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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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Li X, Li M, Li W, Zhou J, Han Q, Lu W, Luo Q, Zhu S, Xiong A, Tan G, Zheng Y. Comparative Analysis of the Complete Mitochondrial Genomes of Apium graveolens and Apium leptophyllum Provide Insights into Evolution and Phylogeny Relationships. Int J Mol Sci 2023; 24:14615. [PMID: 37834070 PMCID: PMC10572446 DOI: 10.3390/ijms241914615] [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: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in Apium plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of A. graveolens and A. leptophyllum. The complete lengths of the mitochondrial genomes of A. graveolens and A. leptophyllum were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both A. graveolens and A. leptophyllum showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of A. graveolens, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of A. leptophyllum. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both A. graveolens and A. leptophyllum exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of A. graveolens and A. leptophyllum into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that A. graveolens, A. leptophyllum, and Daucus carota form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of A. graveolens and A. leptophyllum, thereby enhancing comprehension of the traits and evolutionary patterns within the Apium genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family.
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Affiliation(s)
- Xiaoyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Weilong Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Jin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Qiuju Han
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Wei Lu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
| | - Qin Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Shunhua Zhu
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing 611130, China;
| | - Guofei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China; (Q.L.); (S.Z.)
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (X.L.); (M.L.); (W.L.); (J.Z.); (Q.H.); (W.L.)
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Sun Y, Li M, Li X, Du J, Li W, Lin Y, Zhang Y, Wang Y, He W, Chen Q, Zhang Y, Wang X, Luo Y, Xiong A, Tang H. Characterization of Volatile Organic Compounds in Five Celery ( Apium graveolens L.) Cultivars with Different Petiole Colors by HS-SPME-GC-MS. Int J Mol Sci 2023; 24:13343. [PMID: 37686147 PMCID: PMC10488006 DOI: 10.3390/ijms241713343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Celery (Apium graveolens L.) is an important vegetable crop cultivated worldwide for its medicinal properties and distinctive flavor. Volatile organic compound (VOC) analysis is a valuable tool for the identification and classification of species. Currently, less research has been conducted on aroma compounds in different celery varieties and colors. In this study, five different colored celery were quantitatively analyzed for VOCs using HS-SPME, GC-MS determination, and stoichiometry methods. The result revealed that γ-terpinene, d-limonene, 2-hexenal,-(E)-, and β-myrcene contributed primarily to the celery aroma. The composition of compounds in celery exhibited a correlation not only with the color of the variety, with green celery displaying a higher concentration compared with other varieties, but also with the specific organ, whereby the content and distribution of volatile compounds were primarily influenced by the leaf rather than the petiole. Seven key genes influencing terpenoid synthesis were screened to detect expression levels. Most of the genes exhibited higher expression in leaves than petioles. In addition, some genes, particularly AgDXS and AgIDI, have higher expression levels in celery than other genes, thereby influencing the regulation of terpenoid synthesis through the MEP and MVA pathways, such as hydrocarbon monoterpenes. This study identified the characteristics of flavor compounds and key aroma components in different colored celery varieties and explored key genes involved in the regulation of terpenoid synthesis, laying a theoretical foundation for understanding flavor chemistry and improving its quality.
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Affiliation(s)
- Yue Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Xiaoyan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Jiageng Du
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Weilong Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China; (Y.S.); (M.L.); (X.L.); (J.D.); (W.L.); (Y.L.); (Y.Z.); (Y.W.); (W.H.); (Q.C.); (Y.Z.); (X.W.); (Y.L.)
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Sun L, Wang J, Cui Y, Cui R, Kang R, Zhang Y, Wang S, Zhao L, Wang D, Lu X, Fan Y, Han M, Chen C, Chen X, Guo L, Ye W. Changes in terpene biosynthesis and submergence tolerance in cotton. BMC PLANT BIOLOGY 2023; 23:330. [PMID: 37344795 DOI: 10.1186/s12870-023-04334-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
BACKGROUND Flooding is among the most severe abiotic stresses in plant growth and development. The mechanism of submergence tolerance of cotton in response to submergence stress is unknown. RESULTS The transcriptome results showed that a total of 6,893 differentially expressed genes (DEGs) were discovered under submergence stress. Gene Ontology (GO) enrichment analysis showed that DEGs were involved in various stress or stimulus responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs related to plant hormone signal transduction, starch and sucrose metabolism, glycolysis and the biosynthesis of secondary metabolites were regulated by submergence stress. Eight DEGs related to ethylene signaling and 3 ethylene synthesis genes were identified in the hormone signal transduction. For respiratory metabolism, alcohol dehydrogenase (ADH, GH_A02G0728) and pyruvate decarboxylase (PDC, GH_D09G1778) were significantly upregulated but 6-phosphofructokinase (PFK, GH_D05G0280), phosphoglycerate kinase (PGK, GH_A01G0945 and GH_D01G0967) and sucrose synthase genes (SUS, GH_A06G0873 and GH_D06G0851) were significantly downregulated in the submergence treatment. Terpene biosynthetic pathway-related genes in the secondary metabolites were regulated in submergence stress. CONCLUSIONS Regulation of terpene biosynthesis by respiratory metabolism may play a role in enhancing the tolerance of cotton to submergence under flooding. Our findings showed that the mevalonate pathway, which occurs in the cytoplasm of the terpenoid backbone biosynthesis pathway (ko00900), may be the main response to submergence stress.
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Affiliation(s)
- Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
- Cotton Research Institute of Jiangxi Province, Jiujiang, 332105, Jiangxi, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Ruiqing Kang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
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Li M, Zhang R, Zhou J, Du J, Li X, Zhang Y, Chen Q, Wang Y, Lin Y, Zhang Y, He W, Wang X, Xiong A, Luo Y, Tang H. Comprehensive analysis of HSF genes from celery ( Apium graveolens L.) and functional characterization of AgHSFa6-1 in response to heat stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1132307. [PMID: 37223803 PMCID: PMC10202177 DOI: 10.3389/fpls.2023.1132307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
High temperature stress is regarded as one of the significant abiotic stresses affecting the composition and distribution of natural habitats and the productivity of agriculturally significant plants worldwide. The HSF family is one of the most important transcription factors (TFs) families in plants and capable of responding rapidly to heat and other abiotic stresses. In this study, 29 AgHSFs were identified in celery and classified into three classes (A, B, and C) and 14 subgroups. The gene structures of AgHSFs in same subgroups were conserved, whereas in different classes were varied. AgHSF proteins were predicted to be involved in multiple biological processes by interacting with other proteins. Expression analysis revealed that AgHSF genes play a significant role in response to heat stress. Subsequently, AgHSFa6-1, which was significantly induced by high temperature, was selected for functional validation. AgHSFa6-1 was identified as a nuclear protein, and can upregulate the expression of certain downstream genes (HSP98.7, HSP70-1, BOB1, CPN60B, ADH2, APX1, GOLS1) in response to high-temperature treatment. Overexpression of AgHSFa6-1 in yeast and Arabidopsis displayed higher thermotolerance, both morphologically and physiologically. In response to heat stress, the transgenic plants produced considerably more proline, solute protein, antioxidant enzymes, and less MDA than wild-type (WT) plants. Overall, this study revealed that AgHSF family members perform a key role in response to high temperature, and AgHSFa6-1 acts as a positive regulator by augmenting the ROS-scavenging system to maintain membrane integrity, reducing stomatal apertures to control water loss, and upregulating the expression level of heat-stress sensitive genes to improve celery thermotolerance.
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Affiliation(s)
- Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ran Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Jin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Jiageng Du
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyan Li
- 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 and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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