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Back S, Kim JM, Choi H, Lee JH, Han K, Hwang D, Kwon JK, Kang BC. Genetic characterization of a locus responsible for low pungency using EMS-induced mutants in Capsicum annuum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:101. [PMID: 38607449 PMCID: PMC11014816 DOI: 10.1007/s00122-024-04602-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/16/2024] [Indexed: 04/13/2024]
Abstract
KEY MESSAGE The pepper mutants ('221-2-1a' and '1559-1-2h') with very low pungency were genetically characterized. The Pun4 locus, responsible for the reduced pungency of the mutant fruits, was localized to a 208 Mb region on chromosome 6. DEMF06G16460, encoding 3-ketoacyl-CoA synthase, was proposed as a strong candidate gene based on the genetic analyses of bulked segregants, DEG, and expression analyses. Capsaicinoids are unique alkaloids present in pepper (Capsicum spp.), synthesized through the condensation of by-products from the phenylpropanoid and branched-chain fatty acid pathways, and accumulating in the placenta. In this study, we characterized two allelic ethyl methanesulfonate-induced mutant lines with extremely low pungency ('221-2-1a' and '1559-1-2h'). These mutants, derived from the pungent Korean landrace 'Yuwolcho,' exhibited lower capsaicinoid content than Yuwolcho but still contained a small amount of capsaicinoid with functional capsaicinoid biosynthetic genes. Genetic crosses between the mutants and Yuwolcho or pungent lines indicated that a single recessive mutation was responsible for the low-pungency phenotype of mutant 221-2-1a; we named the causal locus Pungency 4 (Pun4). To identify Pun4, we combined genome-wide polymorphism analysis and transcriptome analysis with bulked-segregant analysis. We narrowed down the location of Pun4 to a 208-Mb region on chromosome 6 containing five candidate genes, of which DEMF06G16460, encoding a 3-ketoacyl-CoA synthase associated with branched-chain fatty acid biosynthesis, is the most likely candidate for Pun4. The expression of capsaicinoid biosynthetic genes in placental tissues in Yuwolcho and the mutant was consistent with the branched-chain fatty acid pathway playing a pivotal role in the lower pungency observed in the mutant. We also obtained a list of differentially expressed genes in placental tissues between the mutant and Yuwolcho, from which we selected candidate genes using gene co-expression analysis. In summary, we characterized the capsaicinoid biosynthesis-related locus Pun4 through integrated of genetic, genomic, and transcriptome analyses. These findings will contribute to our understanding of capsaicinoid biosynthesis in pepper.
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Affiliation(s)
- Seungki Back
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jung-Min Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hayoung Choi
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Koeun Han
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Doyeon Hwang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul, 08826, Republic of Korea.
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Kusaka H, Nakasato S, Sano K, Kobata K, Ohno S, Doi M, Tanaka Y. An evolutionary view of vanillylamine synthase pAMT, a key enzyme of capsaicinoid biosynthesis pathway in chili pepper. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1453-1465. [PMID: 38117481 DOI: 10.1111/tpj.16573] [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: 05/30/2023] [Revised: 11/03/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
Pungent capsaicinoid is synthesized only in chili pepper (Capsicum spp.). The production of vanillylamine from vanillin is a unique reaction in the capsaicinoid biosynthesis pathway. Although putative aminotransferase (pAMT) has been isolated as the vanillylamine synthase gene, it is unclear how Capsicum acquired pAMT. Here, we present a phylogenetic overview of pAMT and its homologs. The Capsicum genome contained 5 homologs, including pAMT, CaGABA-T1, CaGABA-T3, and two pseudogenes. Phylogenetic analysis indicated that pAMT is a member of the Solanaceae cytoplasmic GABA-Ts. Comparative genome analysis found that multiple copies of GABA-T exist in a specific Solanaceae genomic region, and the cytoplasmic GABA-Ts other than pAMT are located in the region. The cytoplasmic GABA-T was phylogenetically close to pseudo-GABA-T harboring a plastid transit peptide (pseudo-GABA-T3). This suggested that Solanaceae cytoplasmic GABA-Ts occurred via duplication of a chloroplastic GABA-T ancestor and subsequent loss of the plastid transit signal. The cytoplasmic GABA-T may have been translocated from the specific Solanaceae genomic region during Capsicum divergence, resulting in the current pAMT locus. A recombinant protein assay demonstrated that pAMT had higher vanillylamine synthase activity than those of other plant GABA-Ts. pAMT was expressed exclusively in the placental septum of mature green fruit, whereas tomato orthologs SlGABA-T2/4 exhibit a ubiquitous expression pattern in plants. These findings suggested that both the increased catalytic efficiency and transcriptional changes in pAMT may have contributed to establish vanillylamine synthesis in the capsaicinoid biosynthesis pathway. This study provides insights into the establishment of pungency in the evolution of chili peppers.
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Affiliation(s)
- Hirokazu Kusaka
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Saika Nakasato
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama, 350-0295, Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, Saitama, 350-0295, Japan
| | - Kenji Kobata
- Graduate School of Pharmaceutical Sciences, Josai University, Saitama, 350-0295, Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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Burgos-Valencia E, Echevarría-Machado I, Ortega-Lule G, Medina-Lara F, García-Laynes F, Martínez-Estévez M, Narváez-Zapata J. Haplotype analysis, regulatory elements and docking simulation of structural models of different AT3 copies in the genus Capsicum. J Biomol Struct Dyn 2024:1-14. [PMID: 38354741 DOI: 10.1080/07391102.2024.2317991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
Capsaicinoids are responsible for the pungency in Capsicum species. These are synthesized by the Capsaicin synthase (CS) encoded by the AT3 gene, which catalyzes the transference of an acyl moiety from a branched-chain fatty acid-CoA ester to the vanillylamine to produce capsaicinoids. Some AT3 gene copies have been identified on the Capsicum genome. The absence of capsaicinoid in some nonpungent accessions is related to mutant AT3 alleles. The differences between CS protein copies can affect the tridimensional structure of the protein and the affinity for its substrates, and this could affect fruit pungency. This study characterized 32 AT3 sequences covering Capsicum pungent and non-pungent accessions. These were clustered in AT3-D1 and AT3-D2 groups and representative sequences were analyzed. Genomic upstream analysis shows different regulatory elements, mainly responsive to light and abiotic stress. AT3-D1 and AT3-D2 gene expression was confirmed in fruit tissues of C. annuum. Amino acid substitutions close to the predictable HXXXD and DFGWG motifs were also identified. AT3 sequences were modeled showing a BAHD acyltransferase structure with two connected domains. A pocket with different shape, size and composition between AT3 models was found inside the protein, with the conserved motif HXXXD exposed to it, and a channel for their accessibility. CS substrates exhibit high interaction energies with the His and Asp conserved residues. AT3 models have different interaction affinities with the (E)-8-methylnon-6-enoyl-CoA, 8-methylnonanoyl-CoA and vanillylamine substrates. These results suggested that AT3-D1 and AT3-D2 sequences encode CS enzymes with different regulatory factors and substratum affinities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Eduardo Burgos-Valencia
- Unidad de Biología Integrativa. Centro de Investigación Científica de Yucatán, Calle 43 # 130, Chuburna de Hidalgo, Mérida, Yucatán, México
| | - Ileana Echevarría-Machado
- Unidad de Biología Integrativa. Centro de Investigación Científica de Yucatán, Calle 43 # 130, Chuburna de Hidalgo, Mérida, Yucatán, México
| | - Gustavo Ortega-Lule
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Fátima Medina-Lara
- Unidad de Biología Integrativa. Centro de Investigación Científica de Yucatán, Calle 43 # 130, Chuburna de Hidalgo, Mérida, Yucatán, México
| | - Federico García-Laynes
- Unidad de Biología Integrativa. Centro de Investigación Científica de Yucatán, Calle 43 # 130, Chuburna de Hidalgo, Mérida, Yucatán, México
| | - Manuel Martínez-Estévez
- Unidad de Biología Integrativa. Centro de Investigación Científica de Yucatán, Calle 43 # 130, Chuburna de Hidalgo, Mérida, Yucatán, México
| | - José Narváez-Zapata
- Instituto Politécnico Nacional - Centro de Biotecnología Genómica, Reynosa, Tamaulipas, México
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Koeda S, Noda T, Hachisu S, Kubo A, Tanaka Y, Yamamoto H, Ozaki S, Kinoshita M, Ohno K, Tanaka Y, Tomi K, Kamiyoshihara Y. Expression of alcohol acyltransferase is a potential determinant of fruit volatile ester variations in Capsicum. PLANT CELL REPORTS 2023; 42:1745-1756. [PMID: 37642676 DOI: 10.1007/s00299-023-03064-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
KEY MESSAGE The transcript level of alcohol acyltransferase 1 (AAT1) may be the main factor influencing the variations in volatile esters that characterizing the fruity/exotic aroma of pepper fruit. Volatile esters are key components for characterizing the fruity/exotic aroma of pepper (Capsicum spp.) fruit. In general, the volatile ester content in the fruit is the consequence of a delicate balance between their synthesis by alcohol acyltransferases (AATs) and degradation by carboxylesterases (CXEs). However, the precise role of these families of enzymes with regard to volatile ester content remains unexplored in Capsicum. In this study, we found that the volatile ester content was relatively low in C. annuum and much higher in C. chinense, particularly in pungent varieties. Additionally, fruits collected from multiple non-pungent C. chinense varieties, which harbor loss-of-function mutations in capsaicinoid biosynthetic genes, acyltransferase (Pun1), putative aminotransferase (pAMT), or putative ketoacyl-ACP reductase (CaKR1) were analyzed. The volatile ester contents of non-pungent C. chinense varieties (pamt/pamt) were equivalent to those of pungent varieties, but their levels were significantly lower in non-pungent NMCA30036 (pun12/pun12) and C. chinense (Cakr1/Cakr1) varieties. Multiple AAT-like sequences were identified from the pepper genome sequences, whereas only one CXE-like sequence was identified. Among these, AAT1, AAT2, and CXE1 were isolated from fruits of C. chinense and C. annuum. Gene expression analysis revealed that the AAT1 transcript level is a potential determinant of fruit volatile ester variations in Capsicum. Furthermore, enzymatic assays demonstrated that AAT1 is responsible for the biosynthesis of volatile esters in pepper fruit. Identification of a key gene for aroma biosynthesis in pepper fruit will provide a theoretical basis for the development of molecular tools for flavor improvement.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan.
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan.
| | - Tomona Noda
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Shinkai Hachisu
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Akiha Kubo
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Yasuto Tanaka
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Hiroto Yamamoto
- Graduate School of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Sayaka Ozaki
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | | | - Kouki Ohno
- Faculty of Agriculture, Kindai University, Nara, 3327-204, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenichi Tomi
- Japan Society for Scientific Aromatherapy, Tokyo, 164-0003, Japan
| | - Yusuke Kamiyoshihara
- College of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan
- Graduate School of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan
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Xu L, Zang E, Sun S, Li M. Main flavor compounds and molecular regulation mechanisms in fruits and vegetables. Crit Rev Food Sci Nutr 2023; 63:11859-11879. [PMID: 35816297 DOI: 10.1080/10408398.2022.2097195] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fruits and vegetables (F&V) are an indispensable part of a healthy diet. The volatile and nonvolatile compounds present in F&V constitute unique flavor substances. This paper reviews the main flavor substances present in F&V, as well as the biosynthetic pathways and molecular regulation mechanisms of these compounds. A series of compounds introduced include aromatic substances, soluble sugars and organic acids, which constitute the key flavor substances of F&V. Esters, phenols, alcohols, amino acids and terpenes are the main volatile aromatic substances, and nonvolatile substances are represented by amino acids, fatty acids and carbohydrates; The combination of these ingredients is the cause of the sour, sweet, bitter, astringent and spicy taste of these foods. This provides a theoretical basis for the study of the interaction between volatile and nonvolatile substances in F&V, and also provides a research direction for the healthy development of food in the future.
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Affiliation(s)
- Ling Xu
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Erhuan Zang
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China
| | - Shuying Sun
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Minhui Li
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China
- Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, China
- Inner Mongolia Traditional Chinese and Mongolian Medical Research Institute, Hohhot, China
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6
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Islam K, Rawoof A, Kumar A, Momo J, Ahmed I, Dubey M, Ramchiary N. Genetic Regulation, Environmental Cues, and Extraction Methods for Higher Yield of Secondary Metabolites in Capsicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37289974 DOI: 10.1021/acs.jafc.3c01901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Capsicum (chili pepper) is a widely popular and highly consumed fruit crop with beneficial secondary metabolites such as capsaicinoids, carotenoids, flavonoids, and polyphenols, among others. Interestingly, the secondary metabolite profile is a dynamic function of biosynthetic enzymes, regulatory transcription factors, developmental stage, abiotic and biotic environment, and extraction methods. We propose active manipulable genetic, environmental, and extraction controls for the modulation of quality and quantity of desired secondary metabolites in Capsicum species. Specific biosynthetic genes such as Pun (AT3) and AMT in the capsaicinoids pathway and PSY, LCY, and CCS in the carotenoid pathway can be genetically engineered for enhanced production of capsaicinoids and carotenoids, respectively. Generally, secondary metabolites increase with the ripening of the fruit; however, transcriptional regulators such as MYB, bHLH, and ERF control the extent of accumulation in specific tissues. The precise tuning of biotic and abiotic factors such as light, temperature, and chemical elicitors can maximize the accumulation and retention of secondary metabolites in pre- and postharvest settings. Finally, optimized extraction methods such as ultrasonication and supercritical fluid method can lead to a higher yield of secondary metabolites. Together, the integrated understanding of the genetic regulation of biosynthesis, elicitation treatments, and optimization of extraction methods can maximize the industrial production of secondary metabolites in Capsicum.
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Affiliation(s)
- Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod 671316, Kerala, India
| | - John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ilyas Ahmed
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Meenakshi Dubey
- Department of Biotechnology, Delhi Technological University, New Delhi 110042, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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7
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MYB24 Negatively Regulates the Biosynthesis of Lignin and Capsaicin by Affecting the Expression of Key Genes in the Phenylpropanoid Metabolism Pathway in Capsicum chinense. Molecules 2023; 28:molecules28062644. [PMID: 36985616 PMCID: PMC10054932 DOI: 10.3390/molecules28062644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The wide application of pepper is mostly related to the content of capsaicin, and phenylpropanoid metabolism and its branch pathways may play an important role in the biosynthesis of capsaicin. The expression level of MYB24, a transcription factor screened from the transcriptome data of the pepper fruit development stage, was closely related to the spicy taste. In this experiment, CcMYB24 was cloned from Hainan Huangdenglong pepper, a hot aromatic pepper variety popular in the world for processing, and its function was confirmed by tissue expression characteristics, heterologous transformation in Arabidopsis thaliana, and VIGS technology. The results showed that the relative expression level of CcMYB24 was stable in the early stage of pepper fruit development, and increased significantly from 30 to 50 days after flowering. Heterologous expression led to a significant increase in the expression of CcMYB24 and decrease in lignin content in transgenic Arabidopsis thaliana plants. CcMYB24 silencing led to a significant increase in the expression of phenylpropanoid metabolism pathway genes PAL, 4CL, and pAMT; lignin branch CCR1 and CAD; and capsaicin pathway CS, AT3, and COMT genes in the placenta of pepper, with capsaicin content increased by more than 31.72% and lignin content increased by 20.78%. However, the expression of PAL, pAMT, AT3, COMT, etc., in the corresponding pericarps did not change significantly. Although CS, CCR1, and CAD increased significantly, the relative expression amount was smaller than that in placental tissue, and the lignin content did not change significantly. As indicated above, CcMYB24 may negatively regulate the formation of capsaicin and lignin by regulating the expression of genes from phenylpropanoid metabolism and its branch pathways.
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Kondo F, Umeda K, Sudasinghe SP, Yamaguchi M, Aratani S, Kumanomido Y, Nemoto K, Nagano AJ, Matsushima K. Genetic analysis of pungency deficiency in Japanese chili pepper 'Shishito' (Capsicum annuum) revealed its unique heredity and brought the discovery of two genetic loci involved with the reduction of pungency. Mol Genet Genomics 2023; 298:201-212. [PMID: 36374297 DOI: 10.1007/s00438-022-01975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/30/2022] [Indexed: 11/16/2022]
Abstract
The sensation of pungency generated by capsaicinoids is a characteristic trait of chili peppers (Capsicum spp.), and the presence or absence of pungency is central in determining its usage as a spice or a vegetable. In the present study, we aimed to clarify the heredity and genetic factors involved in the deficiency of pungency (quite low pungency) that is uniquely observed in the Japanese chili pepper 'Shishito' (Capsicum annuum). First, the F2 population ('Shishito' × pungent variety 'Takanotsume') was used for segregation analysis, and pungency level was investigated using capsaicinoid quantification with high-performance liquid chromatography. Also, restriction site associated DNA sequencing of the F2 population was performed, and genetic map construction and quantitative trait locus (QTL) mapping were implemented. The results indicated that the F2 population showed varying capsaicinoid content and two major QTLs were detected, Shql3 and Shql7, which explained 39.8 and 19.7% of the genetic variance, respectively. According to these results, the quite low pungency of 'Shishito' was a quantitative trait that involved at least the two loci. Further, this trait was completely separate from general non-pungent traits controlled by individual recessive genes, as described in previous studies. The present study is the first report to investigate the genetic mechanism of pungency deficiency in Japanese chili peppers, and our results provide new insights into the genetic regulation of pungency in chili pepper.
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Affiliation(s)
- Fumiya Kondo
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan.,Japan Society for the Promotion of Science (JSPS), Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan
| | - Koyuki Umeda
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan
| | - Sathya Prabandaka Sudasinghe
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan
| | - Moe Yamaguchi
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan
| | - Shintaro Aratani
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan
| | - Yui Kumanomido
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan
| | - Kazuhiro Nemoto
- Institute of Agriculture, Academic Assembly Faculty, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta, Ohe-Cho, Otsu, Shiga, 520-2194, Japan.,Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Kenichi Matsushima
- Institute of Agriculture, Academic Assembly Faculty, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan.
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9
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Zhang W, Wu D, Zhang L, Zhao C, Shu H, Cheng S, Wang Z, Zhu J, Liu P. Identification and expression analysis of capsaicin biosynthesis pathway genes at genome level in Capsicum chinense. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2071633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Wei Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Dan Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Liping Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Chengzhi Zhao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Jie Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, College of Horticulture, Hainan University, Haikou, Hainan, PR China
| | - Pingwu Liu
- Fang Zhiyuan Academician Team Innovation Center of Hainan Province, Haikou, Hainan, PR China
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10
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Yi S, Lee DG, Back S, Hong JP, Jang S, Han K, Kang BC. Genetic mapping revealed that the Pun2 gene in Capsicum chacoense encodes a putative aminotransferase. FRONTIERS IN PLANT SCIENCE 2022; 13:1039393. [PMID: 36388488 PMCID: PMC9664168 DOI: 10.3389/fpls.2022.1039393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Several genes regulating capsaicinoid biosynthesis including Pun1 (also known as CS), Pun3, pAMT, and CaKR1 have been studied. However, the gene encoded by Pun2 in the non-pungent Capsicum chacoense is unknown. This study aimed to identify the Pun2 gene by genetic mapping using interspecific (C. chacoense × Capsicum annuum) and intraspecific (C. chacoense × C. chacoense) populations. QTL mapping using the interspecific F2 population revealed two major QTLs on chromosomes 3 and 9. Two bin markers within the QTL regions on two chromosomes were highly correlated with the capsaicinoid content in the interspecific population. The major QTL, Pun2_PJ_Gibbs_3.11 on chromosome 3, contained the pAMT gene, indicating that the non-pungency of C. chacoense may be attributed to a mutation in the pAMT gene. Sequence analysis revealed a 7 bp nucleotide insertion in the 8th exon of pAMT of the non-pungent C. chacoense. This mutation resulted in the generation of an early stop codon, resulting in a truncated mutant lacking the PLP binding site, which is critical for pAMT enzymatic activity. This insertion co-segregated with the pungency phenotype in the intraspecific F2 population. We named this novel pAMT allele pamt11 . Taken together, these data indicate that the non-pungency of C. chacoense is due to the non-functional pAMT allele, and Pun2 encodes the pAMT gene.
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11
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Koeda S, Mori N, Horiuchi R, Watanabe C, Nagano AJ, Shiragane H. PepYLCIV and PepYLCAV resistance gene Pepy-2 encodes DFDGD-Class RNA-dependent RNA polymerase in Capsicum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2437-2452. [PMID: 35652932 DOI: 10.1007/s00122-022-04125-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F2 and F3 segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Namiko Mori
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Ryo Horiuchi
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Chiho Watanabe
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Atsushi J Nagano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
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12
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Shoji T, Umemoto N, Saito K. Genetic divergence in transcriptional regulators of defense metabolism: insight into plant domestication and improvement. PLANT MOLECULAR BIOLOGY 2022; 109:401-411. [PMID: 34114167 DOI: 10.1007/s11103-021-01159-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/29/2021] [Indexed: 05/23/2023]
Abstract
A number of mutational changes in transcriptional regulators of defense metabolism have occurred during plant domestication and improvement. Plant domestication and improvement entail genetic changes that underlie divergence in development and metabolism, providing a tremendous model of biological evolution. Plant metabolism produces numerous specialized alkaloids, terpenoids, phenolics, and cyanogenic glucosides with indispensable roles in defense against herbivory and microbial infection. Many compounds toxic or deterrent to predators have been eliminated through domestication and breeding. Series of genes involved in defense metabolism are coordinately regulated by transcription factors that specifically recognize cis-regulatory elements in promoter regions of downstream target genes. Recent developments in DNA sequencing technologies and genomic approaches have facilitated studies of the metabolic and genetic changes in chemical defense that have occurred via human-mediated selection, many of which result from mutations in transcriptional regulators of defense metabolism. In this article, we review such examples in almond (Prunus dulcis), cucumber (Cucumis sativus), pepper (Capsicum spp.), potato (Solanum tuberosum), quinoa (Chenopodium quinoa), sorghum (Sorghum bicolor), and related species and discuss insights into the evolution and regulation of metabolic pathways for specialized defense compounds.
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Affiliation(s)
- Tsubasa Shoji
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Naoyuki Umemoto
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Plant Molecular Science Center, Chiba University, Chuo-ku, Chiba, 260-8675, Japan
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13
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Fiesel PD, Parks HM, Last RL, Barry CS. Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae. Nat Prod Rep 2022; 39:1438-1464. [PMID: 35332352 DOI: 10.1039/d2np00003b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary metabolites, are conserved across the plant kingdom and are required for processes essential to growth and development. These include amino acids, sugars, lipids, and organic acids. In contrast, specialized metabolites, historically termed secondary metabolites, are structurally diverse, exhibit lineage-specific distribution and provide selective advantage to host species to facilitate reproduction and environmental adaptation. Due to their potent bioactivities, plant specialized metabolites attract considerable attention for use as flavorings, fragrances, pharmaceuticals, and bio-pesticides. The Solanaceae (Nightshade family) consists of approximately 2700 species and includes crops of significant economic, cultural, and scientific importance: these include potato, tomato, pepper, eggplant, tobacco, and petunia. The Solanaceae has emerged as a model family for studying the biochemical evolution of plant specialized metabolism and multiple examples exist of lineage-specific metabolites that influence the senses and physiology of commensal and harmful organisms, including humans. These include, alcohols, phenylpropanoids, and carotenoids that contribute to fruit aroma and color in tomato (fruity), glandular trichome-derived terpenoids and acylsugars that contribute to plant defense (stinky & sticky, respectively), capsaicinoids in chilli-peppers that influence seed dispersal (spicy), and steroidal glycoalkaloids (bitter) from Solanum, nicotine (addictive) from tobacco, as well as tropane alkaloids (deadly) from Deadly Nightshade that deter herbivory. Advances in genomics and metabolomics, coupled with the adoption of comparative phylogenetic approaches, resulted in deeper knowledge of the biosynthesis and evolution of these metabolites. This review highlights recent progress in this area and outlines opportunities for - and challenges of-developing a more comprehensive understanding of Solanaceae metabolism.
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Affiliation(s)
- Paul D Fiesel
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Hannah M Parks
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L Last
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
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Tanaka Y, Watachi M, Nemoto W, Goto T, Yoshida Y, Yasuba KI, Ohno S, Doi M. Capsaicinoid biosynthesis in the pericarp of chili pepper fruits is associated with a placental septum-like transcriptome profile and tissue structure. PLANT CELL REPORTS 2021; 40:1859-1874. [PMID: 34283265 DOI: 10.1007/s00299-021-02750-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
CAP biosynthesis in the pericarp of chili pepper fruits occurs with an ambiguous boundary in the placental septum and pericarp. Capsaicinoid (CAP) is a pungent ingredient of chili pepper fruits. Generally, CAP biosynthesis is limited to the placental septum of fruits, but it has been reported that its biosynthesis occurs even in the pericarp of some extremely pungent varieties, resulting in a substantial increase in total content. To examine the mechanism of CAP biosynthesis in the pericarp, comparative transcriptome analysis of a variety that produces CAP in the pericarp (MY) and a variety that does not (HB) was carried out. RNA-seq revealed that 2264 genes were differentially expressed in the MY pericarp compared with the HB pericarp. PCA analysis and GO enrichment analysis indicated that the MY pericarp has a gene expression profile more like placental septum than the HB pericarp. The gene expression of CAP biosynthesis-related genes in the MY pericarp changed coordinately with the placental septum during fruit development. In most Capsicum accessions including HB, the distribution of slender epidermal cells producing CAP was limited to the placental septum, and the morphological boundary between the placental septum and pericarp was clear. In some extremely pungent varieties such as MY, slender epidermal cells ranged from the placental septum to the pericarp region, and the pericarp was morphologically similar to the placental septum, such as the absence of large sub-epidermal cells and abundant spaces in the parenchymal tissue. Our data suggest that CAP biosynthesis in the pericarp occurred with an ambiguous boundary in the placental septum and pericarp. These findings contribute to further enhancement of CAP production in chili pepper fruits.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
| | - Mayuko Watachi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Wakana Nemoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tanjuro Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuichi Yoshida
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Ken-Ichiro Yasuba
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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Koeda S, Onouchi M, Mori N, Pohan NS, Nagano AJ, Kesumawati E. A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2947-2964. [PMID: 34081151 DOI: 10.1007/s00122-021-03870-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/24/2021] [Indexed: 05/25/2023]
Abstract
A begomovirus resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, was identified in pepper (C. annuum) through map-based cloning and functional characterization. Pepper yellow leaf curl disease caused by begomoviruses seriously affects pepper (Capsicum spp.) production in a number of regions around the world. Ty genes of tomato, which confer resistance to the tomato yellow leaf curl virus, are the only begomovirus resistance genes cloned to date. In this study, we focused on the identification of begomovirus resistance genes in Capsicum annuum. BaPep-5 was identified as a novel source of resistance against pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV). A single recessive locus, which we named as pepper yellow leaf curl disease virus resistance 1 (pepy-1), responsible for PepYLCAV resistance in BaPep-5 was identified on chromosome 5 in an F2 population derived from a cross between BaPep-5 and the begomovirus susceptible accession BaPep-4. In the target region spanning 34 kb, a single candidate gene, the messenger RNA surveillance factor Pelota, was identified. Whole-genome resequencing of BaPep-4 and BaPep-5 and comparison of their genomic DNA sequences revealed a single nucleotide polymorphism (A to G) located at the splice site of the 9th intron of CaPelota in BaPep-5, which caused the insertion of the 9th intron into the transcript, resulting in the addition of 28 amino acids to CaPelota protein without causing a frameshift. Virus-induced gene silencing of CaPelota in the begomovirus susceptible pepper No.218 resulted in the gain of resistance against PepYLCIV, a phenotype consistent with BaPep-5. The DNA marker developed in this study will greatly facilitate marker-assisted breeding of begomovirus resistance in peppers.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Mika Onouchi
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Namiko Mori
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Nadya Syafira Pohan
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Atsushi J Nagano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
| | - Elly Kesumawati
- Faculty of Agriculture, Syiah Kuala University, Banda Aceh, Aceh , 23111, Indonesia
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16
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The pungent-variable sweet chili pepper 'Shishito' (Capsicum annuum) provides insights regarding the relationship between pungency, the number of seeds, and gene expression involving capsaicinoid biosynthesis. Mol Genet Genomics 2021; 296:591-603. [PMID: 33599813 DOI: 10.1007/s00438-021-01763-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Pungent traits caused by capsaicinoids are characteristic of chili peppers (Capsicum spp.), and the pungent-variable sweet chili pepper 'Shishito' (Capsicum annuum) is unique in being known for the pungency in fruits with few seeds. In the present study, we tried to clarify the relationship between the number of seeds and pungency in 'Shishito'. First, we investigated the pungency of 'Shishito' by simple sensory evaluations and quantifications of capsaicinoids by high-performance liquid chromatography. As a result, few-seeded fruits had a larger fluctuation of capsaicinoid content than many-seeded ones. This indicates that the number of seeds, in particular a decrease of the seeds, has some sort of connection with the pungency of 'Shishito'. Then, we analyzed the relationship between pungency and gene expression involving capsaicinoid biosynthesis at the individual fruit level. We vertically separated the placental septum in which capsaicinoids are synthesized and performed quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for 18 genes involved in capsaicinoid biosynthesis. We also used the placental septum for capsaicinoid quantification so that the gene expression levels and capsaicinoid contents in the same fruits were obtained, and their correlations were analyzed using 20 biological replicates. Among the 18 genes, expression levels of 11 genes (WRKY9, CaMYB31, AT3, BCAT, BCKDH, KAS I, KAS III, ACL, CaKR1, FAT, and pAMT) had a significant positive correlation with the capsaicinoid concentration, and they were considered to upregulate capsaicinoid biosynthesis. These results provide new insights regarding the environmental variation of the pungency traits in chili peppers and the relationship between pungency, the number of seeds, and gene expression involved in capsaicinoid biosynthesis.
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Zhang B, Hu F, Cai X, Cheng J, Zhang Y, Lin H, Hu K, Wu Z. Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin ( Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:783496. [PMID: 35069640 PMCID: PMC8767146 DOI: 10.3389/fpls.2021.783496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/13/2021] [Indexed: 05/14/2023]
Abstract
Pungency is a unique characteristic of chili peppers (Capsicum spp.) caused by capsaicinoids. The evolutionary emergence of pungency is thought to be a derived trait within the genus Capsicum. However, it is not well-known how pungency has varied during Capsicum domestication and specialization. In this study, we applied a comparative metabolomics along with transcriptomics analysis to assess various changes between two peppers (a mildly pungent cultivated pepper BB3 and its hot progenitor chiltepin) at four stages of fruit development, focusing on pungency variation. A total of 558 metabolites were detected in two peppers. In comparison with chiltepin, capsaicinoid accumulation in BB3 was almost negligible at the early stage. Next, 412 DEGs associated with the capsaicinoid accumulation pathway were identified through coexpression analysis, of which 18 genes (14 TFs, 3 CBGs, and 1 UGT) were deemed key regulators due to their high coefficients. Based on these data, we speculated that downregulation of these hub genes during the early fruit developmental stage leads to a loss in pungency during Capsicum domestication (from chiltepin to BB3). Of note, a putative UDP-glycosyltransferase, GT86A1, is thought to affect the stabilization of capsaicinoids. Our results lay the foundation for further research on the genetic diversity of pungency traits during Capsicum domestication and specialization.
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Affiliation(s)
- Bipei Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xiaotao Cai
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ying Zhang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hui Lin
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
- *Correspondence: Kailin Hu,
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Zhiming Wu,
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Wang J, Liu Y, Tang B, Dai X, Xie L, Liu F, Zou X. Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the R2R3-MYB Gene Family in Capsicum annuum L. Front Genet 2020; 11:598183. [PMID: 33408738 PMCID: PMC7779616 DOI: 10.3389/fgene.2020.598183] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Capsaicinoids are naturally specialized metabolites in pepper and are the main reason that Capsicum fruits have a pungent smell. During the synthesis of capsaicin, MYB transcription factors play key regulatory roles. In particular, R2R3-MYB subfamily genes are the most important members of the MYB family and are critical candidate factors in capsaicinoid biosynthesis. The 108 R2R3-MYB genes in pepper were identified in this study and all are shown to have two highly conserved MYB binding domains. Phylogenetic and structural analyses clustered CaR2R3-MYB genes into seven groups. Interspecies collinearity analysis found that the R2R3-MYB family contains 16 duplicated gene pairs and the highest gene density is on chromosome 00 and 03. The expression levels of CaR2R3-MYB differentially expressed genes (DEGs) and capsaicinoid-biosynthetic genes (CBGs) in fruit development stages were obtained via RNA-seq and quantitative polymerase chain reaction (qRT-PCR). Co-expression analyses reveal that highly expressed CaR2R3-MYB genes are co-expressed with CBGs during early stages of pericarp and placenta development processes. It is speculated that six candidate CaR2R3-MYB genes are involved in regulating the synthesis of capsaicin and dihydrocapsaicin. This study is the first systematic analysis of the CaR2R3-MYB gene family and provided references for studying their molecular functions. At the same time, these results also laid the foundation for further research on the capsaicin characteristics of CaR2R3-MYB genes in pepper.
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Affiliation(s)
- Jin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Yi Liu
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Bingqian Tang
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Xiongze Dai
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Lingling Xie
- Hunan Vegetable Research Institute, Changsha, China
| | - Feng Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Hunan Vegetable Research Institute, Changsha, China
| | - Xuexiao Zou
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
- College of Horticulture, Hunan Agricultural University, Changsha, China
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An extreme-phenotype genome-wide association study identifies candidate cannabinoid pathway genes in Cannabis. Sci Rep 2020; 10:18643. [PMID: 33122674 PMCID: PMC7596533 DOI: 10.1038/s41598-020-75271-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
Cannabis produces a class of isoprenylated resorcinyl polyketides known as cannabinoids, a subset of which are medically important and exclusive to this plant. The cannabinoid alkyl group is a critical structural feature that governs therapeutic activity. Genetic enhancement of the alkyl side-chain could lead to the development of novel chemical phenotypes (chemotypes) for pharmaceutical end-use. However, the genetic determinants underlying in planta variation of cannabinoid alkyl side-chain length remain uncharacterised. Using a diversity panel derived from the Ecofibre Cannabis germplasm collection, an extreme-phenotype genome-wide association study (XP-GWAS) was used to enrich for alkyl cannabinoid polymorphic regions. Resequencing of chemotypically extreme pools revealed a known cannabinoid synthesis pathway locus as well as a series of chemotype-associated genomic regions. One of these regions contained a candidate gene encoding a β-keto acyl carrier protein (ACP) reductase (BKR) putatively associated with polyketide fatty acid starter unit synthesis and alkyl side-chain length. Association analysis revealed twenty-two polymorphic variants spanning the length of this gene, including two nonsynonymous substitutions. The success of this first reported application of XP-GWAS for an obligate outcrossing and highly heterozygote plant genus suggests that this approach may have generic application for other plant species.
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20
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Sun B, Zhou X, Chen C, Chen C, Chen K, Chen M, Liu S, Chen G, Cao B, Cao F, Lei J, Zhu Z. Coexpression network analysis reveals an MYB transcriptional activator involved in capsaicinoid biosynthesis in hot peppers. HORTICULTURE RESEARCH 2020; 7:162. [PMID: 33082969 PMCID: PMC7527512 DOI: 10.1038/s41438-020-00381-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/18/2020] [Accepted: 07/13/2020] [Indexed: 05/24/2023]
Abstract
Plant biosynthesis involves numerous specialized metabolites with diverse chemical natures and biological activities. The biosynthesis of metabolites often exclusively occurs in response to tissue-specific combinatorial developmental cues that are controlled at the transcriptional level. Capsaicinoids are a group of specialized metabolites that confer a pungent flavor to pepper fruits. Capsaicinoid biosynthesis occurs in the fruit placenta and combines its developmental cues. Although the capsaicinoid biosynthetic pathway has been largely characterized, the regulatory mechanisms that control capsaicinoid metabolism have not been fully elucidated. In this study, we combined fruit placenta transcriptome data with weighted gene coexpression network analysis (WGCNA) to generate coexpression networks. A capsaicinoid-related gene module was identified in which the MYB transcription factor CaMYB48 plays a critical role in regulating capsaicinoid in pepper. Capsaicinoid biosynthetic gene (CBG) and CaMYB48 expression primarily occurs in the placenta and is consistent with capsaicinoid biosynthesis. CaMYB48 encodes a nucleus-localized protein that primarily functions as a transcriptional activator through its C-terminal activation motif. CaMYB48 regulates capsaicinoid biosynthesis by directly regulating the expression of CBGs, including AT3a and KasIa. Taken together, the results of this study indicate ways to generate robust networks optimized for the mining of CBG-related regulators, establishing a foundation for future research elucidating capsaicinoid regulation.
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Affiliation(s)
- Binmei Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Xin Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Jiangxi Agricultural Engineering College, Zhangshu, 331200 Jiangxi China
| | - Changming Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Chengjie Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Kunhao Chen
- Guangdong Helinong Seeds, Co., Ltd., Shantou, 515800 Guangdong China
- Guangdong Helinong Agricultural Research Institute, Co., Ltd., Shantou, 515800 Guangdong China
| | - Muxi Chen
- Guangdong Helinong Seeds, Co., Ltd., Shantou, 515800 Guangdong China
- Guangdong Helinong Agricultural Research Institute, Co., Ltd., Shantou, 515800 Guangdong China
| | - Shaoqun Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Guoju Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Fanrong Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
| | - Jianjun Lei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Henry School of Agricultural Science and Engineering, Shaoguan University, Guangdong, 512005 China
| | - Zhangsheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642 China
- Peking University—Southern University of Science and Technology Joint Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055 China
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21
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Liu H, Hong Y, Lu Q, Li H, Gu J, Ren L, Deng L, Zhou B, Chen X, Liang X. Integrated Analysis of Comparative Lipidomics and Proteomics Reveals the Dynamic Changes of Lipid Molecular Species in High-Oleic Acid Peanut Seed. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:426-438. [PMID: 31855429 DOI: 10.1021/acs.jafc.9b04179] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Modern peanut contains fatty acid desaturase 2 (FAD2) mutation, which is capable of producing high oleic acid for human health. However, the dynamic changes of the lipidome regarding fad2 remain elusive in peanut seed. In the present study, 547 lipid features were identified in high- and normal-oleic peanut seeds by utilizing the mass spectrometric approach. The fad2-induced differently expressed lipids (DELs) were polarly distributed at early and maturation stages during high-oleic acid (OA) seed development. Subsequently, integration of previously published proteomic data and lipidomic data revealed that 21 proteins and 149 DELs were annotated into the triacylglycerol assembly map, of which nine enzymes and 31 lipid species shared similar variation tendencies. Additionally, the variation tendencies of 17 acyl fatty acids were described in a hypothetical biosynthetic pathway. Collectively, the understanding of the lipid composition correlated with fad2 established a foundation for future high-OA peanut breeding based on lipidomic data.
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Affiliation(s)
- Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement , Crops Research Institute, Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , China
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement , Crops Research Institute, Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , China
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement , Crops Research Institute, Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , China
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement , Crops Research Institute, Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , China
| | - Jianzhong Gu
- Peanut Research Institute , Kaifeng Academy of Agriculture and Forestry , Kaifeng 475004 , China
| | - Li Ren
- Peanut Research Institute , Kaifeng Academy of Agriculture and Forestry , Kaifeng 475004 , China
| | - Li Deng
- Peanut Research Institute , Kaifeng Academy of Agriculture and Forestry , Kaifeng 475004 , China
| | - Baojin Zhou
- Shenzhen Deepxomics Biotechnology Co. Ltd. , Shenzhen 518000 , China
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement , Crops Research Institute, Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , China
| | - Xuanqiang Liang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement , Crops Research Institute, Guangdong Academy of Agricultural Sciences , Guangzhou 510640 , China
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22
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Tanaka Y, Asano T, Kanemitsu Y, Goto T, Yoshida Y, Yasuba K, Misawa Y, Nakatani S, Kobata K. Positional differences of intronic transposons in pAMT affect the pungency level in chili pepper through altered splicing efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:693-705. [PMID: 31323150 DOI: 10.1111/tpj.14462] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Capsaicinoids are unique compounds that give chili pepper fruits their pungent taste. Capsaicinoid levels vary widely among pungent cultivars, which range from low pungency to extremely pungent. However, the molecular mechanisms underlying this quantitative variation have not been elucidated. Our previous study identified various loss-of-function alleles of the pAMT gene which led to low pungency. The mutations in these alleles are commonly defined by Tcc transposon insertion and its footprint. In this study, we identified two leaky pamt alleles (pamtL1 and pamtL2 ) with different levels of putative aminotransferase (pAMT) activity. Notably, both alleles had a Tcc transposon insertion in intron 3, but the locations of the insertions within the intron were different. Genetic analysis revealed that pamtL1 , pamtL2 and a loss-of-function pamt allele reduced capsaicinoid levels to about 50%, 10% and less than 1%, respectively. pamtL1 and pamtL2 encoded functional pAMT proteins, but they exhibited lower transcript levels than the functional type. RNA sequencing analysis showed that intronic transposons disrupted splicing in intron 3, which resulted in simultaneous expression of functional pAMT mRNA and non-functional splice variants containing partial sequences of Tcc. The non-functional splice variants were more dominant in pamtL2 than in pamtL1 . This suggested that the difference in position of the intronic transposons could alter splicing efficiency, leading to different pAMT activities and reducing capsaicinoid content to different levels. Our results provide a striking example of allelic variations caused by intronic transposons; these variations contribute to quantitative differences in secondary metabolite contents.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takaya Asano
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yorika Kanemitsu
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Tanjuro Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuichi Yoshida
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenichiro Yasuba
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Misawa
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Sachie Nakatani
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama, 350-0295, Japan
| | - Kenji Kobata
- Graduate School of Pharmaceutical Sciences, Josai University, 1-1 Keyakidai, Sakado, Saitama, 350-0295, Japan
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23
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Han K, Jang S, Lee JH, Lee DG, Kwon JK, Kang BC. A MYB transcription factor is a candidate to control pungency in Capsicum annuum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1235-1246. [PMID: 30607439 DOI: 10.1007/s00122-018-03275-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/22/2018] [Indexed: 05/13/2023]
Abstract
Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F2 plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.
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Affiliation(s)
- Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Siyoung Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Do-Gyeong Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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24
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Park M, Lee JH, Han K, Jang S, Han J, Lim JH, Jung JW, Kang BC. A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:515-529. [PMID: 30426173 DOI: 10.1007/s00122-018-3238-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/09/2018] [Indexed: 05/09/2023]
Abstract
A major QTL and candidate genes controlling capsaicinoid content in the pericarp were identified by QTL-seq and RNA-seq in Capsicum chinense. Capsaicinoid biosynthesis was previously thought to be restricted to the placental tissue; however, the recent discovery of their biosynthesis in the pericarp provides new opportunities to increase the capsaicinoid content in pepper fruits. Currently, the genetic mechanisms regulating capsaicinoid biosynthesis in the pericarp remain unknown. Here, we performed quantitative trait loci (QTL) mapping and RNA sequencing (RNA-seq) to reveal the genes controlling capsaicinoid biosynthesis in the pericarp. A whole-genome sequencing-based QTL-seq strategy was employed, identifying a major QTL on chromosome 6. To validate the QTL on chromosome 6, we performed traditional QTL mapping using the same population in QTL-seq with an additional biparental population. A total of 15 QTLs for capsaicinoid content distributed on chromosomes 3, 6, and 11 were newly identified. Among these QTLs, the genetic loci on the lower arm of chromosome 6 were commonly detected in the two mapping populations, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. Our RNA-seq analysis identified candidate genes within the common QTL that were differentially expressed in the pungent and non-pungent pericarp tissues. Our results are expected to contribute to the elucidation of the regulation of capsaicinoid biosynthesis. We also demonstrated that a combination of QTL mapping and RNA-seq is helpful for refining the candidate genes of a complicated trait of interest.
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Affiliation(s)
- Minjeong Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Siyoung Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jiwoong Han
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jung-Hyun Lim
- Research Institute of Biotechnology, CJ CheilJedang Corp., Suwon, 16495, Republic of Korea
| | - Ji-Won Jung
- Research Institute of Biotechnology, CJ CheilJedang Corp., Suwon, 16495, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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