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Jia C, Huang Y, Cheng Z, Zhang N, Shi T, Ma X, Zhang G, Zhang C, Hua R. Combined Transcriptomics and Metabolomics Analysis Reveals Profenofos-Induced Invisible Injury in Pakchoi ( Brassica rapa L.) through Inhibition of Carotenoid Accumulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15321-15333. [PMID: 38917998 DOI: 10.1021/acs.jafc.4c03262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Profenofos insecticide poses risks to nontarget organisms including mammals and hydrobionts, and its effects on crops are not known. This study examined the invisible toxicity of profenofos on pakchoi (Brassica rapa L.), using transcriptome and metabolome analyses. Profenofos inhibited the photosynthetic efficiency and light energy absorption by leaves and severely damaged the chloroplasts, causing the accumulation of reactive oxygen species (ROS). Metabolomic analysis confirmed that profenofos promoted the conversion of β-carotene into abscisic acid (ABA), as evidenced by the upregulation of the carotenoid biosynthesis pathway genes: zeaxanthin epoxidase (ZEP), 9-cis-epoxycarotenoid dioxygenase (NCED3), and xanthoxin dehydrogenase (XanDH). The inhibitory effects on carotenoid accumulation, photosynthesis, and increased ABA and ROS contents of the leaves led to invisible injury and stunted growth of the pakchoi plants. The findings of this study revealed the toxicological risk of profenofos to nontarget crops and provide guidance for the safe use of insecticides.
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Affiliation(s)
- Caiyi Jia
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Youkun Huang
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Zechao Cheng
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Nan Zhang
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Taozhong Shi
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Xin Ma
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Genrong Zhang
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
| | - Chao Zhang
- College of Agronomy, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, P. R. China
| | - Rimao Hua
- Key Laboratory of Agri-Food Safety of Anhui Province, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
- College of Resources and Environment, Anhui Agricultural University, No. 130 Changjiangxilu, Hefei 230036, China
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Niu J, Xu M, Zong N, Sun J, Zhao L, Hui W. Ascorbic acid releases dormancy and promotes germination by an integrated regulation of abscisic acid and gibberellin in Pyrus betulifolia seeds. PHYSIOLOGIA PLANTARUM 2024; 176:e14271. [PMID: 38566130 DOI: 10.1111/ppl.14271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Seed dormancy is an important life history state in which intact viable seeds delay or prevent germination under suitable conditions. Ascorbic acid (AsA) acts as a small molecule antioxidant, and breaking seed dormancy and promoting subsequent growth are among its numerous functions. In this study, a germination test using Pyrus betulifolia seeds treated with exogenous AsA or AsA synthesis inhibitor lycorine (Lyc) and water absorption was conducted. The results indicated that AsA released dormancy and increased germination and 20 mmol L-1 AsA promoted cell division, whereas Lyc reduced germination. Seed germination showed typical three phases of water absorption; and seeds at five key time points were sampled for transcriptome analysis. It revealed that multiple pathways were involved in breaking dormancy and promoting germination through transcriptome data, and 12 differentially expressed genes (DEGs) related to the metabolism and signal transduction of abscisic acid (ABA) and gibberellins (GA) were verified by subsequent RT-qPCR. For metabolites, exogenous AsA increased endogenous AsA and GA3 but reduced ABA and the ABA/GA3 ratio. In addition, three genes regulating ABA synthesis were downregulated by AsA, while five genes mediating ABA degradation were upregulated. Taken together, AsA regulates the pathways associated with ABA and GA synthesis, catalysis, and signal transduction, with subsequent reduction in ABA and increase in GA and further the balance of ABA/GA, ultimately releasing dormancy and promoting germination.
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Affiliation(s)
- Junpeng Niu
- College of Life Sciences, Shaanxi Normal University, China
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Mingzhen Xu
- College of Life Sciences, Shaanxi Normal University, China
| | - Na Zong
- College of Life Sciences, Shaanxi Normal University, China
| | - Jia Sun
- College of Life Sciences, Shaanxi Normal University, China
| | - Lei Zhao
- College of Life Sciences, Shaanxi Normal University, China
| | - Wei Hui
- College of Life Sciences, Shaanxi Normal University, China
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Li H, Che R, Zhu J, Yang X, Li J, Fernie AR, Yan J. Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:999-1017. [PMID: 38009661 DOI: 10.1111/tpj.16545] [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: 11/18/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Zhao J, Xu Y, Li H, Zhu X, Yin Y, Zhang X, Qin X, Zhou J, Duan L, Liang X, Huang T, Zhang B, Wan R, Shi Z, Cao Y, An W. ERF5.1 modulates carotenoid accumulation by interacting with CCD4.1 in Lycium. HORTICULTURE RESEARCH 2023; 10:uhad230. [PMID: 38143484 PMCID: PMC10745278 DOI: 10.1093/hr/uhad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/01/2023] [Indexed: 12/26/2023]
Abstract
Carotenoids are important natural pigments and have medical and health functions for humans. Carotenoid cleavage dioxygenase 4 (CCD4) and ethylene responsive factor (ERF) participate in carotenoid metabolism, but their roles in Lycium have not been discovered. Here, we annotated LbCCDs from the Lycium reference genome and found that LbCCD4.1 expression was significantly correlated with the carotenoid metabolites during Lycium five fruit developmental stages. Over-expression of LbCCD4.1 in NQ's leaves resulted in a series of significantly lower contents of carotenoid metabolites, including β-carotene and β-cryptoxanthin. Moreover, LbERF5.1, a transcription factor belonging to the ERF family that was located in the nucleus, was isolated. Significant reductions in the carotenoids, especially lutein, violaxanthin and their derivatives, were observed in over-expressing ERF5.1 transgenic NQ's leaves. Over-expression or virus-induced gene silencing of LbERF5.1 in NQ's leaves induced a consistent up- or down-expression, respectively, of LbCCD4.1. Furthermore, yeast one-hybrid and dual-luciferase reporter assays showed that ERF5.1 interacted with the promoter of CCD4.1 to increase its expression, and LbERF5.1 could bind to any one of the three predicted binding sites in the promoter of LbCCD4.1. A transcriptome analysis of LbERF5.1 and LbCCD4.1 over-expressed lines showed similar global transcript expression, and geranylgeranyl diphosphate synthase, phytoene synthase, lycopene δ-cyclase cytochrome, cytochrome P450-type monooxygenase 97A, cytochrome P450-type monooxygenase 97C, and zeaxanthin epoxidase in the carotenoid biosynthesis pathway were differentially expressed. In summary, we uncovered a novel molecular mechanism of carotenoid accumulation that involved an interaction between ERF5.1 and CCD4.1, which may be used to enhance carotenoid in Lycium.
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Affiliation(s)
- Jianhua Zhao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yuhui Xu
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Haoxia Li
- Institute of Forestry and Grassland Ecology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xinlei Zhu
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yue Yin
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xiyan Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | | | - Jun Zhou
- College of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China
| | - Linyuan Duan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xiaojie Liang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Ting Huang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Bo Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Ru Wan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Zhigang Shi
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Youlong Cao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Wei An
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
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Cruet-Burgos C, Rhodes DH. Unraveling transcriptomics of sorghum grain carotenoids: a step forward for biofortification. BMC Genomics 2023; 24:233. [PMID: 37138226 PMCID: PMC10157909 DOI: 10.1186/s12864-023-09323-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Sorghum (Sorghum bicolor [L.] Moench) is a promising target for pro-vitamin A biofortification as it is a global staple crop, particularly in regions where vitamin A deficiency is prevalent. As with most cereal grains, carotenoid concentrations are low in sorghum, and breeding could be a feasible strategy to increase pro-vitamin A carotenoids to biologically relevant concentrations. However, there are knowledge gaps in the biosynthesis and regulation of sorghum grain carotenoids, which can limit breeding effectiveness. The aim of this research was to gain an understanding of the transcriptional regulation of a priori candidate genes in carotenoid precursor, biosynthesis, and degradation pathways. RESULTS We used RNA sequencing of grain to compare the transcriptional profile of four sorghum accessions with contrasting carotenoid profiles through grain development. Most a priori candidate genes involved in the precursor MEP, carotenoid biosynthesis, and carotenoid degradation pathways were found to be differentially expressed between sorghum grain developmental stages. There was also differential expression of some of the a priori candidate genes between high and low carotenoid content groups at each developmental time point. Among these, we propose geranyl geranyl pyrophosphate synthase (GGPPS), phytoene synthase (PSY), and phytoene desaturase (PDS) as promising targets for pro-vitamin A carotenoid biofortification efforts in sorghum grain. CONCLUSIONS A deeper understanding of the controls underlying biosynthesis and degradation of sorghum grain carotenoids is needed to advance biofortification efforts. This study provides the first insights into the regulation of sorghum grain carotenoid biosynthesis and degradation, suggesting potential gene targets to prioritize for molecular breeding.
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Affiliation(s)
- Clara Cruet-Burgos
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Davina H Rhodes
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA.
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Morote L, Rubio-Moraga Á, López-Jiménez AJ, Argandoña J, Niza E, Ahrazem O, Gómez-Gómez L. A carotenoid cleavage dioxygenase 4 from Paulownia tomentosa determines visual and aroma signals in flowers. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111609. [PMID: 36737005 DOI: 10.1016/j.plantsci.2023.111609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Paulownia tomentosa is an economically important fast-growing tree, and its flowers and fruits are a rich source of biologically active secondary metabolites. In addition, the flowers of P. tomentosa are distinguished by a strong aroma and are also excellent nectariferous plants. The flowers are pale lilac and characterized by the presence of yellow nectar guides, whose color changes during the development of the flower, representing reliable signals to pollinators while enhancing reproductive success. The chemical analyses of the nectar guides revealed the presence of carotenoids as the pigments responsible for the observed coloration, with β-carotene levels determining the color changes observed after anthesis, with a reduction at anthesis and further increase and accumulation in post anthesis. To understand how β-carotene accumulation was controlled in the nectar guides, the expression of genes related to carotenoid biosynthesis and metabolism was analyzed. Carotenogenic gene expression was not associated with the observed changes in β-carotene during flower development. However, the expression of a gene encoding a carotenoid cleavage dioxygenase, CCD4-4, was co-related with the levels of β-carotene in the nectar guides. In addition, CCD4-4 cleavage β-carotene at C9-C10 and C9'-C10' positions, resulting in the generation of β-ionone, which was detected in flowers at anthesis. The obtained results indicated a developmental stage specific regulation of apocarotenoid formation through β-carotene cleavage, resulting in color changes and volatile production as key traits for plant-pollinator interactions. DATA AVAILABILITY: Data will be made available on request.
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Affiliation(s)
- Lucía Morote
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Ángela Rubio-Moraga
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Alberto José López-Jiménez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Javier Argandoña
- Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Enrique Niza
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain; Facultad de Farmacia, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Oussama Ahrazem
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain; Facultad de Farmacia, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain.
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Kumar V, Khan A, Srivastava A, Saxena G. Toxicity assessment of metribuzin and its amelioration through plant growth regulators in Vigna radiata (L.) R. Wilczek. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:33307-33321. [PMID: 36478549 DOI: 10.1007/s11356-022-24534-z] [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: 08/31/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The present experiment was conducted to evaluate the metribuzin-induced stress response in Vigna radiata and to explore the ameliorative role of exogenous application of plant growth regulators (PGRs) against metribuzin toxicity by assessing important biochemical and yield parameters. Prior to the field experiment, dose standardization experiments were performed, and EC50 was calculated for metribuzin. On day 21, field grown V. radiata plants were treated with graded concentrations of metribuzin (0-1000 mg [Formula: see text]). Plants treated with 600 mg [Formula: see text] (EC50) and 1000 mg [Formula: see text] (highest dose) of metribuzin were co-treated individually and simultaneously with gibberellic acid-3 (GA), indole-3 acetic acid (IAA), and salicylic acid (SA). After 7 days of treatment, leaf tissues were analyzed for biochemical parameters, whereas those related to yield were recorded during harvest. The result of this study indicated that metribuzin treatment to V. radiata resulted in increase in lipid peroxidation and reduce chlorophyll and carotenoid contents as well as yield parameters. However, metribuzin-treated plants induced proline accumulation and activity of antioxidant enzymes. Exogenous application of GA, IAA, and SA significantly reduced lipid peroxidation and increased contents of photosynthetic pigments, proline, and antioxidant enzymes thereby increasing yield parameters. It was observed that during metribuzin stress, SA exhibited a better ameliorative response out of the three exogenously applied PGRs, while the combined use of all PGRs exhibited much improved ameliorative response on biochemical and yield parameters of plants.
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Affiliation(s)
- Vaibhav Kumar
- In Vitro Culture and Plant Genetics Unit, Department of Botany, University of Lucknow, Lucknow, 226007, Uttar Pradesh, India
| | - Adiba Khan
- In Vitro Culture and Plant Genetics Unit, Department of Botany, University of Lucknow, Lucknow, 226007, Uttar Pradesh, India
| | - Alka Srivastava
- In Vitro Culture and Plant Genetics Unit, Department of Botany, University of Lucknow, Lucknow, 226007, Uttar Pradesh, India
| | - Gauri Saxena
- In Vitro Culture and Plant Genetics Unit, Department of Botany, University of Lucknow, Lucknow, 226007, Uttar Pradesh, India.
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Xiao S, Dai X, Zhao L, Zhou Z, Zhao L, Xu P, Gao B, Zhang A, Zhao D, Yuan R, Wang Y, Wang J, Li Q, Cao Q. Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits. HORTICULTURE RESEARCH 2022; 10:uhac234. [PMID: 36643760 PMCID: PMC9832839 DOI: 10.1093/hr/uhac234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4 599 509 SNPs and 846 654 InDels were generated, among which 196 124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40 366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1, IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.
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Affiliation(s)
| | | | | | - Zhilin Zhou
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Lukuan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Pan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Bingqian Gao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - An Zhang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Donglan Zhao
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Rui Yuan
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Yao Wang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Jie Wang
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Qinglian Li
- Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, Chinese Agricultural Academy of Sciences, Xuzhou 221131, China
| | - Qinghe Cao
- Correspondence: Qinghe Cao (); Tel.: 086-0516-82189205; Fax: 086-0516-82189205
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Zhao L, Li M, Ma X, Luo D, Zhou Q, Liu W, Liu Z. Transcriptome analysis and identification of abscisic acid and gibberellin-related genes during seed development of alfalfa (Medicago sativa L.). BMC Genomics 2022; 23:651. [PMID: 36100883 PMCID: PMC9472388 DOI: 10.1186/s12864-022-08875-0] [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: 02/13/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa) is a widely cultivated plant. Unlike many crops, the main goal of breeding alfalfa is to increase its aboveground biomass rather than the biomass of its seeds. However, the low yield of alfalfa seeds limits alfalfa production. Many studies have explored the factors affecting seed development, in which phytohormones, especially ABA and GAs, play an important role in seed development. RESULTS Here, we performed a transcriptome analysis of alfalfa seeds at five development stages. A total of 16,899 differentially expressed genes (DEGs) were identified and classified into 10 clusters, and the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. The contents of ABA, GA1, GA3, GA4 and GA7 in alfalfa seeds at five development stages were determined. In addition, 14 ABA-related DEGs and 20 GA-related DEGs were identified and analysed. These DEGs are involved in plant hormone pathways and play an important role in seed development. Moreover, morphological and physiological analyses revealed the dynamic changes during the development of alfalfa seeds. CONCLUSION Overall, our study is the first to analyse the transcriptome across various stages of seed development in alfalfa. The results of our study could be used to improve alfalfa seed yield. The key ABA and GA related-genes are potential targets for improving alfalfa seed yield via genetic engineering in the future.
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Affiliation(s)
- Lu Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Mingyu Li
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xiaomei Ma
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
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10
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Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC PLANT BIOLOGY 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
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Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
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11
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Li H, Han S, Huo Y, Ma G, Sun Z, Li H, Hou S, Han Y. Comparative metabolomic and transcriptomic analysis reveals a coexpression network of the carotenoid metabolism pathway in the panicle of Setaria italica. BMC PLANT BIOLOGY 2022; 22:105. [PMID: 35260077 PMCID: PMC8903627 DOI: 10.1186/s12870-022-03467-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The grains of foxtail millet are enriched in carotenoids, which endow this plant with a yellow color and extremely high nutritional value. However, the underlying molecular regulation mechanism and gene coexpression network remain unclear. METHODS The carotenoid species and content were detected by HPLC for two foxtail millet varieties at three panicle development stages. Based on a homologous sequence BLAST analysis, these genes related to carotenoid metabolism were identified from the foxtail millet genome database. The conserved protein domains, chromosome locations, gene structures and phylogenetic trees were analyzed using bioinformatics tools. RNA-seq was performed for these samples to identify differentially expressed genes (DEGs). A Pearson correlation analysis was performed between the expression of genes related to carotenoid metabolism and the content of carotenoid metabolites. Furthermore, the expression levels of the key DEGs were verified by qRT-PCR. The gene coexpression network was constructed by a weighted gene coexpression network analysis (WGCNA). RESULT The major carotenoid metabolites in the panicles of DHD and JG21 were lutein and β-carotene. These carotenoid metabolite contents sharply decreased during the panicle development stage. The lutein and β-carotene contents were highest at the S1 stage of DHD, with values of 11.474 μg /100 mg and 12.524 μg /100 mg, respectively. Fifty-four genes related to carotenoid metabolism were identified in the foxtail millet genome. Cis-acting element analysis showed that these gene promoters mainly contain 'plant hormone', 'drought stress resistance', 'MYB binding site', 'endosperm specific' and 'seed specific' cis-acting elements and especially the 'light-responsive' and 'ABA-responsive' elements. In the carotenoid metabolic pathways, SiHDS, SiHMGS3, SiPDS and SiNCED1 were more highly expressed in the panicle of foxtail millet. The expression of SiCMT, SiAACT3, SiPSY1, SiZEP1/2, and SiCCD8c/8d was significantly correlated with the lutein content. The expression of SiCMT, SiHDR, SiIDI2, SiAACT3, SiPSY1, and SiZEP1/2 was significantly correlated with the content of β-carotene. WGCNA showed that the coral module was highly correlated with lutein and β-carotene, and 13 structural genes from the carotenoid biosynthetic pathway were identified. Network visualization revealed 25 intramodular hub genes that putatively control carotenoid metabolism. CONCLUSION Based on the integrative analysis of the transcriptomics and carotenoid metabonomics, we found that DEGs related to carotenoid metabolism had a stronger correlation with the key carotenoid metabolite content. The correlation analysis and WGCNA identified and predicted the gene regulation network related to carotenoid metabolism. These results lay the foundation for exploring the key target genes regulating carotenoid metabolism flux in the panicle of foxtail millet. We hope that these target genes could be used to genetically modify millet to enhance the carotenoid content in the future.
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Affiliation(s)
- Hui Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Shangling Han
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yiqiong Huo
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Guifang Ma
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, 030801, Shanxi, China
| | - Hongying Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, 030801, Shanxi, China
| | - Siyu Hou
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, 030801, Shanxi, China.
| | - Yuanhuai Han
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
- Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taigu, 030801, Shanxi, China.
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12
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Yang S, Liu H, Zhao Y, Su H, Wei X, Wang Z, Zhao X, Zhang XW, Yuan Y. Map-Based Cloning and Characterization of Br-dyp1, a Gene Conferring Dark Yellow Petal Color Trait in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). FRONTIERS IN PLANT SCIENCE 2022; 13:841328. [PMID: 35251110 PMCID: PMC8891484 DOI: 10.3389/fpls.2022.841328] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/27/2022] [Indexed: 05/29/2023]
Abstract
Flower color is an important trait in Brassica species. However, genes responsible for the dark yellow flower trait in Chinese cabbage have not been reported. In this study, we identified a dark-yellow-flowered Chinese cabbage line SD369. Genetic analysis indicated that the dark yellow flower trait in SD369 was controlled by a single recessive locus, Br-dyp1 (dark yellow petal color 1 in Brassica rapa). Using bulked segregant RNA sequencing and kompetitive allele-specific PCR assays, Br-dyp1 was fine-mapped to an interval of 53.6 kb on chromosome A09. Functional annotation analysis, expression analysis, and sequence variation analysis revealed that Bra037130 (BraA09.ZEP), which encodes a zeaxanthin epoxidase, was the most likely candidate gene for Br-dyp1. Carotenoid profile analysis suggested that Bra037130 (BraA09.ZEP) might participate in the epoxidation from zeaxanthin to violaxanthin. The 679 bp insertion in dark yellow petal caused premature stop codon, thus caused the loss-of-function of the enzyme zeaxanthin epoxidase (ZEP), which disturbed the carotenoid metabolism, and caused the increased accumulation of total carotenoid, and finally converted the flower color from yellow to dark yellow. Comparative transcriptome analysis also showed that the "carotenoid biosynthesis" pathway was significantly enriched, and genes involved in carotenoid degradation and abscisic acid biosynthesis and metabolism were significantly downregulated. Furthermore, we developed and validated the functional marker Br-dyp1-InDel for Br-dyp1. Overall, these results provide insight into the molecular basis of carotenoid-based flower coloration in B. rapa and reveal valuable information for marker-assisted selection breeding in Chinese cabbage.
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Affiliation(s)
- Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Honglei Liu
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Henan Su
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaobin Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiao-Wei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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13
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Gupta P, Hirschberg J. The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:806184. [PMID: 35069664 PMCID: PMC8770946 DOI: 10.3389/fpls.2021.806184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.
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Affiliation(s)
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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14
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Geng F, Nie R, Yang N, Cai L, Hu Y, Chen S, Cheng X, Wang Z, Chen L. Integrated transcriptome and metabolome profiling of Camellia reticulata reveal mechanisms of flower color differentiation. Front Genet 2022; 13:1059717. [PMID: 36482888 PMCID: PMC9725097 DOI: 10.3389/fgene.2022.1059717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2023] Open
Abstract
Camellia reticulata (Lindl.) is an important ornamental plant in China. Long-term natural or artificial selections have resulted in diverse phenotypes, especially for flower colors. Modulating flower colors can enhance the visual appeal and economic value in ornamental plants. In this study, we investigated the molecular mechanisms underlying flower color differentiation in C. reticulata. We performed a combined transcriptome and metabolome analysis of the petals of a popular variety C. reticulata (HHYC) (red), and its two cultivars "Xuejiao" (XJ) (pink) and "Tongzimian" (TZM) (white). Targeted metabolome profiling identified 310 flavonoid compounds of which 18 anthocyanins were differentially accumulated among the three samples with an accumulation pattern of HHYC > XJ > TZM. Likewise, transcriptome analysis showed that carotenoid and anthocyanin biosynthetic structural genes were mostly expressed in order of HHYC > XJ > TZM. Two genes (gene-LOC114287745765 and gene-LOC114289234) encoding for anthocyanidin 3-O-glucosyltransferase are predicted to be responsible for red coloration in HHYC and XJ. We also detected 42 MYB and 29 bHLH transcription factors as key regulators of anthocyanin-structural genes. Overall, this work showed that flavonoids, particularly anthocyanins contents are the major determinants of flower color differentiation among the 3 C. reticulata samples. In addition, the main regulatory and structural genes modulating anthocyanin contents in C. reticulata have been unveiled. Our results will help in the development of Camellia varieties with specific flower color and quality.
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Affiliation(s)
- Fang Geng
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
| | - Ruimin Nie
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
| | - Nan Yang
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
| | - Lei Cai
- Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, China
| | - YunChong Hu
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
| | - Shengtong Chen
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
| | - Xiaomao Cheng
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
| | - Zhonglang Wang
- Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, China
| | - Longqing Chen
- College of Landscape Architecture and Horticulture Sciences, Southwest Landscape Architecture Engineering Technology Research Center of National Forestry and Grassland Administration, Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Southwest Forestry University, Kunming, Yunnan, China
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15
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Sun T, Zhu Q, Wei Z, Owens LA, Fish T, Kim H, Thannhauser TW, Cahoon EB, Li L. Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds. ABIOTECH 2021; 2:191-214. [PMID: 36303886 PMCID: PMC9590580 DOI: 10.1007/s42994-021-00046-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023]
Abstract
Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of Phytoene synthase (PSY) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during seed maturation and storage, consistent with previous studies of provitamin A biofortified grains. In contrast, stacking with Orange (OR His ), a gene that initiates chromoplast biogenesis, dramatically enhances provitamin A and total carotenoid content and stability. Up to 65- and 10-fold increases of β-carotene and total carotenoids, respectively, with provitamin A carotenoids composing over 63% were observed in the seeds containing OR His and PSY. Co-expression of Homogentisate geranylgeranyl transferase (HGGT) with OR His and PSY further increases carotenoid accumulation and stability during seed maturation and storage. Moreover, knocking-out of β-carotene hydroxylase 2 (BCH2) by CRISPR/Cas9 not only potentially facilitates β-carotene accumulation but also minimizes the negative effect of carotenoid over production on seed germination. Our findings provide new insights into various processes on carotenoid accumulation and stability in seeds and establish a multiplexed strategy to simultaneously target carotenoid biosynthesis, turnover, and stable storage for carotenoid biofortification in crop seeds. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00046-1.
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Affiliation(s)
- 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
| | - Qinlong Zhu
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Ziqing Wei
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Lauren A Owens
- 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
| | - Hyojin Kim
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Theodore W Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Edgar B Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588 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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Diepenbrock CH, Ilut DC, Magallanes-Lundback M, Kandianis CB, Lipka AE, Bradbury PJ, Holland JB, Hamilton JP, Wooldridge E, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mateos-Hernandez M, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D. Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain. THE PLANT CELL 2021; 33:882-900. [PMID: 33681994 PMCID: PMC8226291 DOI: 10.1093/plcell/koab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/26/2021] [Indexed: 05/03/2023]
Abstract
Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percentage of phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide an in-depth genome-level understanding of the genetic and molecular control of carotenoids in plants. In addition, these findings provide a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.
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Affiliation(s)
| | - Daniel C Ilut
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Catherine B Kandianis
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Alexander E Lipka
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- United States Department of Agriculture—Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - James B Holland
- United States Department of Agriculture—Agricultural Research Service, Plant Science Research Unit, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Edmund Wooldridge
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Elsa Góngora-Castillo
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Jason G Wallace
- Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602
| | - Jason Cepela
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Maria Mateos-Hernandez
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Brenda F Owens
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Tyler Tiede
- Present addresses: Nacre Innovations, Houston, Texas 77002 (C.B.K.); Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (A.E.L.); University of Michigan, Ann Arbor, MI 48109 (E.W.); Centro de Investigación Científica de Yucatan, CONACYT—Unidad de Biotecnologia, Merida, Yucatan 97200, Mexico (E.G.-C.); Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 (J.C.); Bayer, Stonington, Illinois 62567 (M.M.-H.); BASF, Dawson, Georgia 39842 (B.F.O.); and Corteva Agriscience, St. Paul, Minnesota 55108 (T.T.)
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- United States Department of Agriculture—Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853
| | - Torbert Rocheford
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Michael A Gore
- Authors for correspondence: (C.H.D.), (M.A.G.), and (D.D.P.)
| | - Dean DellaPenna
- Authors for correspondence: (C.H.D.), (M.A.G.), and (D.D.P.)
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17
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Sano N, Marion-Poll A. ABA Metabolism and Homeostasis in Seed Dormancy and Germination. Int J Mol Sci 2021; 22:5069. [PMID: 34064729 PMCID: PMC8151144 DOI: 10.3390/ijms22105069] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 02/07/2023] Open
Abstract
Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely achieved by fine-tuning, in the different seed tissues, hormone synthesis by cleavage of carotenoid precursors and inactivation by 8'-hydroxylation. In this review, we provide an overview of the current knowledge on ABA metabolism in developing and germinating seeds; notably, how environmental signals such as light, temperature and nitrate control seed dormancy through the adjustment of hormone levels. A number of regulatory factors have been recently identified which functional relationships with major transcription factors, such as ABA INSENSITIVE3 (ABI3), ABI4 and ABI5, have an essential role in the control of seed ABA levels. The increasing importance of epigenetic mechanisms in the regulation of ABA metabolism gene expression is also described. In the last section, we give an overview of natural variations of ABA metabolism genes and their effects on seed germination, which could be useful both in future studies to better understand the regulation of ABA metabolism and to identify candidates as breeding materials for improving germination properties.
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Affiliation(s)
| | - Annie Marion-Poll
- IJPB Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France;
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18
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Jiang L, Strobbe S, Van Der Straeten D, Zhang C. Regulation of plant vitamin metabolism: backbone of biofortification for the alleviation of hidden hunger. MOLECULAR PLANT 2021; 14:40-60. [PMID: 33545049 DOI: 10.1016/j.molp.2020.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 05/04/2023]
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19
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Martina M, Tikunov Y, Portis E, Bovy AG. The Genetic Basis of Tomato Aroma. Genes (Basel) 2021; 12:genes12020226. [PMID: 33557308 PMCID: PMC7915847 DOI: 10.3390/genes12020226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.
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Affiliation(s)
- Matteo Martina
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
| | - Ezio Portis
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands;
- Correspondence: (E.P.); (A.G.B.); Tel.: +39-011-6708807 (E.P.); +31-317-480762 (A.G.B.)
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20
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Liu Y, Ye S, Yuan G, Ma X, Heng S, Yi B, Ma C, Shen J, Tu J, Fu T, Wen J. Gene silencing of BnaA09.ZEP and BnaC09.ZEP confers orange color in Brassica napus flowers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:932-949. [PMID: 32808386 DOI: 10.1111/tpj.14970] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/20/2020] [Accepted: 07/29/2020] [Indexed: 05/28/2023]
Abstract
Brassica napus is currently cultivated as an important ornamental crop in China. Flower color has attracted much attention in rapeseed genetics and breeding. Here, we characterize an orange-flowered mutant of B. napus that exhibits an altered carotenoid profile in its petals. As revealed by map-based cloning, the change in color from yellow to orange is attributed to the loss of BnaC09.ZEP (zeaxanthin epoxidase) and a 1695-bp deletion in BnaA09.ZEP. HPLC analysis, genetic complementation and CRISPR/Cas9 experiments demonstrated that BnaA09.ZEP and BnaC09.ZEP have similar functions, and the abolishment of both genes led to a substantial increase in lutein content and a sharp decline in violaxanthin content in petals but not leaves. BnaA09.ZEP and BnaC09.ZEP are predominantly expressed in floral tissues, whereas their homologs, BnaA07.ZEP and BnaC07.ZEP, mainly function in leaves, indicating redundancy and tissue-specific diversification of BnaZEP function. Transcriptome analysis in petals revealed differences in the expression of carotenoid and flavonoid biosynthesis-related genes between the mutant and its complementary lines. Flavonoid profiles in the petals of complementary lines were greatly altered compared to the mutant, indicating potential cross-talk between the regulatory networks underlying the carotenoid and flavonoid pathways. Additionally, our results indicate that there is functional compensation by BnaA07.ZEP and BnaC07.ZEP in the absence of BnaA09.ZEP and BnaC09.ZEP. Cloning and characterization of BnaZEPs provide insights into the molecular mechanisms underlying flower pigmentation in B. napus and would facilitate breeding of B. napus varieties with higher ornamental value.
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Affiliation(s)
- Yingjun Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shenhua Ye
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gaigai Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaowei Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangping Heng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China
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21
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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22
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Cruet-Burgos C, Cox S, Ioerger BP, Perumal R, Hu Z, Herald TJ, Bean SR, Rhodes DH. Advancing provitamin A biofortification in sorghum: Genome-wide association studies of grain carotenoids in global germplasm. THE PLANT GENOME 2020; 13:e20013. [PMID: 33016639 DOI: 10.1002/tpg2.20013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/19/2020] [Indexed: 06/11/2023]
Abstract
Vitamin A deficiency is one of the most prevalent nutritional deficiencies worldwide. Sorghum [Sorghum bicolor L. (Moench)] is a major cereal crop consumed by millions of people in regions with high vitamin A deficiency. We quantified carotenoid concentrations in a diverse sorghum panel using high-performance liquid chromatography and conducted a genome-wide association study (GWAS) of grain carotenoids to identify genes underlying carotenoid variation. There was moderate variation for β-carotene (00.8 μg g-1 ), lutein (0.3-9.4 μg g-1 ), and zeaxanthin (0.2-9.1 μg g-1 ), but β-cryptoxanthin and α-carotene were nearly undetectable. Genotype had the largest effect size, at 81% for zeaxanthin, 62% for β-carotene, and 53% for lutein. Using multiple models, GWAS identified several significant associations between carotenoids and single nucleotide polymorphisms (SNPs), some of which colocalized with known carotenoid genes that have not been previously implicated in carotenoid variation. Several of the candidate genes identified have also been identified in maize (Zea mays L.) and Arabidopsis (Arabidopsis thaliana) carotenoid GWAS studies. Notably, an SNP inside the putative ortholog of maize zeaxanthin epoxidase (ZEP) had the most significant association with zeaxanthin and with the ratio between lutein and zeaxanthin, suggesting that ZEP is a major gene controlling sorghum carotenoid variation. Overall findings suggest there is oligogenic inheritance for sorghum carotenoids and suitable variation for marker-assisted selection. The high carotenoid germplasm and significant associations identified in this study can be used in biofortification efforts to improve the nutritional quality of sorghum.
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Affiliation(s)
- Clara Cruet-Burgos
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Sarah Cox
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Brian P Ioerger
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Thomas J Herald
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Scott R Bean
- Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Davina H Rhodes
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
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23
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Zheng X, Giuliano G, Al-Babili S. Carotenoid biofortification in crop plants: citius, altius, fortius. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158664. [PMID: 32068105 DOI: 10.1016/j.bbalip.2020.158664] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/24/2022]
Abstract
Carotenoids are indispensable for human health, required as precursors of vitamin A and efficient antioxidants. However, these plant pigments that play a vital role in photosynthesis are represented at insufficient levels in edible parts of several crops, which creates a need for increasing their content or optimizing their composition through biofortification. In particular, vitamin A deficiency, a severe health problem affecting the lives of millions in developing countries, has triggered the development of a series of high-provitamin A crops, including Golden Rice as the best-known example. Further carotenoid-biofortified crops have been generated by using genetic engineering approaches or through classical breeding. In this review, we depict carotenoid metabolism in plants and provide an update on the development of carotenoid-biofortified plants and their potential to meet needs and expectations. Furthermore, we discuss the possibility of using natural variation for carotenoid biofortification and the potential of gene editing tools. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Affiliation(s)
- Xiongjie Zheng
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, the BioActives Lab, Thuwal 23955-6900, Saudi Arabia
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Center, Via Anguillarese 301, Roma 00123, Italy
| | - Salim Al-Babili
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, the BioActives Lab, Thuwal 23955-6900, Saudi Arabia.
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24
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Zheng X, Zhu K, Sun Q, Zhang W, Wang X, Cao H, Tan M, Xie Z, Zeng Y, Ye J, Chai L, Xu Q, Pan Z, Xiao S, Fraser PD, Deng X. Natural Variation in CCD4 Promoter Underpins Species-Specific Evolution of Red Coloration in Citrus Peel. MOLECULAR PLANT 2019; 12:1294-1307. [PMID: 31102783 DOI: 10.1016/j.molp.2019.04.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/26/2019] [Accepted: 04/29/2019] [Indexed: 05/06/2023]
Abstract
Carotenoids and apocarotenoids act as phytohormones and volatile precursors that influence plant development and confer aesthetic and nutritional value critical to consumer preference. Citrus fruits display considerable natural variation in carotenoid and apocarotenoid pigments. In this study, using an integrated genetic approach we revealed that a 5' cis-regulatory change at CCD4b encoding CAROTENOID CLEAVAGE DIOXYGENASE 4b is a major genetic determinant of natural variation in C30 apocarotenoids responsible for red coloration of citrus peel. Functional analyses demonstrated that in addition the known role in synthesizing β-citraurin, CCD4b is also responsible for the production of another important C30 apocarotenoid pigment, β-citraurinene. Furthermore, analyses of the CCD4b promoter and transcripts from various citrus germplasm accessions established a tight correlation between the presence of a putative 5' cis-regulatory enhancer within an MITE transposon and the enhanced allelic expression of CCD4b in C30 apocarotenoid-rich red-peeled accessions. Phylogenetic analysis provided further evidence that functional diversification of CCD4b and naturally occurring variation of the CCD4b promoter resulted in the stepwise evolution of red peels in mandarins and their hybrids. Taken together, our findings provide new insights into the genetic and evolutionary basis of apocarotenoid diversity in plants, and would facilitate breeding efforts that aim to improve the nutritional and aesthetic value of citrus and perhaps other fruit crops.
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Affiliation(s)
- Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Kaijie Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Quan Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Hongbo Cao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Meilian Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Yunliu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.
| | - Shunyuan Xiao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China; Department of Plant Science and Landscape Architecture, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.
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25
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Chlorophyll degradation and carotenoid biosynthetic pathways: Gene expression and pigment content in broccoli during yellowing. Food Chem 2019; 297:124964. [PMID: 31253313 DOI: 10.1016/j.foodchem.2019.124964] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 11/23/2022]
Abstract
Broccoli undergoes yellowing in unfavorable conditions, thereby diminishing the sensory quality and commodity value. This study aimed to investigate systematically cellular and/or biomolecular changes involved in broccoli yellowing by analyzing changes in microstructural integrity, pigment content, and gene expression. On day-5 of storage at 20 °C, the buds turned yellow without blooming and showed structural damage; ultrastructural analysis revealed plastid transformation and abnormal chloroplast development. Genes regulating pigment content and chloroplast structure directly were identified. More specifically, BoCAO and BoNYC1 regulated chlorophyll turnover, affecting chlorophyll a and b contents. Changes in the β-cryptoxanthin content were influenced by the combined action of up- (BoHYD) and downstream (BoZEP) genes. BoZEP and BoVDE were activated after cold-temperature induction. High BoHO1 expression delayed yellowing at low temperature, inducing BoZEP expression. Color intensity correlated significantly with the chlorophyll b, β-cryptoxanthin, and β-carotene contents, which were associated with increased yellowing of plant tissues.
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26
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Zheng X, Tang Y, Ye J, Pan Z, Tan M, Xie Z, Chai L, Xu Q, Fraser PD, Deng X. SLAF-Based Construction of a High-Density Genetic Map and Its Application in QTL Mapping of Carotenoids Content in Citrus Fruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:994-1002. [PMID: 30589260 DOI: 10.1021/acs.jafc.8b05176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Carotenoids are important antioxidant components in the human diet. To develop carotenoid-rich agricultural products by genetic intervention, understanding the genetic basis of carotenoids variation is essential. In this study, we constructed a high-density integrated genetic map with 3817 molecular markers using specific locus amplified fragment (SLAF) sequencing from a C. reticulata × P. trifoliata F1 pseudotestcross population. A total of 17 significant quantitative trait loci (QTLs) distributed on Chromosomes (Chr) 2, 3, 5, 6, and 9 were detected to determine the carotenoid variation in the population. In particular, three QTL colocalizations for multiple carotenoid constituents were observed on Chr 2, 3, and 9, one of which was located on Chr2:34,654,608-35430715 accounted for 20.1-25.4% of the variation of luteoxanthin, auroxanthin, lutein, violaxanthin, and total carotenoid content. Overall, this study provides a genetic foundation for marker-assisted selection (MAS) breeding of nutritionally enhanced citrus fruit.
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Affiliation(s)
- Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Yuqing Tang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Meilian Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway , University of London , Egham, Surrey TW20 0EX , United Kingdom
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
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Cabrera-Soto L, Pixley KV, Rosales-Nolasco A, Galicia-Flores LA, Palacios-Rojas N. Carotenoid and Tocochromanol Profiles during Kernel Development Make Consumption of Biofortified "Fresh" Maize an Option to Improve Micronutrient Nutrition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9391-9398. [PMID: 30130402 DOI: 10.1021/acs.jafc.8b01886] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Biofortification is a strategy to reduce micronutrient malnutrition. The aim of this study was to investigate whether consumption of biofortified fresh maize can supply nutritionally meaningful amounts of provitamin A carotenoids (PVA), zinc, lysine, and tryptophan. The accumulation patterns for PVA and tocochromanol compounds in developing grain of 23 PVA hybrids was studied, and nutritionally meaningful amounts of those compounds were found in grain by milk stage, when fresh maize is eaten. The highest PVA and tocochromanol accumulation occurred by physiological maturity. The percent apparent retention in boiled fresh maize was 92%, 117%, 99%, and 66% for PVA, zinc, lysine, and tryptophan, respectively. Consumption of 0.5 to 2 ears of fresh maize daily could supply 33-62.2%, 11-24% and more than 85% of the estimated average requirement of PVA, tryptophan, and zinc, respectively. The results indicate that eating biofortified fresh maize can contribute to improved micronutrient nutrition.
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Affiliation(s)
- Luisa Cabrera-Soto
- International Maize and Wheat Improvement Center (CIMMYT), CIMMYT Research Station , Km. 45 Carretera Mexico-Veracruz, El Batán , Texcoco , CP 56237 Edo. de México , México
| | - Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), CIMMYT Research Station , Km. 45 Carretera Mexico-Veracruz, El Batán , Texcoco , CP 56237 Edo. de México , México
| | - Aldo Rosales-Nolasco
- International Maize and Wheat Improvement Center (CIMMYT), CIMMYT Research Station , Km. 45 Carretera Mexico-Veracruz, El Batán , Texcoco , CP 56237 Edo. de México , México
| | - Luis A Galicia-Flores
- International Maize and Wheat Improvement Center (CIMMYT), CIMMYT Research Station , Km. 45 Carretera Mexico-Veracruz, El Batán , Texcoco , CP 56237 Edo. de México , México
| | - Natalia Palacios-Rojas
- International Maize and Wheat Improvement Center (CIMMYT), CIMMYT Research Station , Km. 45 Carretera Mexico-Veracruz, El Batán , Texcoco , CP 56237 Edo. de México , México
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Effects of Aromatic Herb Flavoring on Carotenoids and Volatile Compounds in Edible Oil From Blue Sweet Lupin (Lupinus angustifolius). EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201800227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Yan F, Shi M, He Z, Wu L, Xu X, He M, Chen J, Deng X, Cheng Y, Xu J. Largely different carotenogenesis in two pummelo fruits with different flesh colors. PLoS One 2018; 13:e0200320. [PMID: 29985936 PMCID: PMC6037374 DOI: 10.1371/journal.pone.0200320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/23/2018] [Indexed: 02/03/2023] Open
Abstract
Carotenoids in citrus fruits have health benefits and make the fruits visually attractive. Red-fleshed ‘Chuhong’ (‘CH’) and pale green-fleshed ‘Feicui’ (‘FC’) pummelo (Citrus maxima (Burm) Merr.) fruits are interesting materials for studying the mechanisms of carotenoid accumulation. In this study, particularly high contents of linear carotenes were observed in the albedo tissue, segment membranes and juice sacs of ‘CH’. However, carotenoids, especially β-carotene and xanthophylls, accumulated more in the flavedo tissue of ‘FC’ than in that of ‘CH’. Additionally, the contents of other terpenoids such as limonin, nomilin and abscisic acid significantly differed in the juice sacs at 150 days postanthesis. A dramatic increase in carotenoid production was observed at 45 to 75 days postanthesis in the segment membranes and juice sacs of ‘CH’. Different expression levels of carotenogenesis genes, especially the ζ-carotene desaturase (CmZDS), β-carotenoid hydroxylase (CmBCH) and zeaxanthin epoxidase (CmZEP) genes, in combination are directly responsible for the largely different carotenoid profiles between these two pummelo fruits. The sequences of eleven genes involved in carotenoid synthesis were investigated; different alleles of seven of eleven genes might also explain the largely different carotenogenesis observed between ‘CH’ and ‘FC’. These results enhance our understanding of carotenogenesis in pummelo fruits.
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Affiliation(s)
- Fuhua Yan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
- Forestry Science Academy of Lishui, Lishui, Zhejiang, P.R. China
| | - Meiyan Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Zhenyu He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Lianhai Wu
- Forestry Science Academy of Lishui, Lishui, Zhejiang, P.R. China
| | - Xianghua Xu
- Forestry Science Academy of Lishui, Lishui, Zhejiang, P.R. China
| | - Min He
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Jiajing Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, Hubei, P.R. China
- * E-mail:
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30
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Comparative transcriptome analysis provides global insight into gene expression differences between two orchid cultivars. PLoS One 2018; 13:e0200155. [PMID: 29975782 PMCID: PMC6033423 DOI: 10.1371/journal.pone.0200155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022] Open
Abstract
The orchids GL and YL are two cultivars of Cymbidium longibracteatum. YL displays an obviously yellowing rhizome and yellow leaves, while GL ('Longchangsu') shows dark green leaves and greenish rhizome. But the molecular mechanism for the differences between the two cultivars is poorly understood. In the present study, we showed that the structure of chloroplasts was significantly damaged in YL. Biochemical analysis uncovered the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoid were notably decreased in YL. Using RNA-Seq technology, more than 38 million clean reads were generated in each pool, and 116,422 unigenes were assembled de novo. 6,660 unigenes with differential expression patterns (FDR≤0.01 and |log2 ratio|≥1) were totally identified between the two cultivars. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed unigenes (DEGs) suggested 33 KEGG pathways were notably enriched, including biological processes such as “phenylpropanoid biosynthesis”, “phagosome”, “starch and sucrose metabolism”, “drug metabolism—cytochrome P450”, “fatty acid elongation”, and “flavone and flavonol biosynthesis”. Further analysis revealed that chlorophyll degeneration related unigene (c48794_g1) and flavonoid biosynthesis related unigenes (c16388_g1, c48963_g1, c63571_g1, c4492_g1, c52282_g1, c78740_g1, c4645_g1) were up-regulated while carotenoid biosynthesis related unigene (c7212_g1) were down-regulated in YL. Additionally, six of NAC, R2R3-MYB, bHLH transcription factors (c42861_g1, c105949_g1, c61265_g1, c42659_g1, c82171_g1, c19158_g1) might be involved in regulation of pigment biosynthesis. The chlorophyll degeneration and the flavonoid biosynthesis related unigenes up-regulation together with the carotenoid biosynthesis related unigenes down-regulation may contribute to the yellowing phenotype of YL.
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Wang X, Zou B, Shao Q, Cui Y, Lu S, Zhang Y, Huang Q, Huang J, Hua J. Natural variation reveals that OsSAP16 controls low-temperature germination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:413-421. [PMID: 29237030 PMCID: PMC5853544 DOI: 10.1093/jxb/erx413] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/25/2017] [Indexed: 05/06/2023]
Abstract
Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Baohong Zou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Qiaolin Shao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yongmei Cui
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shan Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Quansheng Huang
- Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Correspondence: ,
| | - Jian Hua
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY, USA
- Correspondence: ,
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Sun T, Yuan H, Cao H, Yazdani M, Tadmor Y, Li L. Carotenoid Metabolism in Plants: The Role of Plastids. MOLECULAR PLANT 2018; 11:58-74. [PMID: 28958604 DOI: 10.1016/j.molp.2017.09.010] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/02/2017] [Accepted: 09/13/2017] [Indexed: 05/17/2023]
Abstract
Carotenoids are indispensable to plants and critical in human diets. Plastids are the organelles for carotenoid biosynthesis and storage in plant cells. They exist in various types, which include proplastids, etioplasts, chloroplasts, amyloplasts, and chromoplasts. These plastids have dramatic differences in their capacity to synthesize and sequester carotenoids. Clearly, plastids play a central role in governing carotenogenic activity, carotenoid stability, and pigment diversity. Understanding of carotenoid metabolism and accumulation in various plastids expands our view on the multifaceted regulation of carotenogenesis and facilitates our efforts toward developing nutrient-enriched food crops. In this review, we provide a comprehensive overview of the impact of various types of plastids on carotenoid biosynthesis and accumulation, and discuss recent advances in our understanding of the regulatory control of carotenogenesis and metabolic engineering of carotenoids in light of plastid types in plants.
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Affiliation(s)
- 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
| | - 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
| | - 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 071001, China
| | - Mohammad Yazdani
- 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
| | - Yaakov Tadmor
- Plant Science Institute, Israeli Agricultural Research Organization, Newe Yaar Research Center, P.O. Box 1021, Ramat Yishai 30095, Israel
| | - 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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Gebremeskel S, Garcia-Oliveira AL, Menkir A, Adetimirin V, Gedil M. Effectiveness of predictive markers for marker assisted selection of pro-vitamin A carotenoids in medium-late maturing maize (Zea mays L.) inbred lines. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2017.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lou Y, Sun H, Li L, Zhao H, Gao Z. Characterization and Primary Functional Analysis of a Bamboo ZEP Gene from Phyllostachys edulis. DNA Cell Biol 2017; 36:747-758. [PMID: 28686465 DOI: 10.1089/dna.2017.3705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zeaxanthin epoxidase (ZEP) plays important roles in plant response to various environmental stresses by involving in abscisic acid (ABA) biosynthesis and xanthophyll cycle. A full-length cDNA of PeZEP was isolated from moso bamboo (Phyllostachys edulis), which comprised of a 138-bp 5'-untranslated region (UTR), a 381-bp 3'-UTR, and a 2013-bp open reading frame (ORF) encoding a putative protein of 670 amino acids. PeZEP was mainly expressed in leaf blades and leaf sheaths, and less in roots and culms. The transcript level of PeZEP in bamboo leaf was elevated with the increasing light intensity. PeZEP was significantly upregulated in response to high light (HL: 1200 μmol·m-2·s-1) and reached to a higher level after 1 h treatment, and kept higher levels in the following hours. Besides, PeZEP was upregulated under high temperature (42°C), and downregulated under low temperature (4°C) and exogenous ABA treatment. The expression vector of PeZEP driven by CaMV 35S was constructed and transformed into Arabidopsis thaliana. The transgenic plants overexpressing PeZEP were generated and subjected to drought stress for morphological and physiological assays. Compared with Col-0, the transgenic plants demonstrated enhanced tolerance to drought stress, which appeared later wilting and higher survival rate. Moreover, higher value of Fv/Fm, higher activities of superoxide dismutase, peroxidase, and catalase, and lower concentration of malondialdehyde were also observed in transgenic plants. Transcript levels of AtP5CS and AtRD29b related to drought stress were enhanced in transgenic plants. These results indicated that PeZEP might play an important function in response to drought stress in bamboo.
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Affiliation(s)
- Yongfeng Lou
- 1 State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources , International Center for Bamboo and Rattan, Beijing, China
- 2 Jiangxi Academy of Forestry , Nanchang, China
| | - Huayu Sun
- 1 State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources , International Center for Bamboo and Rattan, Beijing, China
| | - Lichao Li
- 1 State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources , International Center for Bamboo and Rattan, Beijing, China
| | - Hansheng Zhao
- 1 State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources , International Center for Bamboo and Rattan, Beijing, China
| | - Zhimin Gao
- 1 State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources , International Center for Bamboo and Rattan, Beijing, China
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Fernández-Marín B, Míguez F, Méndez-Fernández L, Agut A, Becerril JM, García-Plazaola JI, Kranner I, Colville L. Seed Carotenoid and Tocochromanol Composition of Wild Fabaceae Species Is Shaped by Phylogeny and Ecological Factors. FRONTIERS IN PLANT SCIENCE 2017; 8:1428. [PMID: 28883825 PMCID: PMC5573840 DOI: 10.3389/fpls.2017.01428] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/02/2017] [Indexed: 05/15/2023]
Abstract
Carotenoids distribution and function in seeds have been very scarcely studied, notwithstanding their pivotal roles in plants that include photosynthesis and phytohormone synthesis, pigmentation, membrane stabilization and antioxidant activity. Their relationship with tocochromanols, whose critical role in maintaining seed viability has already been evidenced, and with chlorophylls, whose retention in mature seed is thought to have negative effects on storability, remain also unexplored. Here, we aimed at elucidating seed carotenoids relationship with tocochromanols and chlorophylls with regard to phylogenetic and ecological traits and at understanding their changes during germination. The composition and distribution of carotenoids were investigated in seeds of a wide range of wild species across the Fabaceae (the second-most economically important family after the Poaceae). Photosynthetic pigments and tocochromanols were analyzed by HPLC in mature dry seeds of 50 species representative of 5 subfamilies within the Fabaceae (including taxa that represent all continents, biomes and life forms within the family) and at key timepoints during seedling establishment in three species representative of distinct clades. Total-carotenoids content positively correlated with tocopherols in the basal subfamilies Detarioideae, Cercidoideae, and Dialioideae, and with chlorophylls in the Papilionoideae. Papilionoideae lacked tocotrienols and had the highest total-carotenoids, chlorophyll and γ-tocopherol contents. Interestingly, lutein epoxide was present in 72% of the species including several herbs from different subfamilies. Overall, species original from temperate biomes presented higher carotenoids and lower tocochromanols levels than those from tropical biomes. Also shrub species showed higher carotenoids content than herbs and trees. During germination, total content of photosynthetic pigments increased in parallel to changes in relative abundance of carotenoids: zeaxanthin and anteraxanthin decreased and β-carotene augmented. Notably, the highest contents of nutritionally valuable carotenoids were found in Papilionoideae subfamily to which all pulses of socio-economic importance belong. The major differences in carotenoids and tocochromanols composition across the Fabaceae are apparently related to phylogeny in conjunction with ecological traits such as biome and growth form.
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Affiliation(s)
- Beatriz Fernández-Marín
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU)Bilbao, Spain
| | - Fátima Míguez
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU)Bilbao, Spain
| | - Leire Méndez-Fernández
- Department of Zoology and Animal Cellular Biology, University of the Basque Country (UPV/EHU)Bilbao, Spain
| | - Agustí Agut
- Jardín Botánico de OlarizuVitoria-Gasteiz, Spain
| | - José M. Becerril
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU)Bilbao, Spain
| | - José I. García-Plazaola
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU)Bilbao, Spain
| | - Ilse Kranner
- Department of Botany and Center for Molecular Biosciences, University of InnsbruckInnsbruck, Austria
| | - Louise Colville
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, KewArdingly, United Kingdom
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36
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Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D. Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids. PLANT PHYSIOLOGY 2017; 173:872-886. [PMID: 27872244 PMCID: PMC5210728 DOI: 10.1104/pp.16.01287] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/16/2016] [Indexed: 05/18/2023]
Abstract
Amino acids are essential for proper growth and development in plants. Amino acids serve as building blocks for proteins but also are important for responses to stress and the biosynthesis of numerous essential compounds. In seed, the pool of free amino acids (FAAs) also contributes to alternative energy, desiccation, and seed vigor; thus, manipulating FAA levels can significantly impact a seed's nutritional qualities. While genome-wide association studies (GWAS) on branched-chain amino acids have identified some regulatory genes controlling seed FAAs, the genetic regulation of FAA levels, composition, and homeostasis in seeds remains mostly unresolved. Hence, we performed GWAS on 18 FAAs from a 313-ecotype Arabidopsis (Arabidopsis thaliana) association panel. Specifically, GWAS was performed on 98 traits derived from known amino acid metabolic pathways (approach 1) and then on 92 traits generated from an unbiased correlation-based metabolic network analysis (approach 2), and the results were compared. The latter approach facilitated the discovery of additional novel metabolic interactions and single-nucleotide polymorphism-trait associations not identified by the former approach. The most prominent network-guided GWAS signal was for a histidine (His)-related trait in a region containing two genes: a cationic amino acid transporter (CAT4) and a polynucleotide phosphorylase resistant to inhibition with fosmidomycin. A reverse genetics approach confirmed CAT4 to be responsible for the natural variation of His-related traits across the association panel. Given that His is a semiessential amino acid and a potent metal chelator, CAT4 orthologs could be considered as candidate genes for seed quality biofortification in crop plants.
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Affiliation(s)
- Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.);
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.);
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.);
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Albert Batushansky
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Nicholas Deason
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Sabrina Gonzalez-Jorge
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Michael A Gore
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Aaron Fait
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
| | - Dean DellaPenna
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.)
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.)
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.)
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.)
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