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Wrightstone E, Xu L, Rao S, Hazra A, Li L. ORANGE family proteins: multifunctional chaperones shaping plant carotenoid level, plastid development, stress tolerance, and more. MOLECULAR HORTICULTURE 2025; 5:43. [PMID: 40341160 PMCID: PMC12063368 DOI: 10.1186/s43897-025-00169-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Accepted: 04/11/2025] [Indexed: 05/10/2025]
Abstract
ORANGE (OR) family proteins are DnaJE1 molecular chaperones ubiquitous and highly conserved in all plant species, indicating their important roles in plant growth and development. OR proteins have been found to exert multiple functions in regulating carotenoid and chlorophyll biosynthesis, plastid development, and stress tolerance, with additional functions expected to be discovered. As molecular chaperones, OR proteins directly influence the stability of their target proteins via their holdase activity and may perform other molecular roles through unknown mechanisms. Exploration of OR has uncovered novel mechanisms underlying core plant metabolism pathways and expanded our understanding of processes linked to plastid development. Continued investigation of OR family proteins will not only reveal new functions of molecular chaperones but also provide pioneering tools for crop improvement. Thus, OR family proteins offer a distinctive opportunity to comprehend molecular chaperones in modulating various metabolic and developmental processes and exemplify the importance of chaperones in crop development and adaptability. This review briefly details the history of OR family proteins, highlights recent advancements in understanding their myriad of functions, and discusses the prospects of this fascinating group of chaperones towards generating innovative, more nutritious, and resilient crops alongside other agronomically important traits.
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Affiliation(s)
- Emalee Wrightstone
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
| | - Lilin Xu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sombir Rao
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
| | - Abhijit Hazra
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
| | - Li Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA.
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Gao Y, Zhou X, Huang H, Wang C, Xiao X, Wen J, Wu J, Zhou S, de Dios VR, Rodríguez LG, Yao Y, Liu J, Deng H. ORANGE proteins mediate adaptation to high light and resistance to Pseudomonas syringae in tomato by regulating chlorophylls and carotenoids accumulation. Int J Biol Macromol 2025; 306:141739. [PMID: 40049490 DOI: 10.1016/j.ijbiomac.2025.141739] [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: 01/20/2025] [Revised: 02/19/2025] [Accepted: 03/03/2025] [Indexed: 03/09/2025]
Abstract
Chlorophylls and carotenoids are crucial for photosynthesis and plant survival, with ORANGE (OR) protein being pivotal in pigment accumulation. Despite tomato being rich in carotenoids, the roles of OR proteins in tomato have been overlooked. Herein, we characterized two OR genes in tomato, SlOR and SlOR-like, which are highly expressed in stems, leaves, and flowers, with their proteins being localized to chloroplasts. Overexpression of SlOR in transgenic plants conferred enhanced growth and height, whereas co-silencing of SlOR and SlOR-like resulted in stunted growth, pale-green leaves due to diminished chlorophylls and carotenoids, and fewer thylakoid lamellae and layers. Under normal light, SlOR/SlOR-like-Ri transgenic plants exhibited compromised electron transport and photosynthetic rates; furthermore, high-light exposure exacerbated these effects, resulting in photooxidative stress, elevated reactive oxygen species (ROS) and reduced photosynthetic rates in SlOR/SlOR-like-Ri plants. Transcriptome analysis revealed that photosynthesis-related genes were up-regulated, while defense-related genes were significantly down-regulated in SlOR/SlOR-like-Ri lines relative to wild-type plants. Additionally, SlOR/SlOR-like-Ri plants also displayed enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000. Overall, our study highlights SlOR as a critical protein modulating the accumulation of chlorophylls and carotenoids in tomato, playing a crucial role in adaptation to high light conditions and pathogen resistance.
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Affiliation(s)
- Yongfeng Gao
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Xue Zhou
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Haitao Huang
- Mianyang Academy of Agricultural Sciences, 621023 Mianyang, China
| | - Cheng Wang
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Xiangxia Xiao
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Jing Wen
- Mianyang Academy of Agricultural Sciences, 621023 Mianyang, China
| | - Jiamin Wu
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Shan Zhou
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Víctor Resco de Dios
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Lucas Gutiérrez Rodríguez
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Yinan Yao
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Jikai Liu
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
| | - Heng Deng
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
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Tzuri G, Dafna A, Itzhaki B, Halperin I, Oren E, Isaacson T, Faigenboim A, Yeselson Y, Paris HS, Mazourek M, Burger J, Schaffer AA, Gur A. Meta genetic analysis of melon sweetness. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:68. [PMID: 40067361 PMCID: PMC11897113 DOI: 10.1007/s00122-025-04863-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 02/20/2025] [Indexed: 03/15/2025]
Abstract
KEY MESSAGE Through meta-genetic analysis of Cucumis melo sweetness, we expand the description of the complex genetic architecture of this trait. Integration of extensive new results with published QTL data provides an outline towards construction of a melon sweetness pan-QTLome. An ultimate objective in crop genetics is describing the complete repertoire of genes and alleles that shape the phenotypic variation of a quantitative trait within a species. Flesh sweetness is a primary determinant of fruit quality and consumer acceptance of melons. Cucumis melo is a diverse species that, among other traits, displays extensive variation in total soluble solids (TSS) content in fruit flesh, ranging from 20 Brix in non-sweet to 180 Brix in sweet accessions. We present here meta-genetic analysis of TSS and sugar variation in melon, using six different populations and fruit measurements collected from more than 30,000 open-field and greenhouse-grown plants, integrated with 15 published melon sweetness-related quantitative trait loci (QTL) studies. Starting with characterization of sugar composition variation across 180 diverse accessions that represent 3 subspecies and 12 of their cultivar-groups, we mapped TSS and sugar QTLs, and confirmed that sucrose accumulation is the key variable explaining TSS variation. All modes-of-inheritance for TSS were displayed by multi-season analysis of a broad half-diallel population derived from 20 diverse founders, with significant prevalence of the additive component. Through parallel genetic mapping in four advanced bi-parental populations, we identified common as well as unique TSS QTLs in 12 chromosomal regions. We demonstrate the cumulative less-than-additive nature of favorable TSS QTL alleles and the potential of a QTL-stacking approach. Using our broad dataset, we were additionally able to show that TSS variation displays weak genetic correlations with melon fruit size and ripening behavior, supporting effective breeding for sweetness per se. Our integrated analysis, combined with additional layers of published QTL data, broadens the perspective on the complex genetic landscape of melon sweetness and proposes a scheme towards future construction of a crop community-driven melon sweetness pan-QTLome.
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Affiliation(s)
- Galil Tzuri
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Asaf Dafna
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
- Faculty of Agriculture, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Ben Itzhaki
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Ilan Halperin
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Elad Oren
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Tal Isaacson
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Adi Faigenboim
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7507101, Rishon LeZiyyon, Israel
| | - Yelena Yeselson
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7507101, Rishon LeZiyyon, Israel
| | - Harry S Paris
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Michael Mazourek
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7507101, Rishon LeZiyyon, Israel
| | - Amit Gur
- Plant Science Institute, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, 3009500, Ramat Yishay, Israel.
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Huang JJ, Xu W, Lin S, Cheung PCK. The bioactivities and biotechnological production approaches of carotenoids derived from microalgae and cyanobacteria. Crit Rev Biotechnol 2025; 45:276-304. [PMID: 39038957 DOI: 10.1080/07388551.2024.2359966] [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: 12/18/2023] [Revised: 04/03/2024] [Accepted: 05/13/2024] [Indexed: 07/24/2024]
Abstract
Microalgae and cyanobacteria are a rich source of carotenoids that are well known for their potent bioactivities, including antioxidant, anti-cancer, anti-proliferative, anti-inflammatory, and anti-obesity properties. Recently, many interests have also been focused on the biological activities of these microalgae/cyanobacteria-derived carotenoids, such as fucoxanthin and β-carotene potential to be the salutary nutraceuticals, on treating or preventing human common diseases (e.g., cancers). This is due to their special chemical structures that demonstrate unique bioactive functions, in which the biologically active discrepancies might attribute to the different spatial configurations of their molecules. In addition, their abundance and bioaccessibilities make them more popularly applied in food and pharmaceutical industries, as compared to the macroalgal/fungal-derived ones. This review is focused on the recent studies on the bioactivities of fucoxanthin and some carotenoids derived from microalgae and cyanobacteria in relationship with human health and diseases, with emphasis on their potential applications as natural antioxidants. Various biotechnological approaches employed to induce the production of these specific carotenoids from the culture of microalgae/cyanobacteria are also critically reviewed. These well-developed and emerging biotechnologies present promise to be applied in food and pharmaceutical industries to facilitate the efficient manufacture of the bioactive carotenoid products derived from microalgae and cyanobacteria.
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Affiliation(s)
- Jim Junhui Huang
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, People's Republic of China
- Department of Food Science and Technology, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Wenwen Xu
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, People's Republic of China
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Shaoling Lin
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, People's Republic of China
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, People's Republic of China
| | - Peter Chi Keung Cheung
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, People's Republic of China
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Li S, Wang H, Li Y, Jing F, Xu Y, Deng S, Wang N, Zhang Z, Chai S. Mapping and functional characterization of the golden fruit 1 (gf1) in melon (Cucumis melo L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:59. [PMID: 40009196 DOI: 10.1007/s00122-025-04849-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 02/07/2025] [Indexed: 02/27/2025]
Abstract
KEY MESSAGE A missense mutation that causes premature termination of the CmEGY1 protein leads to golden fruit in melon. Melon (Cucumis melo L.) is an economically important fruit crop that has been cultivated for thousands of years. Fruit color, a crucial trait influencing the appearance quality and economic value of melons, is primarily determined mainly by the type and concentration of pigments such as chlorophyll, carotenoids, and flavonoids. Identifying the genetic loci that govern melon fruit color contributes to breeding efforts aimed at enhancing melon rind coloration. This study reports an EMS-induced mutant, designated as gf1 (golden fruit 1), which produces fruit with both golden peel and flesh. Through MutMap and map-based cloning, we localized the gf1 locus to an 862 kb region containing 42 SNPs. Of these, a single SNP in the coding region caused a stop-gained mutation in the gene Cme13C08g017690, which exhibits the highest sequence similarity to Arabidopsis ETHYLENE-DEPENDENT GRAVITROPISM-DEFICIENT AND YELLOW-GREEN 1 (EGY1). Genome editing of CsEGY1, the cucumber homolog, confirmed its role in golden-fruit formation. Transcriptome and metabolome analyses revealed reduced flavonoid and carotenoid contents, accompanied by the downregulation of related biosynthetic genes. The identification and characterization of egy1 provide novel genetic insights and a valuable resource for improving melon appearance through breeding.
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Affiliation(s)
- Shuai Li
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huihui Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yang Li
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Feng Jing
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuanchao Xu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shijun Deng
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Naonao Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Sen Chai
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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Sturaro M. Carotenoids in Potato Tubers: A Bright Yellow Future Ahead. PLANTS (BASEL, SWITZERLAND) 2025; 14:272. [PMID: 39861622 PMCID: PMC11768161 DOI: 10.3390/plants14020272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 01/13/2025] [Accepted: 01/16/2025] [Indexed: 01/27/2025]
Abstract
Carotenoids, the bright yellow, orange, and red pigments of many fruits and vegetables, are essential components of the human diet as bioactive compounds not synthesized in animals. As a staple crop potato has the potential to deliver substantial amounts of these nutraceuticals despite their lower concentration in tubers compared to edible organs of other plant species. Even small gains in tuber carotenoid levels could have a significant impact on the nutritional value of potatoes. This review will focus on the current status and future perspectives of carotenoid biofortification in potato with conventional breeding and biotechnological approaches. The high biodiversity of tuber carotenoid levels and composition is presented, with an emphasis on the under-exploited native germplasm that represents a wide reservoir of useful genetic variants to breed carotenoid-rich varieties. The following section describes the structural genes involved in carotenoid metabolism and storage known to have a major impact on carotenoid accumulation in potato, together with the strategies that harnessed their expression changes to increase tuber carotenoid content. Finally, the little information available on the regulation of carotenoid metabolism and the desirable future advances in potato carotenoid biofortification are discussed.
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Affiliation(s)
- Monica Sturaro
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca Cerealicoltura e Colture Industriali, via Stezzano 24, 24126 Bergamo, Italy
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Zhang X, Tang C, Jiang B, Zhang R, Li M, Wu Y, Yao Z, Huang L, Luo Z, Zou H, Yang Y, Wu M, Chen A, Wu S, Hou X, Liu X, Fei Z, Fu J, Wang Z. Refining polyploid breeding in sweet potato through allele dosage enhancement. NATURE PLANTS 2025; 11:36-48. [PMID: 39668213 DOI: 10.1038/s41477-024-01873-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 11/08/2024] [Indexed: 12/14/2024]
Abstract
Allele dosage plays a key role in the phenotypic variation of polyploids. Here we present a genome-wide variation map of hexaploid sweet potato that captures allele dosage information, constructed from deep sequencing of 294 hexaploid accessions. Genome-wide association studies identified quantitative trait loci with dosage effects on 23 agronomic traits. Our analyses reveal that sweet potato breeding has progressively increased the dosage of favourable alleles to enhance trait performance. Notably, the Mesoamerican gene pool has evolved towards higher dosages of favourable alleles at multiple loci, which have been increasingly introgressed into modern Chinese cultivars. We substantiated the breeding-driven dosage accumulation through transgenic validation of IbEXPA4, an expansin gene influencing tuberous root weight. In addition, we explored causative sequence variations that alter the expression of the Orange gene, which regulates flesh colour. Our findings illuminate the breeding history of sweet potato and establish a foundation for leveraging allele dosages in polyploid breeding practices.
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Affiliation(s)
- Xiangbo Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Chaochen Tang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Bingzhi Jiang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Rong Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Ming Li
- College of Life Sciences, Chongqing Normal University, Chongqing, China
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yaoyao Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhufang Yao
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Lifei Huang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Zhongxia Luo
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Hongda Zou
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Yiling Yang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China
| | - Minyi Wu
- Guangdong Provincial Key Laboratory of Applied Botany, and State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ao Chen
- Guangdong Provincial Key Laboratory of Applied Botany, and State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany, and State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xu Liu
- Guangdong Provincial Key Laboratory of Applied Botany, and State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA.
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Junjie Fu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhangying Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement of Guangdong Province, Guangzhou, China.
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Palaniswamy R, Kambale R, Mohanavel V, Rajagopalan VR, Manickam S, Muthurajan R. Identifying molecular targets for modulating carotenoid accumulation in rice grains. Biochem Biophys Rep 2024; 40:101815. [PMID: 39290348 PMCID: PMC11406064 DOI: 10.1016/j.bbrep.2024.101815] [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: 05/22/2024] [Revised: 08/07/2024] [Accepted: 08/21/2024] [Indexed: 09/19/2024] Open
Abstract
Carotenoids are potential antioxidants offering extensive human health benefits including protection against chronic diseases. Augmenting the supply of health-benefiting compounds/metabolites through dietary supplements is the most sustainable way for a healthy life. Our study compares the traditional rice cultivar Kavuni and the white rice variety ASD 16. RNA-Seq analysis was carried out in the maturing panicles of Kavuni, which are enriched with antioxidants such as the therapeutic carotenoid lutein, polyphenols, and anthocyanins, along with "ASD 16", a popularly eaten white rice variety, to elucidate the molecular networks regulating accumulation of health benefiting compounds. Systematic analysis of transcriptome data identified preferential up-regulation of carotenoid precursors (OsDXS, OsGGPS) and key carotenoid biosynthetic genes (OsPSY1, OsZ-ISO) in the maturing grains of Kavuni. Our study also identified enhanced expression of OsLYC-E, OsCYP97A, and OsCYP97C transcripts involved in the alpha-carotenoid biosynthetic pathway and thereby leading to elevated lutein content in the grains of Kavuni. Kavuni grains showed preferential down-regulation of negative regulators of carotenoid metabolism viz., AP2 and HY5 and preferential up-regulation of positive modulators of carotenoid metabolism viz., Orange, OsDjB7, and OsSET29, thus creating a favorable molecular framework for carotenoid accumulation. Our study has unearthed valuable gene control points for precise manipulation of carotenoid profiles through CRISPR-based gene editing in rice grains. Perturbation of carotenoid biosynthesis holds unprecedented potential for the rapid development of the next generation of 'Golden rice'.
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Affiliation(s)
- Rakshana Palaniswamy
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Rohit Kambale
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Vignesh Mohanavel
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sudha Manickam
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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9
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Mayobre C, Garcia-Mas J, Pujol M. A matter of smell: The complex regulation of aroma production in melon. Food Chem 2024; 460:140640. [PMID: 39096801 DOI: 10.1016/j.foodchem.2024.140640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 08/05/2024]
Abstract
Melon fruit flavor is one of the most valuable traits for consumers. Aroma, formed by volatile organic compounds (VOCs), is a major component of flavor but has been neglected in breeding programs because of its complex regulation. Although the genetic regulation of VOCs biosynthesis is not fully understood, several advances have been recently achieved. VOCs originate from the degradation of fatty acids, aminoacids and terpenes, and the role of newly described enzymes, transcription factors and putative regulators is here discussed. Furthermore, ethylene plays a key role in fruit aroma production in melon, triggering the conversion of green-flavored aldehydes into fruity-flavored esters. A current challenge is to understand the ethylene-independent regulation of VOCs formation. Environmental conditions and human processing can also shape the melon volatile profile, and future research should focus on studying the effect of climate change in aroma formation.
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Affiliation(s)
- Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain.
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain.
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10
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Bowers RR, Slonecki TJ, Olukolu BA, Yencho GC, Wadl PA. Genome-Wide Association Study of Sweet Potato Storage Root Traits Using GWASpoly, a Gene Dosage-Sensitive Model. Int J Mol Sci 2024; 25:11727. [PMID: 39519288 PMCID: PMC11546673 DOI: 10.3390/ijms252111727] [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: 09/20/2024] [Revised: 10/28/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024] Open
Abstract
Sweet potato (Ipomoea batatas) is an important food crop that plays a pivotal role in preserving worldwide food security. Due to its polyploid genome, high heterogeneity, and phenotypic plasticity, sweet potato genetic characterization and breeding is challenging. Genome-wide association studies (GWASs) can provide important resources for breeders to improve breeding efficiency and effectiveness. GWASpoly was used to identify 28 single nucleotide polymorphisms (SNPs), comprising 21 unique genetic loci, associated with sweet potato storage root traits including dry matter (4 loci), subjective flesh color (5 loci), flesh hue angle (3 loci), and subjective skin color and skin hue angle (9 loci), in 384 accessions from the USDA sweet potato germplasm collection. The I. batatas 'Beauregard' and I. trifida reference genomes were utilized to identify candidate genes located within 100 kb from the SNPs that may affect the storage traits of dry matter, flesh color, and skin color. These candidate genes include transcription factors (especially Myb, bHLH, and WRKY family members), metabolite transporters, and metabolic enzymes and associated proteins involved in starch, carotenoid, and anthocyanin synthesis. A greater understanding of the genetic loci underlying sweet potato storage root traits will enable marker-assisted breeding of new varieties with desired traits. This study not only reinforces previous research findings on genes associated with dry matter and β-carotene content but also introduces novel genetic loci linked to these traits as well as other root characteristics.
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Affiliation(s)
- Robert R. Bowers
- United States Department of Agriculture, Agricultural Research Service, United States Vegetable Laboratory, Charleston, SC 29414, USA;
| | | | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA;
| | - G. Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Phillip A. Wadl
- United States Department of Agriculture, Agricultural Research Service, United States Vegetable Laboratory, Charleston, SC 29414, USA;
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11
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Peng J, Gao Y, Qiao Y, Wang G. A point mutation in the zinc-finger transcription factor CqLOL1 controls the green flesh color in chieh-qua ( Benincasa hispida Cogn. var. Chieh-qua How). FRONTIERS IN PLANT SCIENCE 2024; 15:1388115. [PMID: 39498399 PMCID: PMC11532076 DOI: 10.3389/fpls.2024.1388115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 09/17/2024] [Indexed: 11/07/2024]
Abstract
Introduction Flesh color is an essential trait in chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How); however, the inheritance and molecular basis of green flesh trait remain unclear. Methods In the present study, two F2 populations, derived from 1742 (white flesh) × FJ3211 (green flesh) and J16 (white flesh) × FJ5 (green flesh), were used to identify the green flesh (Cqgf) locus. Results Genetic analysis revealed that the presence of green flesh was a quantitative trait that closely followed a normal distribution. Combining the results from QTL mapping and BSA-seq analysis, the Cqgf locus was preliminarily determined to be located on chromosome 05 and was narrowed down to a 2.55-Mb interval by linkage analysis. A large J16 × FJ5 F2 population comprising 3,180 individuals was subsequently used to screen the recombinants, and the Cqgf locus was fine-mapped to a region of 329.70 kb that harbors six genes. One of the candidate genes, Bch05G003700, the zinc-finger transcription factor LOL1 (lsd one like 1 protein; CqLOL1), was the strongest candidate gene for the Cqgf locus according to sequence variation and expression analysis. Additionally, a point mutation (A > C) in CqLOL1 resulted in the substitution of threonine (T) with proline (P) in the amino acid sequence, showing a complete relationship linked with flesh color in a panel of 45 germplasms. Discussion The study suggests that CqLOL1 promotes the accumulation of chlorophyll content in chieh-qua and lead to green flesh. Our findings establish a theoretical and technical foundation for breeding different flesh color lines and elucidating the underlying mechanisms of flesh color in chieh-qua.
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Affiliation(s)
- Jiazhu Peng
- Vegetable Research Science Department, Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou, China
- Vegetable Research Institute, Guangzhou Academy of Agricultural Sciences, Guangzhou, China
| | - Yin Gao
- Vegetable Research Science Department, Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yanchun Qiao
- Vegetable Research Science Department, Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou, China
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou, China
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12
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Liu J, Fang X, Yu F, Zhang C, Fan P, Wang N, Shao Q, Gan N, Lv X, Ouyang B, Zhang M, Wu X, Liao N. Genetic mapping and molecular marker development for white flesh color in tomato. FRONTIERS IN PLANT SCIENCE 2024; 15:1459013. [PMID: 39290736 PMCID: PMC11405233 DOI: 10.3389/fpls.2024.1459013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/13/2024] [Indexed: 09/19/2024]
Abstract
Introduction Fruit color significantly influences the quality of horticultural crops, which affects phytochemical diversity and consumer preferences. Despite its importance, the genetic basis of the white-colored fruit in tomatoes remains poorly understood. Methods In this study, we demonstrate that white-fleshed tomato varieties accumulate fewer carotenoids than yellow-fleshed varieties. We developed various segregating populations by hybridizing red, yellow, and white fruit tomato cultivars. Results Genetic analysis revealed that the white fruit color trait is controlled by a single gene that dominates both red and yellow fruits. Bulk segregant RNA sequencing provided a preliminary map of a 3.17 Mb region on chromosome 3 associated with the white color trait. Based on kompetitive allele-specific PCR (KASP) markers, we narrowed the candidate gene region to 819 kb. Within this region, we identified a 4906-bp sequence absence variation near Phytoene Synthase 1 (SlPSY1) specific to white-colored tomatoes. Genotyping of the progeny and natural populations using a single nucleotide polymorphism adjacent to this absence of variation confirmed its key role in white fruit formation. Discussion Collectively, our findings provide insights into white fruit trait formation in tomatoes, enabling tomato breeders to precisely introduce white fruit traits for commercial exploitation.
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Affiliation(s)
- Jie Liu
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Xiaoxue Fang
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Fangjie Yu
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Chengfeng Zhang
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Pengfei Fan
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Ningdong Wang
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Qiao Shao
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Ning Gan
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Xiaolong Lv
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bo Ouyang
- Department of Vegetable Science, College of Horticultural and Forest Sciences, Huazhong Agricultural University, Wuhan, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xinsheng Wu
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
| | - Nanqiao Liao
- Department of Molecular Assistant Breeding, Weimeng Seed Co. Ltd., Ningbo, China
- Key Laboratory of digital seed industry of watermelon, melon & cabbage, Ministry of Agriculture and Rural Areas, Ningbo, China
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13
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Wang YG, Zhang YM, Wang YH, Zhang K, Ma J, Hang JX, Su YT, Tan SS, Liu H, Xiong AS, Xu ZS. The Y locus encodes a REPRESSOR OF PHOTOSYNTHETIC GENES protein that represses carotenoid biosynthesis via interaction with APRR2 in carrot. THE PLANT CELL 2024; 36:2798-2817. [PMID: 38593056 PMCID: PMC11289637 DOI: 10.1093/plcell/koae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Little is known about the factors regulating carotenoid biosynthesis in roots. In this study, we characterized DCAR_032551, the candidate gene of the Y locus responsible for the transition of root color from ancestral white to yellow during carrot (Daucus carota) domestication. We show that DCAR_032551 encodes a REPRESSOR OF PHOTOSYNTHETIC GENES (RPGE) protein, named DcRPGE1. DcRPGE1 from wild carrot (DcRPGE1W) is a repressor of carotenoid biosynthesis. Specifically, DcRPGE1W physically interacts with DcAPRR2, an ARABIDOPSIS PSEUDO-RESPONSE REGULATOR2 (APRR2)-like transcription factor. Through this interaction, DcRPGE1W suppresses DcAPRR2-mediated transcriptional activation of the key carotenogenic genes phytoene synthase 1 (DcPSY1), DcPSY2, and lycopene ε-cyclase (DcLCYE), which strongly decreases carotenoid biosynthesis. We also demonstrate that the DcRPGE1W-DcAPRR2 interaction prevents DcAPRR2 from binding to the RGATTY elements in the promoter regions of DcPSY1, DcPSY2, and DcLCYE. Additionally, we identified a mutation in the DcRPGE1 coding region of yellow and orange carrots that leads to the generation of alternatively spliced transcripts encoding truncated DcRPGE1 proteins unable to interact with DcAPRR2, thereby failing to suppress carotenoid biosynthesis. These findings provide insights into the transcriptional regulation of carotenoid biosynthesis and offer potential target genes for enhancing carotenoid accumulation in crop plants.
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Affiliation(s)
- Ying-Gang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu-Min Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Ma
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Jia-Xin Hang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu-Ting Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan-Shan Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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14
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Chen X, Li H, Dong Y, Xu Y, Xu K, Zhang Q, Yao Z, Yu Q, Zhang H, Zhang Z. A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:144. [PMID: 38809285 DOI: 10.1007/s00122-024-04647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
KEY MESSAGE A wild melon reference genome elucidates the genomic basis of fruit acidity domestication. Structural variants (SVs) have been reported to impose major effects on agronomic traits, representing a significant contributor to crop domestication. However, the landscape of SVs between wild and cultivated melons is elusive and how SVs have contributed to melon domestication remains largely unexplored. Here, we report a 379-Mb chromosome-scale genome of a wild progenitor melon accession "P84", with a contig N50 of 14.9 Mb. Genome comparison identifies 10,589 SVs between P84 and four cultivated melons with 6937 not characterized in previously analysis of 25 melon genome sequences. Furthermore, the population-scale genotyping of these SVs was determined in 1175 accessions, and 18 GWAS signals including fruit acidity, fruit length, fruit weight, fruit color and sex determination were detected. Based on these genotyped SVs, we identified 3317 highly diverged SVs between wild and cultivated melons, which could be the potential SVs associated with domestication-related traits. Furthermore, we identify novel SVs affecting fruit acidity and proposed the diverged evolutionary trajectories of CmPH, a key regulator of melon fruit acidity, during domestication and selection of different populations. These results will offer valuable resources for genomic studies and genetic improvement in melon.
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Affiliation(s)
- Xinxiu Chen
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hongbo Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuanhua Dong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuanchao Xu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Kuipeng Xu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiqi Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwang Yao
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing Yu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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15
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Rao S, Cao H, O’Hanna FJ, Zhou X, Lui A, Wrightstone E, Fish T, Yang Y, Thannhauser T, Cheng L, Dudareva N, Li L. Nudix hydrolase 23 post-translationally regulates carotenoid biosynthesis in plants. THE PLANT CELL 2024; 36:1868-1891. [PMID: 38299382 PMCID: PMC11653588 DOI: 10.1093/plcell/koae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/12/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Carotenoids are essential for photosynthesis and photoprotection. Plants must evolve multifaceted regulatory mechanisms to control carotenoid biosynthesis. However, the regulatory mechanisms and the regulators conserved among plant species remain elusive. Phytoene synthase (PSY) catalyzes the highly regulated step of carotenogenesis and geranylgeranyl diphosphate synthase (GGPPS) acts as a hub to interact with GGPP-utilizing enzymes for the synthesis of specific downstream isoprenoids. Here, we report a function of Nudix hydrolase 23 (NUDX23), a Nudix domain-containing protein, in post-translational regulation of PSY and GGPPS for carotenoid biosynthesis. NUDX23 expresses highly in Arabidopsis (Arabidopsis thaliana) leaves. Overexpression of NUDX23 significantly increases PSY and GGPPS protein levels and carotenoid production, whereas knockout of NUDX23 dramatically reduces their abundances and carotenoid accumulation in Arabidopsis. NUDX23 regulates carotenoid biosynthesis via direct interactions with PSY and GGPPS in chloroplasts, which enhances PSY and GGPPS protein stability in a large PSY-GGPPS enzyme complex. NUDX23 was found to co-migrate with PSY and GGPPS proteins and to be required for the enzyme complex assembly. Our findings uncover a regulatory mechanism underlying carotenoid biosynthesis in plants and offer promising genetic tools for developing carotenoid-enriched food crops.
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Affiliation(s)
- Sombir Rao
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, NY 14853, USA
| | - Hongbo Cao
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
- College of Horticulture, Hebei Agricultural University,
Baoding, Hebei 071000, China
| | - Franz Joseph O’Hanna
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
| | - Xuesong Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, NY 14853, USA
| | - Andy Lui
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, NY 14853, USA
| | - Emalee Wrightstone
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, NY 14853, USA
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
| | - Theodore Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant Science, Cornell
University, Ithaca, NY 14853, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University,
West Lafayette, IN 47907-2063, USA
- Department of Horticulture and Landscape Architecture, Purdue
University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University,
West Lafayette, IN 47907, USA
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell
University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science,
Cornell University, Ithaca, NY 14853, USA
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16
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Zhang P, Wang Y, Zhu G, Zhu H. Developing carotenoids-enhanced tomato fruit with multi-transgene stacking strategies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108575. [PMID: 38554536 DOI: 10.1016/j.plaphy.2024.108575] [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: 02/06/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024]
Abstract
As natural dominant pigments, carotenoids and their derivatives not only contribute to fruit color and flavor quality but are regarded as phytochemicals beneficial to human health because of various bioactivities. Tomato is one of the most important vegetables as well as a main dietary source of carotenoids. So, it's of great importance to generate carotenoid-biofortified tomatoes. The carotenoid biosynthesis pathway is a network co-regulated by multiple enzymes and regulatory genes. Here, we assembled four binary constructs containing different combinations of four endogenous carotenoids metabolic-related genes, including SlORHis, SlDXS, SlPSY, and SlBHY by using a high efficiency multi-transgene stacking system and a series of fruit-specific promotors. Transgenic lines overexpression SlORHis alone, three genes (SlORHis/SlDXS/SlPSY), two genes (SlORHis/SlBHY), and all these four genes (SlORHis/SlDXS/SlPSY/SlBHY) were enriched with carotenoids to varying degrees. Notably, overexpressing SlORHis alone showed comparable effects with simultaneous overexpression of the key regulatory enzyme coding genes SlDXS, SlPSY, and SlORHis in promoting carotenoid accumulation. Downstream carotenoid derivatives zeaxanthin and violaxanthin were detected only in lines containing SlBHY. In addition, the sugar content and total antioxidant capacity of these carotenoids-enhanced tomatoes was also increased. These data provided useful information for the future developing of biofortified tomatoes with different carotenoid profiles, and confirmed a promising system for generation of nutrients biofortified tomatoes by multiple engineering genes stacking strategy.
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Affiliation(s)
- Peiyu Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Yifan Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Guoning Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, PR China; Sichuan Advanced Agricultural & Industrial Institute, China Agriculture University, Chengdu, 611430, Sichuan, PR China.
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17
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Sugumar T, Shen G, Smith J, Zhang H. Creating Climate-Resilient Crops by Increasing Drought, Heat, and Salt Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1238. [PMID: 38732452 PMCID: PMC11085490 DOI: 10.3390/plants13091238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Over the years, the changes in the agriculture industry have been inevitable, considering the need to feed the growing population. As the world population continues to grow, food security has become challenged. Resources such as arable land and freshwater have become scarce due to quick urbanization in developing countries and anthropologic activities; expanding agricultural production areas is not an option. Environmental and climatic factors such as drought, heat, and salt stresses pose serious threats to food production worldwide. Therefore, the need to utilize the remaining arable land and water effectively and efficiently and to maximize the yield to support the increasing food demand has become crucial. It is essential to develop climate-resilient crops that will outperform traditional crops under any abiotic stress conditions such as heat, drought, and salt, as well as these stresses in any combinations. This review provides a glimpse of how plant breeding in agriculture has evolved to overcome the harsh environmental conditions and what the future would be like.
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Affiliation(s)
- Tharanya Sugumar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (T.S.); (J.S.)
| | - Guoxin Shen
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Jennifer Smith
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (T.S.); (J.S.)
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (T.S.); (J.S.)
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18
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Sobrino-Mengual G, Alvarez D, Twyman RM, Gerrish C, Fraser PD, Capell T, Christou P. Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus. PLANT CELL REPORTS 2024; 43:118. [PMID: 38632121 PMCID: PMC11024007 DOI: 10.1007/s00299-024-03199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.
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Affiliation(s)
- Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Derry Alvarez
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, BioActives Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Christopher Gerrish
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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19
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Mayobre C, Santo Domingo M, Özkan EN, Fernández-Borbolla A, Ruiz-Lasierra J, Garcia-Mas J, Pujol M. Genetic regulation of volatile production in two melon introgression line collections with contrasting ripening behavior. HORTICULTURE RESEARCH 2024; 11:uhae020. [PMID: 38469382 PMCID: PMC10925849 DOI: 10.1093/hr/uhae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/10/2024] [Indexed: 03/13/2024]
Abstract
The importance of melon aroma in determining fruit quality has been highlighted in recent years. The fruit volatile profile is influenced by the type of fruit ripening. Non-climacteric fruits contain predominantly aldehydes, while climacteric fruits mainly produce esters. Several genes have been described to participate in volatile organic compounds (VOCs) biosynthesis pathways, but knowledge in this area is still incomplete. In this work we analysed the volatile profile of two reciprocal Introgression Line (IL) collections generated from a cross between 'Piel de Sapo' (PS) and 'Védrantais' (VED) melons, differing in their aroma profile and ripening behaviour. SPME GC-MS was performed to identify genes responsible for VOCs formation. More than 1000 QTLs for many volatiles were detected taken together both populations. Introgressions on chromosomes 3, 5, 6, 7 and 8 modified ester-aldehyde balance and were correlated to ripening changes in both genetic backgrounds. Some previously identified QTLs for fruit ripening might be involved in these phenotypes, such as ETHQV8.1 on chromosome 8 and ETHQV6.3 on chromosome 6. PS alleles on chromosomes 2, 6, 10 and 11 were found to increase ester content when introgressed in VED melons. Terpenes showed to be affected by several genomic regions not related to ripening. In addition, several candidate genes have been hypothesized to be responsible for some of the QTLs detected. The analysis of volatile compounds in two reciprocal IL collections has increased our understanding of the relationship between ripening and aroma and offers valuable plant material to improve food quality in melon breeding programs.
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Affiliation(s)
- Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Elif Nur Özkan
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Andrés Fernández-Borbolla
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Javier Ruiz-Lasierra
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
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20
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Nonaka S, Ezura H. Possibility of genome editing for melon breeding. BREEDING SCIENCE 2024; 74:47-58. [PMID: 39246433 PMCID: PMC11375426 DOI: 10.1270/jsbbs.23074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/07/2024] [Indexed: 09/10/2024]
Abstract
Genome editing technologies are promising for conventional mutagenesis breeding, which takes a long time to remove unnecessary mutations through backcrossing and create new lines because they directly modify the target genes of elite strains. In particular, this technology has advantages for traits caused by the loss of function. Many efforts have been made to utilize this technique to introduce valuable features into crops, including maize, soybeans, and tomatoes. Several genome-edited crops have already been commercialized in the US and Japan. Melons are an important vegetable crop worldwide, produced and used in various areas. Therefore, many breeding efforts have been made to improve its fruit quality, resistance to plant diseases, and stress tolerance. Quantitative trait loci (QTL) analysis was performed, and various genes related to important traits were identified. Recently, several studies have shown that the CRISPR/Cas9 system can be applied to melons, resulting in its possible utilization as a breeding technique. Focusing on two productivity-related traits, disease resistance, and fruit quality, this review introduces the progress in genetics, examples of melon breeding through genome editing, improvements required for breeding applications, and the possibilities of genome editing in melon breeding.
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Affiliation(s)
- Satoko Nonaka
- Laboratory of Vegetable and Ornamental Horticulture, Institute of Life and Environmental Sciences and Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Laboratory of Vegetable and Ornamental Horticulture, Institute of Life and Environmental Sciences and Tsukuba-Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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21
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Mishra A, Pandey VP. CRISPR/Cas system: A revolutionary tool for crop improvement. Biotechnol J 2024; 19:e2300298. [PMID: 38403466 DOI: 10.1002/biot.202300298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 02/27/2024]
Abstract
World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Veda P Pandey
- Department of Biochemistry, University of Lucknow, Lucknow, India
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22
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Jin B, Jang G, Park G, Shahwar D, Shin J, Kwon G, Kim Y, Kim H, Lee O, Park Y. Development of a Gene-Based Marker Set for Orange-Colored Watermelon Flesh with a High β-Carotene Content. Int J Mol Sci 2023; 25:210. [PMID: 38203383 PMCID: PMC10778947 DOI: 10.3390/ijms25010210] [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: 11/03/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The fruit flesh of watermelons differs depending on the distinct carotenoid composition. Orange-colored flesh relates to the accumulation of β-carotene, which is beneficial to human health. Canary-yellow-fleshed OTO-DAH and orange-β-fleshed (orange-fleshed with high β-carotene) NB-DAH near-isogenic lines (NILs) were used to determine the genetic mechanism attributed to orange watermelon flesh. For genetic mapping, an F2 population was developed by crossing the two NILs. The segregation ratio of flesh color in the F2 population indicated that the orange-β flesh of the NB-DAH NIL was controlled by a single incompletely dominant gene. Through a comparative analysis of the whole-genome sequences of the parent lines and NILs, a major introgression region unique to the NB-DAH NIL was detected on Chr. 1; this was considered a candidate region for harboring genes that distinguish orange from canary-yellow and red flesh. Among the 13 genes involved in the carotenoid metabolic pathway in watermelons, only ClPSY1 (ClCG01G008470), which encodes phytoene synthase 1, was located within the introgression region. The genotyping of F2 plants using a cleaved amplified polymorphic sequence marker developed from a non-synonymous SNP in ClPSY1 revealed its relationship with orange-β flesh. The insights gained in this study can be applied to marker-assisted breeding for this desirable trait.
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Affiliation(s)
- Bingkui Jin
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea; (B.J.); (G.J.); (G.P.); (D.S.); (J.S.)
| | - Gaeun Jang
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea; (B.J.); (G.J.); (G.P.); (D.S.); (J.S.)
| | - Girim Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea; (B.J.); (G.J.); (G.P.); (D.S.); (J.S.)
| | - Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea; (B.J.); (G.J.); (G.P.); (D.S.); (J.S.)
| | - Jagyeong Shin
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea; (B.J.); (G.J.); (G.P.); (D.S.); (J.S.)
| | - Gibeom Kwon
- Partner Seeds Co., Ltd., Gimje 54324, Republic of Korea; (G.K.); (Y.K.)
| | - Yongjae Kim
- Partner Seeds Co., Ltd., Gimje 54324, Republic of Korea; (G.K.); (Y.K.)
| | - Hoytaek Kim
- Department of Horticulture, Sunchon National University, Sunchon 57922, Republic of Korea
| | - Oakjin Lee
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea;
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea; (B.J.); (G.J.); (G.P.); (D.S.); (J.S.)
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
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23
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Azad MF, Dawar P, Esim N, Rock CD. Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1278320. [PMID: 38023835 PMCID: PMC10656695 DOI: 10.3389/fpls.2023.1278320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.
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Affiliation(s)
- Md. Fakhrul Azad
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Nevzat Esim
- Department of Molecular Biology and Genetics, Bіngöl University, Bingöl, Türkiye
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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24
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Verbeecke V, Custódio L, Strobbe S, Van Der Straeten D. The role of orphan crops in the transition to nutritional quality-oriented crop improvement. Biotechnol Adv 2023; 68:108242. [PMID: 37640278 DOI: 10.1016/j.biotechadv.2023.108242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Micronutrient malnutrition is a persisting problem threatening global human health. Biofortification via metabolic engineering has been proposed as a cost-effective and short-term means to alleviate this burden. There has been a recent rise in the recognition of potential that underutilized, orphan crops can hold in decreasing malnutrition concerns. Here, we illustrate how orphan crops can serve as a medium to provide micronutrients to populations in need, whilst promoting and maintaining dietary diversity. We provide a roadmap, illustrating which aspects to be taken into consideration when evaluating orphan crops. Recent developments have shown successful biofortification via metabolic engineering in staple crops. This review provides guidance in the implementation of these successes to relevant orphan crop species, with a specific focus on the relevant micronutrients iron, zinc, provitamin A and folates.
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Affiliation(s)
- Vincent Verbeecke
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Laura Custódio
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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25
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Fang X, Li S, Zhu Z, Zhang X, Xiong C, Wang X, Luan F, Liu S. Clorf Encodes Carotenoid Isomerase and Regulates Orange Flesh Color in Watermelon ( Citrullus lanatus L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15445-15455. [PMID: 37815876 DOI: 10.1021/acs.jafc.3c02122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Flesh color is a significant characteristic of watermelon. Although various flesh-color genes have been identified, the inheritance and molecular basis of the orange flesh trait remain relatively unexplored. In the present study, the genetic analysis of six generations derived from W1-1 (red flesh) and W1-61 (orange flesh) revealed that the orange flesh color trait was regulated by a single recessive gene, Clorf (orange flesh). Bulk segregant analysis (BSA) locked the range to ∼4.66 Mb, and initial mapping situated the Clorf locus within a 688.35-kb region of watermelon chromosome 10. Another 1,026 F2 plants narrowed the Clorf locus to a 304.62-kb region containing 32 candidate genes. Subsequently, genome sequence variations in this 304.62-kb region were extracted for in silico BSA strategy among 11 resequenced lines (one orange flesh and ten nonorange flesh) and finally narrowed the Clorf locus into an 82.51-kb region containing nine candidate genes. Sequence variation analysis of coding regions and gene expression levels supports Cla97C10G200950 as the most possible candidate for Clorf, which encodes carotenoid isomerase (Crtiso). This study provides a genetic resource for investigating the orange flesh color of watermelon, with Clorf malfunction resulting in low lycopene accumulation and, thus, orange flesh.
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Affiliation(s)
- Xufeng Fang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shenglong Li
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xian Zhang
- College of Horticulture, Northwest of A&F University, Yangling 712100, China
| | - Cheng Xiong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Xuezheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
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26
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Shahwar D, Khan Z, Park Y. Molecular Marker-Assisted Mapping, Candidate Gene Identification, and Breeding in Melon ( Cucumis melo L.): A Review. Int J Mol Sci 2023; 24:15490. [PMID: 37895169 PMCID: PMC10607903 DOI: 10.3390/ijms242015490] [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: 08/21/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Melon (Cucumis melo L.) is an important crop that is cultivated worldwide for its fleshy fruit. Understanding the genetic basis of a plant's qualitative and quantitative traits is essential for developing consumer-favored varieties. This review presents genetic and molecular advances related to qualitative and quantitative phenotypic traits and biochemical compounds in melons. This information guides trait incorporation and the production of novel varieties with desirable horticultural and economic characteristics and yield performance. This review summarizes the quantitative trait loci, candidate genes, and development of molecular markers related to plant architecture, branching patterns, floral attributes (sex expression and male sterility), fruit attributes (shape, rind and flesh color, yield, biochemical compounds, sugar content, and netting), and seed attributes (seed coat color and size). The findings discussed in this review will enhance demand-driven breeding to produce cultivars that benefit consumers and melon breeders.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
| | - Zeba Khan
- Center for Agricultural Education, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India;
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
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27
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Su W, Zhu C, Fan Z, Huang M, Lin H, Chen X, Deng C, Chen Y, Kou Y, Tong Z, Zhang Y, Xu C, Zheng S, Jiang J. Comprehensive metabolome and transcriptome analyses demonstrate divergent anthocyanin and carotenoid accumulation in fruits of wild and cultivated loquats. FRONTIERS IN PLANT SCIENCE 2023; 14:1285456. [PMID: 37900735 PMCID: PMC10611460 DOI: 10.3389/fpls.2023.1285456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
Eriobotrya is an evergreen fruit tree native to South-West China and adjacent countries. There are more than 26 loquat species known in this genus, while E. japonica is the only species yet domesticated to produce fresh fruits from late spring to early summer. Fruits of cultivated loquat are usually orange colored, in contrast to the red color of fruits of wild E. henryi (EH). However, the mechanisms of fruit pigment formation during loquat evolution are yet to be elucidated. To understand these, targeted carotenoid and anthocyanin metabolomics as well as transcriptomics analyses were carried out in this study. The results showed that β-carotene, violaxanthin palmitate and rubixanthin laurate, totally accounted for over 60% of the colored carotenoids, were the major carotenoids in peel of the orange colored 'Jiefangzhong' (JFZ) fruits. Total carotenoids content in JFZ is about 10 times to that of EH, and the expression levels of PSY, ZDS and ZEP in JFZ were 10.69 to 23.26 folds to that in EH at ripen stage. Cyanidin-3-O-galactoside and pelargonidin-3-O-galactoside were the predominant anthocyanins enriched in EH peel. On the contrary, both of them were almost undetectable in JFZ, and the transcript levels of F3H, F3'H, ANS, CHS and CHI in EH were 4.39 to 73.12 folds higher than that in JFZ during fruit pigmentation. In summary, abundant carotenoid deposition in JFZ peel is well correlated with the strong expression of PSY, ZDS and ZEP, while the accumulation of anthocyanin metabolites in EH peel is tightly associated with the notably upregulated expressions of F3H, F3'H, ANS, CHS and CHI. This study was the first to demonstrate the metabolic background of how fruit pigmentations evolved from wild to cultivated loquat species, and provided gene targets for further breeding of more colorful loquat fruits via manipulation of carotenoids and anthocyanin biosynthesis.
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Affiliation(s)
- Wenbing Su
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Changqing Zhu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/State Agriculture Ministry Laboratory of Horticultural Plant Crop Growth and Development, Zhejiang University, Hangzhou, China
| | - Zhongqi Fan
- Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mingkun Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Han Lin
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Xiuping Chen
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Chaojun Deng
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Yongping Chen
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Yidan Kou
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Zhihong Tong
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
- Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yaling Zhang
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Changjie Xu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/State Agriculture Ministry Laboratory of Horticultural Plant Crop Growth and Development, Zhejiang University, Hangzhou, China
| | - Shaoquan Zheng
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Jimou Jiang
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
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Coe K, Bostan H, Rolling W, Turner-Hissong S, Macko-Podgórni A, Senalik D, Liu S, Seth R, Curaba J, Mengist MF, Grzebelus D, Van Deynze A, Dawson J, Ellison S, Simon P, Iorizzo M. Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots. NATURE PLANTS 2023; 9:1643-1658. [PMID: 37770615 PMCID: PMC10581907 DOI: 10.1038/s41477-023-01526-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023]
Abstract
Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and β-carotene orange phenotype. All three genes control high α- and β-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.
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Affiliation(s)
- Kevin Coe
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - William Rolling
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA
| | | | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Douglas Senalik
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA
| | - Su Liu
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Romit Seth
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Julien Curaba
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Molla Fentie Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, CA, USA
| | - Julie Dawson
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shelby Ellison
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Philipp Simon
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA.
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA.
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA.
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29
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Lyu X, Xia Y, Wang C, Zhang K, Deng G, Shen Q, Gao W, Zhang M, Liao N, Ling J, Bo Y, Hu Z, Yang J, Zhang M. Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops. PLANT PHYSIOLOGY 2023; 193:1330-1348. [PMID: 37477947 DOI: 10.1093/plphys/kiad405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Sweetness and appearance of fresh fruits are key palatable and preference attributes for consumers and are often controlled by multiple genes. However, fine-mapping the key loci or genes of interest by single genome-based genetic analysis is challenging. Herein, we present the chromosome-level genome assembly of 1 landrace melon accession (Cucumis melo ssp. agrestis) with wild morphologic features and thus construct a melon pan-genome atlas via integrating sequenced melon genome datasets. Our comparative genomic analysis reveals a total of 3.4 million genetic variations, of which the presence/absence variations (PAVs) are mainly involved in regulating the function of genes for sucrose metabolism during melon domestication and improvement. We further resolved several loci that are accountable for sucrose contents, flesh color, rind stripe, and suture using a structural variation (SV)-based genome-wide association study. Furthermore, via bulked segregation analysis (BSA)-seq and map-based cloning, we uncovered that a single gene, (CmPIRL6), determines the edible or inedible characteristics of melon fruit exocarp. These findings provide important melon pan-genome information and provide a powerful toolkit for future pan-genome-informed cultivar breeding of melon.
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Affiliation(s)
- Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhao Wang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guancong Deng
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qinghui Shen
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wei Gao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
| | - Mengyi Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Yongming Bo
- Key Laboratory of Vegetable Breeding, Ningbo Weimeng Seed Co., Ltd, Ningbo 315100, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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30
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Zhou X, Sun T, Owens L, Yang Y, Fish T, Wrightstone E, Lui A, Yuan H, Chayut N, Burger J, Tadmor Y, Thannhauser T, Guo W, Cheng L, Li L. Carotenoid sequestration protein FIBRILLIN participates in CmOR-regulated β-carotene accumulation in melon. PLANT PHYSIOLOGY 2023; 193:643-660. [PMID: 37233026 DOI: 10.1093/plphys/kiad312] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
Chromoplasts are plant organelles with a unique ability to sequester and store massive carotenoids. Chromoplasts have been hypothesized to enable high levels of carotenoid accumulation due to enhanced sequestration ability or sequestration substructure formation. However, the regulators that control the substructure component accumulation and substructure formation in chromoplasts remain unknown. In melon (Cucumis melo) fruit, β-carotene accumulation in chromoplasts is governed by ORANGE (OR), a key regulator for carotenoid accumulation in chromoplasts. By using comparative proteomic analysis of a high β-carotene melon variety and its isogenic line low-β mutant that is defective in CmOr with impaired chromoplast formation, we identified carotenoid sequestration protein FIBRILLIN1 (CmFBN1) as differentially expressed. CmFBN1 expresses highly in melon fruit tissue. Overexpression of CmFBN1 in transgenic Arabidopsis (Arabidopsis thaliana) containing ORHis that genetically mimics CmOr significantly enhances carotenoid accumulation, demonstrating its involvement in CmOR-induced carotenoid accumulation. Both in vitro and in vivo evidence showed that CmOR physically interacts with CmFBN1. Such an interaction occurs in plastoglobules and results in promoting CmFBN1 accumulation. CmOR greatly stabilizes CmFBN1, which stimulates plastoglobule proliferation and subsequently carotenoid accumulation in chromoplasts. Our findings show that CmOR directly regulates CmFBN1 protein levels and suggest a fundamental role of CmFBN1 in facilitating plastoglobule proliferation for carotenoid sequestration. This study also reveals an important genetic tool to further enhance OR-induced carotenoid accumulation in chromoplasts in crops.
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Affiliation(s)
- Xuesong Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lauren Owens
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Emalee Wrightstone
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andy Lui
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Hui Yuan
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Noam Chayut
- Department of Vegetable Research, ARO, Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Joseph Burger
- Department of Vegetable Research, ARO, Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
| | - Yaakov Tadmor
- Department of Vegetable Research, ARO, Newe Ya'ar Research Center, Ramat Yishay 30095, Israel
| | - Theodore Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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31
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Kang L, Zhang C, Liu J, Ye M, Zhang L, Chen F, Lin X, Yang D, Ren L, Li Y, Kim HS, Kwak SS, Li H, Deng X, Zhang P, Ke Q. Overexpression of potato ORANGE (StOR) and StOR mutant in Arabidopsis confers increased carotenoid accumulation and tolerance to abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107809. [PMID: 37315350 DOI: 10.1016/j.plaphy.2023.107809] [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: 12/01/2022] [Revised: 05/10/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
ORANGE (OR) plays essential roles in regulating carotenoid homeostasis and enhancing the ability of plants to adapt to environmental stress. However, OR proteins have been functionally characterized in only a few plant species, and little is known about the role of potato OR (StOR). In this study, we characterized the StOR gene in potato (Solanum tuberosum L. cv. Atlantic). StOR is predominantly localized to the chloroplast, and its transcripts are tissue-specifically expressed and significantly induced in response to abiotic stress. Compared with wild type, overexpression of StOR increased β-carotene levels up to 4.8-fold, whereas overexpression of StORHis with a conserved arginine to histidine substitution promoted β-carotene accumulation up to 17.6-fold in Arabidopsis thaliana calli. Neither StOR nor StORHis overexpression dramatically affected the transcript levels of carotenoid biosynthetic genes. Furthermore, overexpression of either StOR or StORHis increased abiotic stress tolerance in Arabidopsis, which was associated with higher photosynthetic capacity and antioxidative activity. Taken together, these results indicate that StOR could be exploited as a potential new genetic tool for the improvement of crop nutritional quality and environmental stress tolerance.
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Affiliation(s)
- Le Kang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637002, China; National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chunli Zhang
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Junke Liu
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Muying Ye
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Li Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637002, China
| | - Fengfeng Chen
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637002, China
| | - Xinyue Lin
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Dongjing Yang
- Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture and Rural Affairs, Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou, Jiangsu, 221131, China
| | - Liping Ren
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637002, China
| | - Yunxiang Li
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637002, China
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hongbing Li
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Xiping Deng
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Qingbo Ke
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China.
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32
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Guo Y, Zhao G, Gao X, Zhang L, Zhang Y, Cai X, Yuan X, Guo X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement. PLANTA 2023; 258:36. [PMID: 37395789 DOI: 10.1007/s00425-023-04187-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023]
Abstract
MAIN CONCLUSION This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.
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Affiliation(s)
- Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Guangdong Zhao
- College of Life Sciences, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Lin Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Yanan Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xiaoming Cai
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xuejiao Yuan
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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Wang W, Wang Y, Chen T, Qin G, Tian S. Current insights into posttranscriptional regulation of fleshy fruit ripening. PLANT PHYSIOLOGY 2023; 192:1785-1798. [PMID: 36250906 PMCID: PMC10315313 DOI: 10.1093/plphys/kiac483] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 05/26/2023]
Abstract
Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.
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Affiliation(s)
- Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Liang MH, Xie SR, Dai JL, Chen HH, Jiang JG. Roles of Two Phytoene Synthases and Orange Protein in Carotenoid Metabolism of the β-Carotene-Accumulating Dunaliella salina. Microbiol Spectr 2023; 11:e0006923. [PMID: 37022233 PMCID: PMC10269666 DOI: 10.1128/spectrum.00069-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Phytoene synthase (PSY) is a key enzyme in carotenoid metabolism and often regulated by orange protein. However, few studies have focused on the functional differentiation of the two PSYs and their regulation by protein interaction in the β-carotene-accumulating Dunaliella salina CCAP 19/18. In this study, we confirmed that DsPSY1 from D. salina possessed high PSY catalytic activity, whereas DsPSY2 almost had no activity. Two amino acid residues at positions 144 and 285 responsible for substrate binding were associated with the functional variance between DsPSY1 and DsPSY2. Moreover, orange protein from D. salina (DsOR) could interact with DsPSY1/2. DbPSY from Dunaliella sp. FACHB-847 also had high PSY activity, but DbOR could not interact with DbPSY, which might be one reason why it could not highly accumulate β-carotene. Overexpression of DsOR, especially the mutant DsORHis, could significantly improve the single-cell carotenoid content and change cell morphology (with larger cell size, bigger plastoglobuli, and fragmented starch granules) of D. salina. Overall, DsPSY1 played a dominant role in carotenoid biosynthesis in D. salina, and DsOR promoted carotenoid accumulation, especially β-carotene via interacting with DsPSY1/2 and regulating the plastid development. Our study provides a new clue for the regulatory mechanism of carotenoid metabolism in Dunaliella. IMPORTANCE Phytoene synthase (PSY) as the key rate-limiting enzyme in carotenoid metabolism can be regulated by various regulators and factors. We found that DsPSY1 played a dominant role in carotenogenesis in the β-carotene-accumulating Dunaliella salina, and two amino acid residues critical in the substrate binding were associated with the functional variance between DsPSY1 and DsPSY2. Orange protein from D. salina (DsOR) can promote carotenoid accumulation via interacting with DsPSY1/2 and regulating the plastid development, which provides new insights into the molecular mechanism of massive accumulation of β-carotene in D. salina.
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Affiliation(s)
- Ming-Hua Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Shan-Rong Xie
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Jv-Liang Dai
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Hao-Hong Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Jian-Guo Jiang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
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35
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Clustered regularly interspaced short palindromic repeats tools for plant metabolic engineering: achievements and perspectives. Curr Opin Biotechnol 2023; 79:102856. [PMID: 36473330 DOI: 10.1016/j.copbio.2022.102856] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 12/09/2022]
Abstract
The plant kingdom represents the biggest source of feedstock, food, and added-value compounds. Engineering plant metabolic pathways to increase the phytochemical production or improve the nutraceutical value of crops is challenging because of the intricate interaction networks that link multiple genes, enzymatic steps, and metabolites, even when pathways are fully elucidated. The development of clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) technologies has helped to overcome limitations in metabolic engineering, providing efficient and versatile tools for multigene editing. CRISPR approaches in plants were shown to have a remarkable efficiency in genome editing of different species to improve agronomic and metabolic traits. Here, we give an overview of the different achievements and perspectives of CRISPR technology in plant metabolic engineering.
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36
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Kim HK, Kim JY, Kim JH, Go JY, Jung YS, Lee HJ, Ahn MJ, Yu J, Bae S, Kim HS, Kwak SS, Kim MS, Cho YG, Jung YJ, Kang KK. Biochemical Characterization of Orange-Colored Rice Calli Induced by Target Mutagenesis of OsOr Gene. PLANTS (BASEL, SWITZERLAND) 2022; 12:56. [PMID: 36616184 PMCID: PMC9823629 DOI: 10.3390/plants12010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
We generated an orange-colored (OC) rice callus line by targeted mutagenesis of the orange gene (OsOr) using the CRISPR-Cas9 system. The OC line accumulated more lutein, β-carotene, and two β-carotene isomers compared to the WT callus line. We also analyzed the expression levels of carotenoid biosynthesis genes by qRT-PCR. Among the genes encoding carotenoid metabolic pathway enzymes, the number of transcripts of the PSY2, PSY3, PDS, ZDS and β-LCY genes were higher in the OC line than in the WT line. In contrast, transcription of the ε-LCY gene was downregulated in the OC line compared to the WT line. In addition, we detected increases in the transcript levels of two genes involved in carotenoid oxidation in the OC lines. The developed OC lines also showed increased tolerance to salt stress. Collectively, these findings indicate that targeted mutagenesis of the OsOr gene via CRISPR/Cas9-mediated genome editing results in β-carotene accumulation in rice calli. Accordingly, we believe that this type of genome-editing technology could represent an effective alternative approach for enhancing the β-carotene content of plants.
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Affiliation(s)
- Hee Kyoung Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
| | - Jin Young Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
| | - Jong Hee Kim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
| | - Ji Yun Go
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
| | - Yoo-Seob Jung
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
| | - Hyo Ju Lee
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
| | - Mi-Jeong Ahn
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jihyeon Yu
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Sangsu Bae
- Department of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Me-Sun Kim
- Department of Crop Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yu Jin Jung
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Republic of Korea
| | - Kwon Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea
- Institute of Genetic Engineering, Hankyong National University, Anseong 17579, Republic of Korea
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Grumet R, Lin YC, Rett-Cadman S, Malik A. Morphological and Genetic Diversity of Cucumber ( Cucumis sativus L.) Fruit Development. PLANTS (BASEL, SWITZERLAND) 2022; 12:23. [PMID: 36616152 PMCID: PMC9824707 DOI: 10.3390/plants12010023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 06/03/2023]
Abstract
Cucumber (Cucumis sativus L.) fruits, which are eaten at an immature stage of development, can vary extensively in morphological features such as size, shape, waxiness, spines, warts, and flesh thickness. Different types of cucumbers that vary in these morphological traits are preferred throughout the world. Numerous studies in recent years have added greatly to our understanding of cucumber fruit development and have identified a variety of genetic factors leading to extensive diversity. Candidate genes influencing floral organ establishment, cell division and cell cycle regulation, hormone biosynthesis and response, sugar transport, trichome development, and cutin, wax, and pigment biosynthesis have all been identified as factors influencing cucumber fruit morphology. The identified genes demonstrate complex interplay between structural genes, transcription factors, and hormone signaling. Identification of genetic factors controlling these traits will facilitate breeding for desired characteristics to increase productivity, improve shipping, handling, and storage traits, and enhance consumer-desired qualities. The following review examines our current understanding of developmental and genetic factors driving diversity of cucumber fruit morphology.
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Affiliation(s)
- Rebecca Grumet
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ying-Chen Lin
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Stephanie Rett-Cadman
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ajaz Malik
- Department of Horticulture-Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar 190 025, India
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Oren E, Dafna A, Tzuri G, Halperin I, Isaacson T, Elkabetz M, Meir A, Saar U, Ohali S, La T, Romay C, Tadmor Y, Schaffer AA, Buckler ES, Cohen R, Burger J, Gur A. Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1525-1542. [PMID: 36353749 PMCID: PMC10100132 DOI: 10.1111/tpj.16021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant-genome sequencing have expedited comparisons among multiple-related individuals. The abundance of structural genomic within-species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan-genome concept. For high-resolution forward genetics, this unprecedented access to genomic variation should be paralleled and integrated with phenotypic characterization of genetic diversity. We developed a multi-parental framework for trait dissection in melon (Cucumis melo), leveraging a novel pan-genome constructed for this highly variable cucurbit crop. A core subset of 25 diverse founders (MelonCore25), consisting of 24 accessions from the two widely cultivated subspecies of C. melo, encompassing 12 horticultural groups, and 1 feral accession was sequenced using a combination of short- and long-read technologies, and their genomes were assembled de novo. The construction of this melon pan-genome exposed substantial variation in genome size and structure, including detection of ~300 000 structural variants and ~9 million SNPs. A half-diallel derived set of 300 F2 populations, representing all possible MelonCore25 parental combinations, was constructed as a framework for trait dissection through integration with the pan-genome. We demonstrate the potential of this unified framework for genetic analysis of various melon traits, including rind color intensity and pattern, fruit sugar content, and resistance to fungal diseases. We anticipate that utilization of this integrated resource will enhance genetic dissection of important traits and accelerate melon breeding.
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Affiliation(s)
- Elad Oren
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Asaf Dafna
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of AgricultureThe Hebrew University of JerusalemRehovotIsrael
| | - Galil Tzuri
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Ilan Halperin
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Tal Isaacson
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Meital Elkabetz
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Ayala Meir
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Uzi Saar
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Shachar Ohali
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Thuy La
- Institute for Genomic Diversity, Cornell UniversityIthacaNew York14853USA
| | - Cinta Romay
- Institute for Genomic Diversity, Cornell UniversityIthacaNew York14853USA
| | - Yaakov Tadmor
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Arthur A. Schaffer
- Department of Vegetable SciencesInstitute of Plant Sciences, Agricultural Research Organization, The Volcani CenterP.O. Box 15159Rishon LeZiyyon7507101Israel
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell UniversityIthacaNew York14853USA
- United States Department of Agriculture‐Agricultural Research ServiceRobert W. Holley Center for Agriculture and HealthIthacaNew York14853USA
| | - Roni Cohen
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Joseph Burger
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
| | - Amit Gur
- Cucurbits Section, Department of Vegetable SciencesAgricultural Research Organization, Newe Ya‘ar Research CenterP.O. Box 1021Ramat Yishay3009500Israel
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Santo Domingo M, Mayobre C, Pereira L, Argyris J, Valverde L, Martín-Hernández AM, Garcia-Mas J, Pujol M. Fruit Morphology and Ripening-Related QTLs in a Newly Developed Introgression Line Collection of the Elite Varieties 'Védrantais' and 'Piel de Sapo'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223120. [PMID: 36432848 PMCID: PMC9694011 DOI: 10.3390/plants11223120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 05/28/2023]
Abstract
Melon is an economically important crop with widely diverse fruit morphology and ripening characteristics. Its diploid sequenced genome and multiple genomic tools make this species suitable to study the genetic architecture of fruit traits. With the development of this introgression line population of the elite varieties 'Piel de Sapo' and 'Védrantais', we present a powerful tool to study fruit morphology and ripening traits that can also facilitate characterization or pyramidation of QTLs in inodorous melon types. The population consists of 36 lines covering almost 98% of the melon genome, with an average of three introgressions per chromosome and segregating for multiple fruit traits: morphology, ripening and quality. High variability in fruit morphology was found within the population, with 24 QTLs affecting six different traits, confirming previously reported QTLs and two newly detected QTLs, FLQW5.1 and FWQW7.1. We detected 20 QTLs affecting fruit ripening traits, six of them reported for the first time, two affecting the timing of yellowing of the rind (EYELLQW1.1 and EYELLQW8.1) and four at the end of chromosome 8 affecting aroma, abscission and harvest date (EAROQW8.3, EALFQW8.3, ABSQW8.3 and HARQW8.3). We also confirmed the location of several QTLs, such as fruit-quality-related QTLs affecting rind and flesh appearance and flesh firmness.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
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Zhang YM, Wu RH, Wang L, Wang YH, Liu H, Xiong AS, Xu ZS. Plastid diversity and chromoplast biogenesis in differently coloured carrots: role of the DcOR3 Leu gene. PLANTA 2022; 256:104. [PMID: 36308565 DOI: 10.1007/s00425-022-04016-9] [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: 09/02/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Distinct plastid types and ultrastructural changes are associated with differences in carotenoid pigment profiles in differently coloured carrots, and a variant of the OR gene, DcOR3Leu is vital for chromoplast biogenesis. Accumulation of different types and amounts of carotenoids in carrots impart different colours to their taproots. In this study, the carotenoid pigment profiles, morphology, and ultrastructure of plastids in 25 carrot varieties with orange, red, yellow, or white taproots were investigated by ultra-high performance liquid chromatography as well as light and transmission electron microscopy. α-/β-Carotene and lycopene were identified as colour-determining carotenoids in orange and red carrots, respectively. In contrast, lutein was identified as the colour-determining carotenoid in almost all tested yellow and white carrots. The latter contained only trace amounts of lutein as a unique detectable carotenoid. Striking differences in plastid types that coincided with distinct carotenoid profiles were observed among the differently coloured carrots. Microscopic analysis of the different carotenoid pigment-loaded plastids revealed abundant crystalloid chromoplasts in the orange and red carrots, whereas amyloplasts were dominant in most of the yellow and white carrots, except for the yellow carrot 'Yellow Stone', where yellow chromoplasts were observed. Plastoglobuli and crystal remnants, the carotenoid sequestering substructures, were identified in crystalloid chromoplasts. Crystal remnants were often associated with a characteristic undulated internal membrane in orange carrots or several undulated membranes in red carrots. No crystal remnants, but some plastoglobuli, were observed in the plastids of all tested yellow and white carrots. In addition, the presence of chromoplast in carrot taproots was found to be associated with DcOR3Leu, a natural variant of DcOR3, which was previously reported to be co-segregated with carotene content in carrots. Knocking out DcOR3Leu in the orange carrot 'Kurodagosun' depressed chromoplast biogenesis and led to the generation of yellow carrots. Our results support that DcOR3Leu is vital but insufficient for chromoplasts biogenesis in carrots, and add to the understanding of the formation of chromoplasts in carrots.
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Affiliation(s)
- Yu-Min Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Rong-Hua Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Lu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
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Mapping and Validation of BrGOLDEN: A Dominant Gene Regulating Carotenoid Accumulation in Brassica rapa. Int J Mol Sci 2022; 23:ijms232012442. [PMID: 36293299 PMCID: PMC9603932 DOI: 10.3390/ijms232012442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
In plants, the accumulation of carotenoids can maintain the balance of the photosystem and improve crop nutritional quality. Therefore, the molecular mechanisms underlying carotenoid synthesis and accumulation should be further explored. In this study, carotenoid accumulation differed significantly among parental Brassica rapa. Genetic analysis was carried out using the golden inner leaf ‘1900264′ line and the light−yellow inner leaf ‘1900262′ line, showing that the golden inner leaf phenotype was controlled by a single dominant gene. Using bulked−segregant analysis sequencing, BraA09g007080.3C encoding the ORANGE protein was selected as a candidate gene. Sequence alignment revealed that a 4.67 kb long terminal repeat insertion in the third exon of the BrGOLDEN resulted in three alternatively spliced transcripts. The spatiotemporal expression results indicated that BrGOLDEN might regulate the expression levels of carotenoid−synthesis−related genes. After transforming BrGOLDEN into Arabidopsis thaliana, the seed−derived callus showed that BrGOLDENIns and BrGOLDENDel lines presented a yellow color and the BrGOLDENLdel line presented a transparent phenotype. In addition, using the yeast two−hybrid assay, BrGOLDENIns, BrGOLDENLdel, and Brgoldenwt exhibited strong interactions with BrPSY1, but BrGOLDENDel did not interact with BrPSY1 in the split−ubiquitin membrane system. In the secondary and 3D structure analysis, BrGOLDENDel was shown to have lost the PNFPSFIPFLPPL sequences at the 125 amino acid position, which resulted in the α−helices of BrGOLDENDel being disrupted, restricting the formation of the 3D structure and affecting the functions of the protein. These findings may provide new insights into the regulation of carotenoid synthesis in B. rapa.
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Ampomah-Dwamena C, Tomes S, Thrimawithana AH, Elborough C, Bhargava N, Rebstock R, Sutherland P, Ireland H, Allan AC, Espley RV. Overexpression of PSY1 increases fruit skin and flesh carotenoid content and reveals associated transcription factors in apple ( Malus × domestica). FRONTIERS IN PLANT SCIENCE 2022; 13:967143. [PMID: 36186009 PMCID: PMC9520574 DOI: 10.3389/fpls.2022.967143] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/29/2022] [Indexed: 06/16/2023]
Abstract
Knowledge of the transcriptional regulation of the carotenoid metabolic pathway is still emerging and here, we have misexpressed a key biosynthetic gene in apple to highlight potential transcriptional regulators of this pathway. We overexpressed phytoene synthase (PSY1), which controls the key rate-limiting biosynthetic step, in apple and analyzed its effects in transgenic fruit skin and flesh using two approaches. Firstly, the effects of PSY overexpression on carotenoid accumulation and gene expression was assessed in fruit at different development stages. Secondly, the effect of light exclusion on PSY1-induced fruit carotenoid accumulation was examined. PSY1 overexpression increased carotenoid content in transgenic fruit skin and flesh, with beta-carotene being the most prevalent carotenoid compound. Light exclusion by fruit bagging reduced carotenoid content overall, but carotenoid content was still higher in bagged PSY fruit than in bagged controls. In tissues overexpressing PSY1, plastids showed accelerated chloroplast to chromoplast transition as well as high fluorescence intensity, consistent with increased number of chromoplasts and carotenoid accumulation. Surprisingly, the expression of other carotenoid pathway genes was elevated in PSY fruit, suggesting a feed-forward regulation of carotenogenesis when this enzyme step is mis-expressed. Transcriptome profiling of fruit flesh identified differentially expressed transcription factors (TFs) that also were co-expressed with carotenoid pathway genes. A comparison of differentially expressed genes from both the developmental series and light exclusion treatment revealed six candidate TFs exhibiting strong correlation with carotenoid accumulation. This combination of physiological, transcriptomic and metabolite data sheds new light on plant carotenogenesis and TFs that may play a role in regulating apple carotenoid biosynthesis.
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Affiliation(s)
| | - Sumathi Tomes
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
| | | | - Caitlin Elborough
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
- BioLumic Limited, Palmerston North, New Zealand
| | - Nitisha Bhargava
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
| | - Ria Rebstock
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
| | - Paul Sutherland
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
| | - Hilary Ireland
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
| | - Richard V. Espley
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
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Skaliter O, Livneh Y, Agron S, Shafir S, Vainstein A. A whiff of the future: functions of phenylalanine-derived aroma compounds and advances in their industrial production. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1651-1669. [PMID: 35638340 PMCID: PMC9398379 DOI: 10.1111/pbi.13863] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 05/19/2023]
Abstract
Plants produce myriad aroma compounds-odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry ketone and vanillin. In the last decade, great strides have been made in elucidating this pathway with the identification of numerous aroma-related biosynthetic enzymes and factors regulating metabolic shunts. These scientific achievements, together with public acknowledgment of aroma compounds' medicinal benefits and growing consumer demand for natural products, are driving the development of novel biological sources for wide-scale, eco-friendly, and inexpensive production. Microbes and plants that are readily amenable to metabolic engineering are garnering attention as suitable platforms for achieving this goal. In this review, we discuss the importance of aroma compounds from the perspectives of humans, pollinators and plant-plant interactions. Focusing on vanillin and raspberry ketone, which are of high interest to the industry, we present key knowledge on the biosynthesis and regulation of phenylalanine-derived aroma compounds, describe advances in the adoption of microbes and plants as platforms for their production, and propose routes for improvement.
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Affiliation(s)
- Oded Skaliter
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Yarin Livneh
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Shani Agron
- Department of NeurobiologyThe Weizmann Institute of ScienceRehovotIsrael
| | - Sharoni Shafir
- B. Triwaks Bee Research Center, Department of Entomology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovotIsrael
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Zhao Y, Duan X, Wang L, Gao G, Xu C, Qi H. Transcription Factor CmNAC34 Regulated CmLCYB-Mediated β-Carotene Accumulation during Oriental Melon Fruit Ripening. Int J Mol Sci 2022; 23:9805. [PMID: 36077205 PMCID: PMC9455964 DOI: 10.3390/ijms23179805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
Ripened oriental melon (Cucumis melo) with orange-colored flesh is rich in β-carotene. Lycopene β-cyclase (LCYB) is the synthetic enzyme that directly controls the massive accumulation of β-carotene. However, the regulatory mechanism underlying the CmLCYB-mediated β-carotene accumulation in oriental melon is fairly unknown. Here, we screened and identified a transcription factor, CmNAC34, by combining bioinformatics analysis and yeast one-hybrid screen with CmLCYB promoter. CmNAC34 was located in the nucleus and acted as a transcriptional activator. The expression profile of CmNAC34 was consistent with that of CmLCYB during the fruit ripening. Additionally, the transient overexpression of CmNAC34 in oriental melon fruit promoted the expression of CmLCYB and enhanced β-carotene concentration, while transient silence of CmNAC34 in fruit was an opposite trend, which indicated CmNAC34 could modulate CmLCYB-mediated β-carotene biosynthesis in oriental melon. Finally, the yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), β-glucuronidase (GUS) analysis assay, and luciferase reporter (LUC) assay indicated that CmNAC34 could bind to the promoter of CmLCYB and positively regulated the CmLCYB transcription level. These findings suggested that CmNAC34 acted as an activator to regulate β-carotene accumulation by directly binding the promoter of CmLCYB, which provides new insight into the regulatory mechanism of carotenoid metabolism during the development and ripening of oriental melon.
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Affiliation(s)
| | | | | | | | - Chuanqiang Xu
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, National and Local Joint Engineering Research Centre of Northern Horticultural, Facilities Design and Application Technology (Liaoning), Shenyang 110866, China
| | - Hongyan Qi
- Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, College of Horticulture, Shenyang Agricultural University, National and Local Joint Engineering Research Centre of Northern Horticultural, Facilities Design and Application Technology (Liaoning), Shenyang 110866, China
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Zhao L, Jia T, Jiao Q, Hu X. Research Progress in J-Proteins in the Chloroplast. Genes (Basel) 2022; 13:1469. [PMID: 36011380 PMCID: PMC9407819 DOI: 10.3390/genes13081469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The J-proteins, also called DNAJ-proteins or heat shock protein 40 (HSP40), are one of the famous molecular chaperones. J-proteins, HSP70s and other chaperones work together as constitute ubiquitous types of molecular chaperone complex, which function in a wide variety of physiological processes. J-proteins are widely distributed in major cellular compartments. In the chloroplast of higher plants, around 18 J-proteins and multiple J-like proteins are present; however, the functions of most of them remain unclear. During the last few years, important progress has been made in the research on their roles in plants. There is increasing evidence that the chloroplast J-proteins play essential roles in chloroplast development, photosynthesis, seed germination and stress response. Here, we summarize recent research advances on the roles of J-proteins in the chloroplast, and discuss the open questions that remain in this field.
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Affiliation(s)
- Lu Zhao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Ting Jia
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qingsong Jiao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Xueyun Hu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Kumar D, Yadav A, Ahmad R, Dwivedi UN, Yadav K. CRISPR-Based Genome Editing for Nutrient Enrichment in Crops: A Promising Approach Toward Global Food Security. Front Genet 2022; 13:932859. [PMID: 35910203 PMCID: PMC9329789 DOI: 10.3389/fgene.2022.932859] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022] Open
Abstract
The global malnutrition burden imparts long-term developmental, economic, social, and medical consequences to individuals, communities, and countries. The current developments in biotechnology have infused biofortification in several food crops to fight malnutrition. However, these methods are not sustainable and suffer from several limitations, which are being solved by the CRISPR-Cas-based system of genome editing. The pin-pointed approach of CRISPR-based genome editing has made it a top-notch method due to targeted gene editing, thus making it free from ethical issues faced by transgenic crops. The CRISPR-Cas genome-editing tool has been extensively used in crop improvement programs due to its more straightforward design, low methodology cost, high efficiency, good reproducibility, and quick cycle. The system is now being utilized in the biofortification of cereal crops such as rice, wheat, barley, and maize, including vegetable crops such as potato and tomato. The CRISPR-Cas-based crop genome editing has been utilized in imparting/producing qualitative enhancement in aroma, shelf life, sweetness, and quantitative improvement in starch, protein, gamma-aminobutyric acid (GABA), oleic acid, anthocyanin, phytic acid, gluten, and steroidal glycoalkaloid contents. Some varieties have even been modified to become disease and stress-resistant. Thus, the present review critically discusses CRISPR-Cas genome editing-based biofortification of crops for imparting nutraceutical properties.
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Affiliation(s)
- Dileep Kumar
- Department of Biochemistry, University of Lucknow, Lucknow, India
| | - Anurag Yadav
- Department of Microbiology, College of Basic Science and Humanities, Sardarkrushinagar Dantiwada Agriculture University, Banaskantha, India
| | - Rumana Ahmad
- Department of Biochemistry, Era Medical University and Hospital, Lucknow, India
| | | | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, India
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Hunziker J, Nishida K, Kondo A, Ariizumi T, Ezura H. Phenotypic Characterization of High Carotenoid Tomato Mutants Generated by the Target-AID Base-Editing Technology. FRONTIERS IN PLANT SCIENCE 2022; 13:848560. [PMID: 35874006 PMCID: PMC9301137 DOI: 10.3389/fpls.2022.848560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Our previous study demonstrated that Target-AID which is the modified CRISPR/Cas9 system enabling base-editing is an efficient tool for targeting multiple genes. Three genes, SlDDB1, SlDET1, and SlCYC-B, responsible for carotenoid accumulation were targeted, and allelic variations were previously obtained by Target-AID. In this research, we characterized the effect of new alleles on plant growth and fruit development, as well as carotenoid accumulation, individually in segregating backcross populations or combined in null self-segregant lines. Only lines carrying homozygous substitutions in the three targeted genes and the segregating backcross population of individual mutations were characterized, resulting in the isolation of two allelic versions for SlDDB1, one associated with SlDET1 and the last one with SlCYC-B. All edited lines showed variations in carotenoid accumulation, with an additive effect for each single mutation. These results suggest that Target-AID base-editing technology is an effective tool for creating new allelic variations in target genes to improve carotenoid accumulation in tomato.
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Affiliation(s)
- Johan Hunziker
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
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Identification and Characterization Roles of Phytoene Synthase (PSY) Genes in Watermelon Development. Genes (Basel) 2022; 13:genes13071189. [PMID: 35885972 PMCID: PMC9324402 DOI: 10.3390/genes13071189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/15/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Phytoene synthase (PSY) plays an essential role in carotenoid biosynthesis. In this study, three ClPSY genes were identified through the watermelon genome, and their full-length cDNA sequences were cloned. The deduced proteins of the three ClPSY genes were ranged from 355 to 421 amino acid residues. Phylogenetic analysis suggested that the ClPSYs are highly conserved with bottle gourd compared to other cucurbit crops PSY proteins. Variation in ClPSY1 expression in watermelon with different flesh colors was observed; ClPSY1 was most highly expressed in fruit flesh and associated with the flesh color formation. ClPSY1 expression was much lower in the white-fleshed variety than the colored fruits. Gene expression analysis of ClPSY genes in root, stem, leaf, flower, ovary and flesh of watermelon plants showed that the levels of ClPSY2 transcripts found in leaves was higher than other tissues; ClPSY3 was dominantly expressed in roots. Functional complementation assays of the three ClPSY genes suggested that all of them could encode functional enzymes to synthesize the phytoene from Geranylgeranyl Pyrophosphate (GGPP). Some of the homologous genes clustered together in the phylogenetic tree and located in the synteny chromosome region seemed to have similar expression profiles among different cucurbit crops. The findings provide a foundation for watermelon flesh color breeding with regard to carotenoid synthesis and also provide an insight for the further research of watermelon flesh color formation.
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Flores-León A, Peréz Moro C, Martí R, Beltran J, Roselló S, Cebolla-Cornejo J, Picó B. Spanish Melon Landraces: Revealing Useful Diversity by Genomic, Morphological, and Metabolomic Analysis. Int J Mol Sci 2022; 23:7162. [PMID: 35806170 PMCID: PMC9266967 DOI: 10.3390/ijms23137162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 12/02/2022] Open
Abstract
Spain is a secondary centre of the diversification of the melon (Cucumis melo L.), with high diversity represented in highly appreciated landraces belonging to the Flexuosus and Ibericus groups. A collection of 47 accessions of Flexuosus, Chate, Piel de Sapo, Tendral, Amarillo, Blanco, and Rochet was analysed using a genotyping-by-sequencing (GBS) approach. A total of 66,971 quality SNPs were identified. Genetic analysis differentiated Ibericus accessions and exotic materials (Ameri, Momordica, Kachri, and Agrestis), while Flexuous accessions shared ancestry between them. Within the Ibericus group, no clear genomic distinction could be identified for the different landraces evaluated, with accessions of different landraces showing high genetic similarity. The morphological characterization confirmed that the external colour and fruit shape had been used as recognition patterns for Spanish melon landraces, but variability within a landrace exists. Differences were found in the sugars and acid and volatile profiles of the materials. Flexuosus and Chate melons at the immature commercial stage accumulated malic acid and low levels of hexoses, while Ibericus melons accumulated high contents of sucrose and citric acid. Specific trends could be identified in the Ibericus landraces. Tendral accumulated low levels of sugars and citric acid and high of malic acid, maintaining higher firmness, Rochet reached higher levels of sugars, and Amarillo tended to lower malic acid contents. Interestingly, high variability was found within landraces for the acidic profile, offering possibilities to alter taste tinges. The main volatile organic compounds (VOCs) in Flexuosus and Chate were aldehydes and alcohols, with clear differences between both groups. In the Ibericus landraces, general trends for VOC accumulation could be identified, but, again, a high level of variation exists. This situation highlights the necessity to develop depuration programs to promote on-farm in situ conservation and, at the same time, offers opportunities to establish new breeding program targets and to take advantage of these sources of variation.
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Affiliation(s)
- Alejandro Flores-León
- COMAV, Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain; (A.F.-L.); (C.P.M.); (B.P.)
| | - Clara Peréz Moro
- COMAV, Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain; (A.F.-L.); (C.P.M.); (B.P.)
| | - Raul Martí
- Joint Research Unit UJI/UPV—Improvement of Agri-Food Quality, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain;
| | - Joaquin Beltran
- Instituto Universitario de Plaguicidas y Aguas (IUPA), Campus de Riu Sec, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain;
| | - Salvador Roselló
- Joint Research Unit UJI/UPV—Improvement of Agri-Food Quality, Department de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain;
| | - Jaime Cebolla-Cornejo
- Joint Research Unit UJI/UPV—Improvement of Agri-Food Quality, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain;
| | - Belen Picó
- COMAV, Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain; (A.F.-L.); (C.P.M.); (B.P.)
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Sun T, Rao S, Zhou X, Li L. Plant carotenoids: recent advances and future perspectives. MOLECULAR HORTICULTURE 2022; 2:3. [PMID: 37789426 PMCID: PMC10515021 DOI: 10.1186/s43897-022-00023-2] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/03/2022] [Indexed: 10/05/2023]
Abstract
Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.
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Affiliation(s)
- Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sombir Rao
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Xuesong Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA.
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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