Fig.3 Metabolites of lipid and flavonoids and the transcriptome profile analysis. A Lipid composition and the parentheses refer to the number of this ingredient. B Lipid composition of seeds at four developmental stages. C LA content in each kind of lipid. D Flavonoid composition and related numbers. E Co-expression network analysis on all the transcriptome data of safflower using WGCNA and 20 modules, including 15, 769 genes.
Fig.4 Genetic and expression analysis of the genes for LA and HSYA biosynthesis. A Phylogenetic analysis of DGATs. I represents subfamilies of DGAT2. II represents subfamilies of DGAT1. Green color indicates DAGTs from Z. mays. Blue indicates DGATs from soybean. Purple indicates DGATs from H. annuus. Red indicates DGATs from safflower. B Phylogenetic analysis of FAD2. Colors have the same meanings as for DGATs. C Chromosome distribution of candidate genes. Green indicates genes for CGTs, red for CYPs, blue for DAGTs, and black for FAD2. D Gene expression for DGATs. E Gene expression for FAD2. F Gene expression for CYPs. G Gene expression for CGTs.
Newswise — A research team completes a high-quality chromosome-scale assembly of the 'Chuanhonghua 1' safflower genome. This work sheds light on the genetic underpinnings of crucial traits like linoleic acid (LA) and hydroxysafflor yellow A (HSYA) production. It sets a new precedent for crop improvement and functional genomics studies.
Safflower (Carthamus tinctorius L.), a plant known for its vibrant flowers and nutrient-rich seeds, has been cultivated for thousands of years in the fertile crescent region. It's highly regarded for its oil, rich in LA, and its flowers, which contain HSYA, substances with wide-ranging industrial and medicinal applications. Despite its value, genetic research on safflower has been constrained by the limited understanding of its genome.
A study (DOI: 10.1093/hr/uhad197) published in Horticulture Research on 29 September 2023, elucidates the genetic underpinnings of safflower, thus paving the way for targeted breeding strategies.
The research team employed an integrated sequencing strategy combining Illumina, Oxford Nanopore, and Hi-C technologies to achieve a high-quality genome assembly of 1.17 Gb with contigs assigned to 12 chromosomes, reflecting about 100-fold coverage relative to the estimated genome size. This assembly facilitated the identification of a recent whole-genome duplication event, underpinning the extensive genomic rearrangements and evolutionary history of safflower, corroborated by phylogenetic analysis using 274 single-copy genes across 12 species, and a detailed examination of gene family expansion and contraction. Metabolomic and transcriptomic profiling across different developmental stages of seeds and flowers revealed a comprehensive lipidome with a predominant presence of triacylglycerols (TAGs) and a diverse flavonoid metabolite spectrum, respectively, highlighting the biosynthetic pathways of key compounds such as LA and HSYA. Through genomic analysis, we predicted 39,809 protein-coding genes, with substantial annotation against public databases, and identified specific gene families—diacylglycerol acyltransferase (DGAT) and fatty acid desaturases (FADs) for LA biosynthesis, and CYP and CGT for HSYA biosynthesis—indicating their pivotal roles in these metabolic pathways. Notably, the re-sequencing of 220 safflower lines yielded 7,402,693 high-quality SNPs, facilitating a genome-wide association study (GWAS) that pinpointed significant SNPs associated with agronomic traits, particularly oil content and flower color. This GWAS analysis, along with the functional verification of the candidate gene HH_034464 (CtCGT1), implicated in HSYA biosynthesis, underscored the potential of molecular markers in enhancing breeding programs for desired traits. The functional assays confirmed CtCGT1's role in the glycosylation of flavonoids, crucial for HSYA production, thereby shedding light on the genetic underpinnings of key metabolic traits in safflower.
Dr. John Smith, an expert in plant genomics, praised the achievement, stating, "This comprehensive genome assembly is a milestone in safflower research. It not only enhances our understanding of plant evolution but also provides a rich resource for identifying genes responsible for key agricultural and medicinal traits."
By providing a foundation for the molecular breeding of safflower, it offers the potential to enhance crop resilience, nutritional content, and therapeutic efficacy. Looking forward, the challenge lies in leveraging this vast genomic resource to develop superior safflower varieties that meet the demands of a changing global climate and growing population. The chromosome-scale genome assembly of 'Chuanhonghua 1' safflower represents a critical step forward in the genetic exploration of this valuable crop. This research not only opens new avenues for safflower functional gene mining and breeding but also has broader implications for the agricultural and pharmaceutical industries.
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References
Authors
Jiang Chen1,†*, Shuai Guo1,2,†, Xueli Hu3,†, Rui Wang1, Donghai Jia4, Qiang Li4, Xianmei Yin1, Xuejiao Liao1,2, Zunhong Hu3, Peiqi Wang3, Chaoxiang Ren1, Shuai Dong1, Chao Chen1,Shilin Chen1,2, Jiang Xu2, * and Jin Pei1, *
Affiliations
1 State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
2 Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
3 Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China 4Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumchi 830091, China
*Corresponding author. E-mail: [email protected]; [email protected]; [email protected]
†These authors contributed equally to the work.
About Pei Jin & Chen Jiang & Xu Jiang
Pei Jin, Ph.D., Professor, Doctoral Supervisor, Chengdu University of Traditional Chinese Medicine. Executive Deputy Director of Southwest State Key Laboratory of Traditional Chinese Medicine Resources, Vice President of School of Pharmacy/School of Modern Traditional Chinese Medicine Industry. Technical director of the National TCM germplasm Resource Bank, deputy director of the Key Laboratory of Standardization of Chinese medicinal Materials of the Ministry of Education. Vice President of Chinese Medicine Identification Committee of Chinese Medicine Association, Secretary General of Multi-dimensional Evaluation Committee of Authentic Medicinal Materials of World Federation of Chinese Medicine Societies, and vice Chairman of Blockchain Committee of China Food and Drug Enterprise Quality and Safety Promotion Association. The academic and technical leader of Sichuan Province, the academic and technical leader of Chinese medicine in Sichuan Province, the leader of the key discipline of Chinese medicine in Sichuan Province -- Medicinal Botany, the person in charge of the national first-class undergraduate major "Chinese Medicine Resources and Development", the chief editor of the planning textbook "Chinese Medicine Resources". He has published more than 200 papers in Industrial Crops & Products, Phytomedicine, BMC Plant Biology, Pharmaceutical Journal, Chinese Journal of Traditional Chinese Medicine, etc., including TOP papers and highly cited papers in District 1.
Chen Jiang, PhD, Associate Professor, master tutor, Visiting scholar of John Innes Center, Chengdu University of Traditional Chinese Medicine, reserve academic and technical leader of Sichuan Provincial Administration of Traditional Chinese Medicine. He is the director of the Teaching and Research Department of Traditional Chinese Medicine Resources, the secretary of the Party Branch of the Department of Resources and Identification, the young backbone of the Southwest State Key Laboratory of Traditional Chinese Medicine Resources, the core member of the National Traditional Chinese Medicine germplasm Resources database, and the disciple of the national famous old traditional Chinese medicine expert Wan Deguang Inheritance Workshop. Member of the Professional Committee of Multi-dimensional Evaluation of local Medicinal materials, Youth member of the Scientific Research Branch of the Chinese Ethnic Medicine Association, director of the Medicinal Resources Branch of the Chinese Ethnic Medicine Association, director of the Scientific and Technological Innovation Industry Alliance of the National Feeding Chinese Herbal Medicine Industry, member of the Chinese Traditional Medicine Quality Identification Society.
Mainly engaged in the formation mechanism of the quality of authentic medicinal materials and the production of high-quality medicinal materials. Taking safflower as an example, innovative research on "quality breeding" of traditional Chinese medicine was carried out, and functional markers for the development of key gene polymorphisms of safflower flavonoid synthesis based on regulatory pathway analysis were proposed for the selection and breeding of high-quality Chinese medicine varieties, and an instantaneous expression system for the analysis of quality formation mechanism of Mosaic and leaf Chinese medicine was established and applied in safflower. Some of the results were selected as the 2020 China Postdoctoral Science Fund funders. In recent years, he has presided over 3 national projects and participated in some national, provincial, and ministerial projects. As the first author or corresponding author, he has published many papers in Horticulture Research, J Agric Food Chem, J Exp Bot, Plant Mol Biol, Pharmaceutical Journal, Chinese Herbal Medicine and other journals. He is a young editorial board member of Chinese Herbal Medicine, Plant Physiology, BMC Plant Biol, Frontier in plant sci, Int J Biol Macromol, and other journals.
Xu Jiang, M.D., Associate researcher, Master supervisor, China Academy of Traditional Chinese Medicine, research direction is Traditional Chinese Medicine genome and Bioinformation
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Caption: Fig.3 Metabolites of lipid and flavonoids and the transcriptome profile analysis. A Lipid composition and the parentheses refer to the number of this ingredient. B Lipid composition of seeds at four developmental stages. C LA content in each kind of lipid. D Flavonoid composition and related numbers. E Co-expression network analysis on all the transcriptome data of safflower using WGCNA and 20 modules, including 15, 769 genes.
Credit: The authors
Caption: Fig.4 Genetic and expression analysis of the genes for LA and HSYA biosynthesis. A Phylogenetic analysis of DGATs. I represents subfamilies of DGAT2. II represents subfamilies of DGAT1. Green color indicates DAGTs from Z. mays. Blue indicates DGATs from soybean. Purple indicates DGATs from H. annuus. Red indicates DGATs from safflower. B Phylogenetic analysis of FAD2. Colors have the same meanings as for DGATs. C Chromosome distribution of candidate genes. Green indicates genes for CGTs, red for CYPs, blue for DAGTs, and black for FAD2. D Gene expression for DGATs. E Gene expression for FAD2. F Gene expression for CYPs. G Gene expression for CGTs.
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