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Vincent D, Reddy P, Isenegger D. Integrated Proteomics and Metabolomics of Safflower Petal Wilting and Seed Development. Biomolecules 2024; 14:414. [PMID: 38672431 PMCID: PMC11048707 DOI: 10.3390/biom14040414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Safflower (Carthamus tinctorius L.) is an ancient oilseed crop of interest due to its diversity of end-use industrial and food products. Proteomic and metabolomic profiling of its organs during seed development, which can provide further insights on seed quality attributes to assist in variety and product development, has not yet been undertaken. In this study, an integrated proteome and metabolic analysis have shown a high complexity of lipophilic proteins and metabolites differentially expressed across organs and tissues during seed development and petal wilting. We demonstrated that these approaches successfully discriminated safflower reproductive organs and developmental stages with the identification of 2179 unique compounds and 3043 peptides matching 724 unique proteins. A comparison between cotyledon and husk tissues revealed the complementarity of using both technologies, with husks mostly featuring metabolites (99%), while cotyledons predominantly yielded peptides (90%). This provided a more complete picture of mechanisms discriminating the seed envelope from what it protected. Furthermore, we showed distinct molecular signatures of petal wilting and colour transition, seed growth, and maturation. We revealed the molecular makeup shift occurring during petal colour transition and wilting, as well as the importance of benzenoids, phenylpropanoids, flavonoids, and pigments. Finally, our study emphasizes that the biochemical mechanisms implicated in the growing and maturing of safflower seeds are complex and far-reaching, as evidenced by AraCyc, PaintOmics, and MetaboAnalyst mapping capabilities. This study provides a new resource for functional knowledge of safflower seed and potentially further enables the precision development of novel products and safflower varieties with biotechnology and molecular farming applications.
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (P.R.); (D.I.)
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Lv T, Li J, Zhou L, Zhou T, Pritchard HW, Ren C, Chen J, Yan J, Pei J. Aging-Induced Reduction in Safflower Seed Germination via Impaired Energy Metabolism and Genetic Integrity Is Partially Restored by Sucrose and DA-6 Treatment. PLANTS (BASEL, SWITZERLAND) 2024; 13:659. [PMID: 38475505 DOI: 10.3390/plants13050659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024]
Abstract
Seed storage underpins global agriculture and the seed trade and revealing the mechanisms of seed aging is essential for enhancing seed longevity management. Safflower is a multipurpose oil crop, rich in unsaturated fatty acids that are at high risk of peroxidation as a contributory factor to seed aging. However, the molecular mechanisms responsible for safflower seed viability loss are not yet elucidated. We used controlled deterioration (CDT) conditions of 60% relative humidity and 50 °C to reduce germination in freshly harvested safflower seeds and analyzed aged seeds using biochemical and molecular techniques. While seed malondialdehyde (MDA) and fatty acid content increased significantly during CDT, catalase activity and soluble sugar content decreased. KEGG analysis of gene function and qPCR validation indicated that aging severely impaired several key functional and biosynthetic pathways including glycolysis, fatty acid metabolism, antioxidant activity, and DNA replication and repair. Furthermore, exogenous sucrose and diethyl aminoethyl hexanoate (DA-6) treatment partially promoted germination in aged seeds, further demonstrating the vital role of impaired sugar and fatty acid metabolism during the aging and recovery processes. We concluded that energy metabolism and genetic integrity are impaired during aging, which contributes to the loss of seed vigor. Such energy metabolic pathways as glycolysis, fatty acid degradation, and the tricarboxylic acid cycle (TCA) are impaired, especially fatty acids produced by the hydrolysis of triacylglycerols during aging, as they are not efficiently converted to sucrose via the glyoxylate cycle to provide energy supply for safflower seed germination and seedling growth. At the same time, the reduced capacity for nucleotide synthesis capacity and the deterioration of DNA repair ability further aggravate the damage to DNA, reducing seed vitality.
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Affiliation(s)
- Tang Lv
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Juan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lanyu Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hugh W Pritchard
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, China
- Royal Botanic Gardens, Kew, Wakehurst, Ardingly, Haywards Heath RH17 6TN, West Sussex, UK
| | - Chaoxiang Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jiang Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Fan K, Qin Y, Hu X, Xu J, Ye Q, Zhang C, Ding Y, Li G, Chen Y, Liu J, Wang P, Hu Z, Yan X, Xiong H, Liu H, Qin R. Identification of genes associated with fatty acid biosynthesis based on 214 safflower core germplasm. BMC Genomics 2023; 24:763. [PMID: 38082219 PMCID: PMC10712096 DOI: 10.1186/s12864-023-09874-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Safflower (Carthamus tinctorius L.) is an oilseed crop with substantial medicinal and economic value. However, the methods for constructing safflower core germplasm resources are limited, and the molecular mechanisms of lipid biosynthesis in safflower seeds are not well understood. RESULTS In this study, 11 oil-related quantitative traits and 50 pairs of InDel markers were used to assess the diversity of a collection of 605 safflower germplasms. The original safflower germplasm exhibited rich phenotypic diversity, with high variation for most of the phenotypic traits under investigation. Similarly, high genetic diversity was evaluated in the original germplasm, in which the mean Shannon's information index (I), observed heterozygosity (H0), and expected heterozygosity (He) were 0.553, 0.182, and 0.374, respectively. Four subgroups with strong genetic structures were identified and a core germplasm of 214 cultivars was constructed, which is well represented in the original germplasm. Meanwhile, differential expression analysis of the transcriptomes of high and low linoleic acid safflower varieties at two stages of seed development identified a total of 47 genes associated with lipid biosynthesis. High expression of the genes KAS II and SAD enhanced the synthesis and accumulation of oleic acid, while FAD genes like FAD2 (Chr8G0104100), FAD3, FAD7 and FAD8 promoted the consumption of oleic acid conversion. The coordinated regulation of these multiple genes ensures the high accumulation of oleic acid in safflower seed oil. CONCLUSIONS Based on these findings, a core germplasm of 214 cultivars was constructed and 47 candidate genes related to unsaturated fatty acid biosynthesis and lipid accumulation were identified. These results not only provide guidance for further studies to elucidate the molecular basis of oil lipid accumulation in safflower seeds, but also contribute to safflower cultivar improvements.
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Affiliation(s)
- Kangjun Fan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Yonghua Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Xueli Hu
- Industrial Crop Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Jindong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Qingzhi Ye
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Chengyang Zhang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Yangyang Ding
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Gang Li
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Yan Chen
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Jiao Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Peiqi Wang
- Industrial Crop Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Zunhong Hu
- Industrial Crop Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xingchu Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Hairong Xiong
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central MinZu University, Wuhan, 430074, China.
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Chen J, Guo S, Hu X, Wang R, Jia D, Li Q, Yin X, Liao X, Hu Z, Wang P, Ren C, Dong S, Chen C, Chen S, Xu J, Pei J. Whole-genome and genome-wide association studies improve key agricultural traits of safflower for industrial and medicinal use. HORTICULTURE RESEARCH 2023; 10:uhad197. [PMID: 38023481 PMCID: PMC10673658 DOI: 10.1093/hr/uhad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Safflower (Carthamus tinctorius) is widely cultivated around the world for its seeds and flowers. The presence of linoleic acid (LA) in its seeds and hydroxysafflor yellow A (HSYA) in its flowers are the crucial traits that enable safflower to be used for industrial and medicinal purposes. Understanding the genetic control of these traits is essential for optimizing the quality of safflower and its breeding. To further this research, we present a chromosome-scale assembly of the genome of the safflower variety 'Chuanhonghua 1', which was achieved using an integrated strategy combining Illumina, Oxford Nanopore, and Hi-C sequencing. We obtained a 1.17-Gb assembly with a contig N50 of 1.08 Mb, and all assembled sequences were assigned to 12 pseudochromosomes. Safflower's evolution involved the core eudicot γ-triplication event and a whole-genome duplication event, which led to large-scale genomic rearrangements. Extensive genomic shuffling has occurred since the divergence of the ancestor of dicotyledons. We conducted metabolite and transcriptome profiles with time- and part-dependent changes and screened candidate genes that significantly contribute to seed lipid biosynthesis. We also analyzed key gene families that participate in LA and HSYA biosynthesis. Additionally, we re-sequenced 220 safflower lines and carried out a genome-wide association study using high-quality SNP data for eight agronomic traits. We identified SNPs related to important traits in safflower. Besides, the candidate gene HH_034464 (CtCGT1) was shown to be involved in the biosynthesis of HSYA. Overall, we provide a high-quality reference genome and elucidate the genetic basis of LA and HSYA biosynthesis in safflower. This vast amount of data will benefit further research for functional gene mining and breeding in safflower.
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Affiliation(s)
- Jiang Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shuai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xueli Hu
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Rui Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Donghai Jia
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumchi 830091, China
| | - Qiang Li
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumchi 830091, China
| | - Xianmei Yin
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xuejiao Liao
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zunhong Hu
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Peiqi Wang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Chaoxiang Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shuai Dong
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Chao Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shilin Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Lin YX, Xu HJ, Yin GK, Zhou YC, Lu XX, Xin X. Dynamic Changes in Membrane Lipid Metabolism and Antioxidant Defense During Soybean ( Glycine max L. Merr.) Seed Aging. FRONTIERS IN PLANT SCIENCE 2022; 13:908949. [PMID: 35812982 PMCID: PMC9263854 DOI: 10.3389/fpls.2022.908949] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Seed viability depends upon the maintenance of functional lipids; however, how membrane lipid components dynamically change during the seed aging process remains obscure. Seed storage is accompanied by the oxidation of membrane lipids and loss of seed viability. Understanding membrane lipid changes and their effect on the cell membrane during seed aging can contribute to revealing the mechanism of seed longevity. In this study, the potential relationship between oxidative stress and membrane lipid metabolism was evaluated by using a non-targeted lipidomics approach during artificial aging of Glycine max L. Merr. Zhongdou No. 27 seeds. We determined changes in reactive oxygen species, malondialdehyde content, and membrane permeability and assessed antioxidant system activity. We found that decreased non-enzymatic antioxidant contents and catalase activity might lead to reactive oxygen species accumulation, resulting in higher electrolyte leakage and lipid peroxidation. The significantly decreased phospholipids and increased glycerolipids and lysophospholipids suggested that hydrolysis of phospholipids to form glycerolipids and lysophospholipids could be the primary pathway of membrane metabolism during seed aging. Moreover, the ratio of phosphatidylcholine to phosphatidylethanolamine, double bond index, and acyl chain length of phospholipids were found to jointly regulate membrane function. In addition, the observed changes in lipid metabolism suggest novel potential hallmarks of soybean seed aging, such as diacylglycerol 36:4; phosphatidylcholine 34:2, 36:2, and 36:4; and phosphatidylethanolamine 34:2. This knowledge can be of great significance for elucidating the molecular mechanism underlying seed aging and germplasm conservation.
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Affiliation(s)
- Yi-xin Lin
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Hai-jin Xu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Guang-kun Yin
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan-chang Zhou
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Xin-xiong Lu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xia Xin
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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