367 DOI: 10.3390/ijms24044194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 02/22/2023] Open
Abstract
Male sterility is a common phenomenon in the plant kingdom and based on the organelles harboring the male-sterility genes, it can be classified into the genic male sterility (GMS) and the cytoplasmic male sterility (CMS). In every generation, CMS can generate 100% male-sterile population, which is very important for the breeders to take advantage of the heterosis and for the seed producers to guarantee the seed purity. Celery is a cross-pollinated plant with the compound umbel type of inflorescence which carries hundreds of small flowers. These characteristics make CMS the only option to produce the commercial hybrid celery seeds. In this study, transcriptomic and proteomic analyses were performed to identify genes and proteins that are associated with celery CMS. A total of 1255 differentially expressed genes (DEGs) and 89 differentially expressed proteins (DEPs) were identified between the CMS and its maintainer line, then 25 genes were found to differentially expressed at both the transcript and protein levels. Ten DEGs involved in the fleece layer and outer pollen wall development were identified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, most of which were down-regulated in the sterile line W99A. These DEGs and DEPs were mainly enriched in the pathways of "phenylpropanoid/sporopollenin synthesis/metabolism", "energy metabolism", "redox enzyme activity" and "redox processes". Results obtained in this study laid a foundation for the future investigation of mechanisms of pollen development as well as the reasons for the CMS in celery.
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Affiliation(s)
- Haoran Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Ziqi Zhai
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Xiangyun Cui
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Mingxuan Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Ruiquan Ye
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
- Correspondence: (L.S.); (H.S.); Tel.: +86-10-6273-1014 (L.S.); +86-10-6273-2831 (H.S.)
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- Department of Vegetable Science, College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan Xi Lu, Haidian District, Beijing 100193, China
- Correspondence: (L.S.); (H.S.); Tel.: +86-10-6273-1014 (L.S.); +86-10-6273-2831 (H.S.)
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10
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Cheng Q, He Y, Lu Q, Wang H, Liu S, Liu J, Liu M, Zhang Y, Wang Y, Sun L, Shen H. Mapping of the AgWp1 gene for the white petiole in celery (Apium graveolens L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111563. [PMID: 36509245 DOI: 10.1016/j.plantsci.2022.111563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Celery (Apium graveolens L.) is one of the most popular leafy vegetables worldwide. The main edible parts of celery are the leaf blade and especially the petiole, which typically has a white, green and red color. To date, there are very few reports about the inheritance and gene cloning of celery petiole color. In this study, bulked segregant analysis-sequencing (BSA-Seq) and fine mapping were conducted to delimit the white petiole (wp1) loci into a 668.5-kb region on Chr04. In this region, AgWp1 is a homolog of a DAG protein in Antirrhinum majus and a MORF9 protein in Arabidopsis, and both proteins are involved in chloroplast development. Sequencing alignment shows that there is a 27-bp insertion in the 3'-utr region in AgWp1 in the white petiole. Gene expression analysis indicated that the expression level of AgWp1 in the green petiole was much higher than that in the white petiole. Further cosegregation revealed that the 27-bp insertion was completely cosegregated with the petiole color in 45 observed celery varieties. Therefore, AgWp1 was considered to be the candidate gene controlling the white petiole in celery. Our results could not only improve the efficiency and accuracy of celery breeding but also help in understanding the mechanism of chlorophyll synthesis and chloroplast development in celery.
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Affiliation(s)
- Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yujiao He
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Qiaohua Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Haoran Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Sujun Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Jinkui Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Mengmeng Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yingxue Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yihao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.
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Li M, Li X, Zhou J, Sun Y, Du J, Wang Z, Luo Y, Zhang Y, Chen Q, Wang Y, Lin Y, Zhang Y, He W, Wang X, Tang H. Genome-wide identification and analysis of terpene synthase ( TPS) genes in celery reveals their regulatory roles in terpenoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:1010780. [PMID: 36247575 PMCID: PMC9557977 DOI: 10.3389/fpls.2022.1010780] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/12/2022] [Indexed: 05/31/2023]
Abstract
Terpenes are an important class of secondary metabolites in celery, which determine its flavor. Terpene synthase (TPS) has been established as a key enzyme in the biosynthesis of terpenes. This study systematically analyzed all members of the TPS gene family of celery (Apium graveolens) based on whole genome data. A total of 39 celery TPS genes were identified, among which TPS-a and TPS-b represented the two largest subfamilies. 77 cis-element types were screened in the promoter regions of AgTPS genes, suggesting the functional diversity of members of this family. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that AgTPS genes were enriched in multiple terpenoid biosynthesis pathways. Transcript abundance analysis and qRT-PCR showed that most AgTPS genes were differentially expressed in different tissues and colors of celery, with AgTPS 6, 9, and 11 expressed differentially in tissues, while AgTPS31, 32, and 38 are expressed differently in colors. More than 70% of the celery volatile compounds identified by HS-SPME-GC/MS were terpene, and the most critical compounds were β-Myrcene, D-Limonene, β-Ocimene and γ-Terpinene. Principal component analysis (PCA) showed that compounds (E)-β-Ocimene, D-Limonene, β-Myrcene and γ-Terpinene predominantly accounted for the variation. Further correlation analysis between gene expression and terpenoid accumulation showed that the four genes AgTPS9, 25, 31 and 38 genes may have positive regulatory effects on the synthesis of D-Limonene and β-Myrcene in celery. Overall, this study identified key candidate genes that regulate the biosynthesis of volatile compounds and provide the foothold for the development and utilization of terpenoids in celery.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Jin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yue Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Jiageng Du
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Zhuo Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, China
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