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Ngo TH, Park J, Jo YD, Jin CH, Jung CH, Nam B, Han AR, Nam JW. Content of Two Major Steroidal Glycoalkaloids in Tomato ( Solanum lycopersicum cv. Micro-Tom) Mutant Lines at Different Ripening Stages. Plants (Basel) 2022; 11:2895. [PMID: 36365348 PMCID: PMC9654965 DOI: 10.3390/plants11212895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Esculeoside A and tomatine are two major steroidal alkaloids in tomato fruit (Solanum lycopersicum) that exhibit anti-inflammatory, anticancer, and anti-hyperlipidemia activities. Tomatine contained in immature tomato fruit is converted to esculeoside A as the fruit matures. To develop new tomato varieties based on the content analysis of functional secondary metabolites, 184 mutant lines were generated from the original cultivar (S. lycopersicum cv. Micro-Tom) by radiation breeding. Ultra-performance liquid chromatography coupled with evaporative light scattering detector was used to identify the mutant lines with good traits by analyzing tomatine and esculeoside A content. Compared with the original cultivar, candidates for highly functional cultivars with high esculeoside A content were identified in the mature fruit of the mutant lines. The mutant lines with low and high tomatine content at an immature stage were selected as edible cultivars due to toxicity reduction and as a source of tomatine with various pharmacological activities, respectively. During the process of ripening from green to red tomatoes, the rate of conversion of tomatine to esculeoside A was high in the green tomatoes with a low tomatine content, whereas green tomatoes with a high tomatine content exhibited a low conversion rate. Using methanol extracts prepared from unripe and ripe fruits of the original cultivar and its mutant lines and two major compounds, we examined their cytotoxicity against FaDu human hypopharynx squamous carcinoma cells. Only tomatine exhibited cytotoxicity with an IC50 value of 5.589 μM, whereas the other samples did not exhibit cytotoxicity. Therefore, radiation breeding represents a useful tool for developing new cultivars with high quality, and metabolite analysis is applicable for the rapid and objective selection of potential mutant lines.
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Affiliation(s)
- Trung Huy Ngo
- College of Pharmacy, Yeungnam University, Gyeongsan-si 38541, Gyeongsangbuk-do, Korea
| | - Jisu Park
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Jeollabuk-do, Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Jeollabuk-do, Korea
- College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Chungcheongnam-do, Korea
| | - Chang Hyun Jin
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Jeollabuk-do, Korea
| | - Chan-Hun Jung
- Jeonju AgroBio-Materials Institute, Jeonju-si 54810, Jeollabuk-do, Korea
| | - Bomi Nam
- Institute of Natural Cosmetic Industry for Namwon, Namwon-si 55801, Jeollabuk-do, Korea
| | - Ah-Reum Han
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Jeollabuk-do, Korea
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan-si 38541, Gyeongsangbuk-do, Korea
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Kim DG, Lyu JI, Kim JM, Seo JS, Choi HI, Jo YD, Kim SH, Eom SH, Ahn JW, Bae CH, Kwon SJ. Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool. Int J Mol Sci 2022; 23:ijms231810441. [PMID: 36142354 PMCID: PMC9499481 DOI: 10.3390/ijms231810441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
In this study, we performed a genotyping-by-sequencing analysis and a genome-wide association study of a soybean mutant diversity pool previously constructed by gamma irradiation. A GWAS was conducted to detect significant associations between 37,249 SNPs, 11 agronomic traits, and 6 phytochemical traits. In the merged data set, 66 SNPs on 13 chromosomes were highly associated (FDR p < 0.05) with the following 4 agronomic traits: days of flowering (33 SNPs), flower color (16 SNPs), node number (6 SNPs), and seed coat color (11 SNPs). These results are consistent with the findings of earlier studies on other genetic features (e.g., natural accessions and recombinant inbred lines). Therefore, our observations suggest that the genomic changes in the mutants generated by gamma irradiation occurred at the same loci as the mutations in the natural soybean population. These findings are indicative of the existence of mutation hotspots, or the acceleration of genome evolution in response to high doses of radiation. Moreover, this study demonstrated that the integration of GBS and GWAS to investigate a mutant population derived from gamma irradiation is suitable for dissecting the molecular basis of complex traits in soybeans.
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Affiliation(s)
- Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
| | - Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
- Research Center of Crop Breeding for Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea
| | - Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
| | - Yeong Deuk Jo
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, Institute of Life Sciences & Resources, Kyung Hee University, Yongin 17104, Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
| | - Chang-Hyu Bae
- Department of Life Resources, Graduate School, Sunchon National University, Suncheon 57922, Korea
- Correspondence: (C.-H.B.); (S.-J.K.)
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup 56212, Korea
- Correspondence: (C.-H.B.); (S.-J.K.)
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Kang MC, Kang HJ, Jung SY, Lee HY, Kang MY, Jo YD, Kang BC. The Unstable Restorer-of-fertility locus in pepper (Capsicum annuum. L) is delimited to a genomic region containing PPR genes. Theor Appl Genet 2022; 135:1923-1937. [PMID: 35357525 DOI: 10.1007/s00122-022-04084-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Unstable Restorer-of-fertility (Rfu), conferring unstable fertility restoration in the pepper CGMS system, was delimited to a genomic region near Rf and is syntenic to the PPR-like gene-rich region in tomato. The use of cytoplasmic-genic male sterility (CGMS) systems greatly increases the efficiency of hybrid seed production. Although marker development and candidate gene isolation have been performed for the Restorer-of-fertility (Rf) gene in pepper (Capsicum annuum L.), the broad use of CGMS systems has been hampered by the instability of fertility restoration among pepper accessions, especially sweet peppers, due to the widespread presence of the Unstable Restorer-of-fertility (Rfu) locus. Therefore, to investigate the genetic factors controlling unstable fertility restoration in sweet peppers, we developed a segregation population (BC4F5) from crosses using a male-sterile line and an Rfu-containing line. Segregation did not significantly deviate from a 3:1 ratio for unstable fertility restoration to sterility, indicating single dominant locus control for unstable fertility restoration in this population. Genetic mapping delimited the Rfu locus to a 398 kb genomic region on chromosome 6, which is close to but different from the previously identified Rf-containing region. The Rfu-containing region harbors a pentatricopeptide repeat (PPR) gene, along with 10 other candidate genes. In addition, this region is syntenic to the genomic region containing the largest number of Rf-like PPR genes in tomato. Therefore, the dynamic evolution of PPR genes might be responsible for both the restoration and instability of fertility in pepper. During genetic mapping, we developed various molecular markers, including one that co-segregated with Rfu. These markers showed higher accuracy for genotyping than previously developed markers, pointing to their possible use in marker-assisted breeding of sweet peppers.
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Affiliation(s)
- Moo Chan Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hwa-Jeong Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - So-Young Jung
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hae-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min-Young Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Chang S, Lee U, Hong MJ, Jo YD, Kim JB. Time-Series Growth Prediction Model Based on U-Net and Machine Learning in Arabidopsis. Front Plant Sci 2021; 12:721512. [PMID: 34858446 PMCID: PMC8631871 DOI: 10.3389/fpls.2021.721512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Yield prediction for crops is essential information for food security. A high-throughput phenotyping platform (HTPP) generates the data of the complete life cycle of a plant. However, the data are rarely used for yield prediction because of the lack of quality image analysis methods, yield data associated with HTPP, and the time-series analysis method for yield prediction. To overcome limitations, this study employed multiple deep learning (DL) networks to extract high-quality HTTP data, establish an association between HTTP data and the yield performance of crops, and select essential time intervals using machine learning (ML). The images of Arabidopsis were taken 12 times under environmentally controlled HTPP over 23 days after sowing (DAS). First, the features from images were extracted using DL network U-Net with SE-ResXt101 encoder and divided into early (15-21 DAS) and late (∼21-23 DAS) pre-flowering developmental stages using the physiological characteristics of the Arabidopsis plant. Second, the late pre-flowering stage at 23 DAS can be predicted using the ML algorithm XGBoost, based only on a portion of the early pre-flowering stage (17-21 DAS). This was confirmed using an additional biological experiment (P < 0.01). Finally, the projected area (PA) was estimated into fresh weight (FW), and the correlation coefficient between FW and predicted FW was calculated as 0.85. This was the first study that analyzed time-series data to predict the FW of related but different developmental stages and predict the PA. The results of this study were informative and enabled the understanding of the FW of Arabidopsis or yield of leafy plants and total biomass consumed in vertical farming. Moreover, this study highlighted the reduction of time-series data for examining interesting traits and future application of time-series analysis in various HTPPs.
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Affiliation(s)
- Sungyul Chang
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup-si, South Korea
| | - Unseok Lee
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung-si, South Korea
| | - Min Jeong Hong
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup-si, South Korea
| | - Yeong Deuk Jo
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup-si, South Korea
| | - Jin-Baek Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup-si, South Korea
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Kim SH, Kim SY, Ryu J, Jo YD, Choi HI, Kim JB, Kang SY. Suggested doses of proton ions and gamma-rays for mutation induction in 20 plant species. Int J Radiat Biol 2021; 97:1624-1629. [PMID: 34402731 DOI: 10.1080/09553002.2021.1969053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE Proton ions are expected to be used as a discriminative radiation source to induce different kinds of mutations than those produced by γ-rays and carbon ions; however, there is little systemic information about radiosensitivity in plants. MATERIALS AND METHODS We analyzed the LD30, LD50, and RD50 values in response to proton ions and γ-rays using 20 plant species. Plant seeds were irradiated, and growth responses were measured one month after planting, except for cymbidium, for which in vitro rhizomes were irradiated. The rhizomes were analyzed at six and nine months after subculturing. RESULTS Resistance to proton ions and γ-rays was observed in Chinese cabbage, watermelon, and melon, while Japanese atractylodes, naked barley, and lentil were susceptible. Plants belonging to the Brassicaceae and Cucurbitaceae families were highly resistant to radiation, and plants belonging to the Compositae and Poaceae families were highly susceptible. In addition, plants with genome sizes greater than 8,000 Mbp were highly sensitive to radiation, but there was no clear relationship between radiosensitivity and genome size in plants with genomes smaller than 2,500 Mbp. CONCLUSIONS The biological effectiveness of proton ions was greater than that of γ-rays in 16 plant species, indicating that they could be used as a discriminative radiation source to induce mutations compared with γ-rays.
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Affiliation(s)
- Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sun Young Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea.,Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
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Choi HI, Han SM, Jo YD, Hong MJ, Kim SH, Kim JB. Effects of Acute and Chronic Gamma Irradiation on the Cell Biology and Physiology of Rice Plants. Plants (Basel) 2021; 10:439. [PMID: 33669039 PMCID: PMC7996542 DOI: 10.3390/plants10030439] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 11/23/2022]
Abstract
The response to gamma irradiation varies among plant species and is affected by the total irradiation dose and dose rate. In this study, we examined the immediate and ensuing responses to acute and chronic gamma irradiation in rice (Oryza sativa L.). Rice plants at the tillering stage were exposed to gamma rays for 8 h (acute irradiation) or 10 days (chronic irradiation), with a total irradiation dose of 100, 200, or 300 Gy. Plants exposed to gamma irradiation were then analyzed for DNA damage, oxidative stress indicators including free radical content and lipid peroxidation, radical scavenging, and antioxidant activity. The results showed that all stress indices increased immediately after exposure to both acute and chronic irradiation in a dose-dependent manner, and acute irradiation had a greater effect on plants than chronic irradiation. The photosynthetic efficiency and growth of plants measured at 10, 20, and 30 days post-irradiation decreased in irradiated plants, i.e., these two parameters were more severely affected by acute irradiation than by chronic irradiation. In contrast, acutely irradiated plants produced seeds with dramatically decreased fertility rate, and chronically irradiated plants failed to produce fertile seeds, i.e., reproduction was more severely affected by chronic irradiation than by acute irradiation. Overall, our findings suggest that acute gamma irradiation causes instantaneous and greater damage to plant physiology, whereas chronic gamma irradiation causes long-term damage, leading to reproductive failure.
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Affiliation(s)
- Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (H.-I.C.); (Y.D.J.); (M.J.H.); (S.H.K.)
| | - Sung Min Han
- Division of Ecological Safety, National Institute of Ecology, Seocheon 33657, Korea;
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (H.-I.C.); (Y.D.J.); (M.J.H.); (S.H.K.)
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (H.-I.C.); (Y.D.J.); (M.J.H.); (S.H.K.)
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (H.-I.C.); (Y.D.J.); (M.J.H.); (S.H.K.)
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (H.-I.C.); (Y.D.J.); (M.J.H.); (S.H.K.)
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Lee SW, Kwon YJ, Baek I, Choi HI, Ahn JW, Kim JB, Kang SY, Kim SH, Jo YD. Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis. Front Plant Sci 2021; 12:752108. [PMID: 34777430 PMCID: PMC8581144 DOI: 10.3389/fpls.2021.752108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 05/19/2023]
Abstract
Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.
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Affiliation(s)
- Sang Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Yu-Jeong Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Department of Horticulture, Chonbuk National University, Jeonju-si, South Korea
| | - Inwoo Baek
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Si-Yong Kang
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- *Correspondence: Yeong Deuk Jo,
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Ryu J, Lyu JI, Kim DG, Kim JM, Jo YD, Kang SY, Kim JB, Ahn JW, Kim SH. Comparative Analysis of Volatile Compounds of Gamma-Irradiated Mutants of Rose ( Rosa hybrida). Plants (Basel) 2020; 9:plants9091221. [PMID: 32957603 PMCID: PMC7569881 DOI: 10.3390/plants9091221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 11/17/2022]
Abstract
Roses are one of the most important floricultural crops, and their essential oils have long been used for cosmetics and aromatherapy. We investigated the volatile compound compositions of 12 flower-color mutant variants and their original cultivars. Twelve rose mutant genotypes were developed by treatment with 70 Gy of 60Co gamma irradiation of six commercial rose cultivars. Essential oils from the flowers of the 18 genotypes were analyzed by gas chromatography–mass spectrometry. Seventy-seven volatile compounds were detected, which were categorized into six classes: Aliphatic hydrocarbons, aliphatic alcohols, aliphatic ester, aromatic compounds, terpene alcohols, and others. Aliphatic (hydrocarbons, alcohols, and esters) compounds were abundant categories in all rose flowers. The CR-S2 mutant had the highest terpene alcohols and oil content. Three (CR-S1, CR-S3, and CR-S4) mutant genotypes showed higher ester contents than their original cultivar. Nonacosane, 2-methylhexacosane, and 2-methyltricosane were major volatile compounds among all genotypes. Hierarchical cluster analysis (HCA) of the rose genotypes gave four groups according to grouping among the 77 volatile compounds. In addition, the principal component analysis (PCA) model was successfully applied to distinguish most attractive rose lines. These findings will be useful for the selection of rose genotypes with improved volatile compounds.
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Affiliation(s)
- Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Dong-Gun Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Jung-Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Si-Yong Kang
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea;
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do 56212, Korea; (J.R.); (J.I.L.); (D.-G.K.); (J.-M.K.); (Y.D.J.); (J.-B.K.); (J.-W.A.)
- Correspondence: ; Tel.: +82-63-570-3318
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Lee SI, Park JW, Kwon SJ, Jo YD, Hong MJ, Kim JB, Choi HI. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. Plants (Basel) 2020; 9:plants9091088. [PMID: 32847097 PMCID: PMC7570246 DOI: 10.3390/plants9091088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.
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Jo YD, Ryu J, Kim YS, Kang KY, Hong MJ, Choi HI, Lim GH, Kim JB, Kim SH. Dramatic Increase in Content of Diverse Flavonoids Accompanied with Down-Regulation of F-Box Genes in a Chrysanthemum ( Chrysanthemum × morifolium (Ramat.) Hemsl.) Mutant Cultivar Producing Dark-Purple Ray Florets. Genes (Basel) 2020; 11:E865. [PMID: 32751443 PMCID: PMC7464468 DOI: 10.3390/genes11080865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Anthocyanins (a subclass of flavonoids) and flavonoids are crucial determinants of flower color and substances of pharmacological efficacy, respectively, in chrysanthemum. However, metabolic and transcriptomic profiling regarding flavonoid accumulation has not been performed simultaneously, thus the understanding of mechanisms gained has been limited. We performed HPLC-DAD-ESI-MS (high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization mass spectrometry) and transcriptome analyses using "ARTI-Dark Chocolate" (AD), which is a chrysanthemum mutant cultivar producing dark-purple ray florets, and the parental cultivar "Noble Wine" for metabolic characterization and elucidation of the genetic mechanism determining flavonoid content. Among 26 phenolic compounds identified, three cyanidins and eight other flavonoids were detected only in AD. The total amounts of diverse flavonoids were 8.0 to 10.3 times higher in AD. Transcriptome analysis showed that genes in the flavonoid biosynthetic pathway were not up-regulated in AD at the early flower stage, implying that the transcriptional regulation of the pathway did not cause flavonoid accumulation. However, genes encoding post-translational regulation-related proteins, especially F-box genes in the mutated gene, were enriched among down-regulated genes in AD. From the combination of metabolic and transcriptomic data, we suggest that the suppression of post-translational regulation is a possible mechanism for flavonoid accumulation in AD. These results will contribute to research on the regulation and manipulation of flavonoid biosynthesis in chrysanthemum.
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Affiliation(s)
- Yeong Deuk Jo
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Jaihyunk Ryu
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Ye-Sol Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Kyung-Yun Kang
- Suncheon Research Center for Natural Medicines, Suncheon 57922, Korea;
| | - Min Jeong Hong
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Hong-Il Choi
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Gah-Hyun Lim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Jin-Baek Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
| | - Sang Hoon Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea; (Y.D.J.); (J.R.); (Y.-S.K.); (M.J.H.); (H.-I.C.); (G.-H.L.); (J.-B.K.)
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Chang S, Lee U, Hong MJ, Jo YD, Kim JB. High-Throughput Phenotyping (HTP) Data Reveal Dosage Effect at Growth Stages in Arabidopsis thaliana Irradiated by Gamma Rays. Plants (Basel) 2020; 9:E557. [PMID: 32349236 PMCID: PMC7284948 DOI: 10.3390/plants9050557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 01/25/2023]
Abstract
The effects of radiation dosages on plant species are quantitatively presented as the lethal dose or the dose required for growth reduction in mutation breeding. However, lethal dose and growth reduction fail to provide dynamic growth behavior information such as growth rate after irradiation. Irradiated seeds of Arabidopsis were grown in an environmentally controlled high-throughput phenotyping (HTP) platform to capture growth images that were analyzed with machine learning algorithms. Analysis of digital phenotyping data revealed unique growth patterns following treatments below LD50 value at 641 Gy. Plants treated with 100-Gy gamma irradiation showed almost identical growth pattern compared with wild type; the hormesis effect was observed >21 days after sowing. In 200 Gy-treated plants, a uniform growth pattern but smaller rosette areas than the wild type were seen (p < 0.05). The shift between vegetative and reproductive stages was not retarded by irradiation at 200 and 300 Gy although growth inhibition was detected under the same irradiation dose. Results were validated using 200 and 300 Gy doses with HTP in a separate study. To our knowledge, this is the first study to apply a HTP platform to measure and analyze the dosage effect of radiation in plants. The method enabled an in-depth analysis of growth patterns, which could not be detected previously due to a lack of time-series data. This information will improve our knowledge about the effects of radiation in model plant species and crops.
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Affiliation(s)
- Sungyul Chang
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea; (S.C.); (M.J.H.)
| | - Unseok Lee
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), 679 Saimdang-ro, Gangneung, Gangwon-do 210-340, Korea;
| | - Min Jeong Hong
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea; (S.C.); (M.J.H.)
| | - Yeong Deuk Jo
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea; (S.C.); (M.J.H.)
| | - Jin-Baek Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea; (S.C.); (M.J.H.)
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12
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Kim SH, Kim SW, Lim GH, Lyu JI, Choi HI, Jo YD, Kang SY, Kang BC, Kim JB. Transcriptome analysis to identify candidate genes associated with the yellow-leaf phenotype of a Cymbidium mutant generated by γ-irradiation. PLoS One 2020; 15:e0228078. [PMID: 31995594 PMCID: PMC6988911 DOI: 10.1371/journal.pone.0228078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/07/2020] [Indexed: 11/23/2022] Open
Abstract
Leaf color is an important agronomic trait in flowering plants, including orchids. However, factors underlying leaf phenotypes in plants remain largely unclear. A mutant displaying yellow leaves was obtained by the γ-ray-based mutagenesis of a Cymbidium orchid and characterized using RNA sequencing. A total of 144,918 unigenes obtained from over 25 million reads were assigned to 22 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, gene ontology was used to classify the predicted functions of transcripts into 73 functional groups. The RNA sequencing analysis identified 2,267 differentially expressed genes between wild-type and mutant Cymbidium sp. Genes involved in the chlorophyll biosynthesis and degradation, as well as ion transport, were identified and assayed for their expression levels in wild-type and mutant plants using quantitative real-time profiling. No critical expression changes were detected in genes involved in chlorophyll biosynthesis. In contrast, seven genes involved in ion transport, including two metal ion transporters, were down-regulated, and chlorophyllase 2, associated with chlorophyll degradation, was up-regulated. Together, these results suggest that alterations in chlorophyll metabolism and/or ion transport might contribute to leaf color in Cymbidium orchids.
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Affiliation(s)
- Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Se Won Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Gah-Hyun Lim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jae Il Lyu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 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, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
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Kim SH, Jo YD, Ryu J, Hong MJ, Kang BC, Kim JB. Effects of the total dose and duration of γ-irradiation on the growth responses and induced SNPs of a Cymbidium hybrid. Int J Radiat Biol 2019; 96:545-551. [PMID: 31852368 DOI: 10.1080/09553002.2020.1704303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose: Ionizing radiation has been used for developing new cultivars of diverse plant species, including Cymbidium orchid species. The effects of the total dose on mutation induction have been investigated; however, there is relatively little research on the influence of the dose rate or irradiation duration.Materials and methods: Thus, we analyzed the effects of the total dose and irradiation duration on the growth of Cymbidium hybrid RB001 protocorm-like bodies (PLBs). We completed a genotyping-by-sequencing analysis to compare the induced SNPs among five γ-irradiated populations with similar growth responses (LD50) to γ-rays.Results: The optimal time to assess the effects of the γ-irradiation was at 6 months after the treatment. On the basis of the survival rate of γ-irradiated PLBs, the optimal doses (LD50) for each irradiation duration were estimated: 1 h, 16.1 Gy; 4 h, 23.6 Gy; 8 h, 37.9 Gy; 16 h, 37.9 Gy; and 24 h, 40.0 Gy. The estimated optimal doses were duration-dependent at irradiation durations shorter than 8 h, but not at irradiation durations exceeding 8 h. A SNP comparison revealed a lack of significant differences among the mutations induced by γ-irradiations.Conclusions: These results indicate the irradiation duration affects PLB growth in response to γ-rays. Moreover, the mutations induced by a short-term treatment may be similar to those induced by a treatment over a longer period.
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Affiliation(s)
- Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 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, Republic of Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
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Jo YD, Lee HY, Ro NY, Kim SH, Kim JB, Kang BC, Kang SY. Mitotypes Based on Structural Variation of Mitochondrial Genomes Imply Relationships With Morphological Phenotypes and Cytoplasmic Male Sterility in Peppers. Front Plant Sci 2019; 10:1343. [PMID: 31708952 PMCID: PMC6822277 DOI: 10.3389/fpls.2019.01343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Plant mitochondrial genomes characteristically contain extensive structural variation that can be used to define and classify cytoplasm types. We developed markers based on structural variation in the mitochondrial genomes of fertile and cytoplasmic male sterility (CMS) pepper lines and applied them to a panel of Capsicum accessions. We designed a total of 20 sequence characterized amplified region (SCAR) markers based on DNA rearrangement junctions or cytoplasm-specific segments that did not show high similarity to any nuclear mitochondrial DNA segments. We used those markers to classify the mitotypes of 96 C. annuum accessions into 15 groups. Precise genotyping of other Capsicum species (C. frutescens, C. chinense, and C. baccatum) was hampered because of various stoichiometric levels of marker amplicons. We developed a multiplex PCR system based on four of the markers that efficiently classified the C. annuum accessions into five mitotype groups. Close relationships between specific mitotypes and morphological phenotypes implied that diversification or domestication of C. annuum germplasm might have been accompanied by structural rearrangements of mitochondrial DNA or the selection of germplasms with specific mitotypes. Meanwhile, CMS lines shared the same amplification profile of markers with another mitotype. Further analysis using mitochondrial DNA (mtDNA) markers based on single-nucleotide polymorphisms (SNPs) or insertions and deletions (InDels) and CMS-specific open reading frames (orfs) provided new information about the origin of the CMS-specific mitotype and evaluation of candidates for CMS-associated genes, respectively.
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Affiliation(s)
- Yeong Deuk Jo
- Radiation Breeding Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Hea-Young Lee
- Department of Plant Science and Vegetable Breeding Research Center, Seoul National University, Seoul, South Korea
| | - Na-Young Ro
- National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Sang Hoon Kim
- Radiation Breeding Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Jin-Baek Kim
- Radiation Breeding Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science and Vegetable Breeding Research Center, Seoul National University, Seoul, South Korea
| | - Si-Yong Kang
- Radiation Breeding Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, South Korea
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15
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Kim JH, Jo YD, Jin CH. Isolation of soluble epoxide hydrolase inhibitor of capsaicin analogs from Capsicum chinense Jacq. cv. Habanero. Int J Biol Macromol 2019; 135:1202-1207. [DOI: 10.1016/j.ijbiomac.2019.06.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 12/16/2022]
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Affiliation(s)
- Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Ye-Sol Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Hyo-Jeong Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
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Ryu J, Kwon SJ, Ahn JW, Jo YD, Kim SH, Jeong SW, Lee MK, Kim JB, Kang SY. Phytochemicals and antioxidant activity in the kenaf plant (Hibiscus cannabinus L.). ACTA ACUST UNITED AC 2017. [DOI: 10.5010/jpb.2017.44.2.191] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jaihyunk Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Sang Wook Jeong
- Jangheung Research Institute for Mushroom Industry, Jangheung 59338, Korea
| | - Min Kyu Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, Jeonbuk 56212, Korea
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Kim SB, Kang WH, Huy HN, Yeom SI, An JT, Kim S, Kang MY, Kim HJ, Jo YD, Ha Y, Choi D, Kang BC. Divergent evolution of multiple virus-resistance genes from a progenitor in Capsicum spp. New Phytol 2017; 213:886-899. [PMID: 27612097 DOI: 10.1111/nph.14177] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/31/2016] [Indexed: 05/11/2023]
Abstract
Plants have evolved hundreds of nucleotide-binding and leucine-rich domain proteins (NLRs) as potential intracellular immune receptors, but the evolutionary mechanism leading to the ability to recognize specific pathogen effectors is elusive. Here, we cloned Pvr4 (a Potyvirus resistance gene in Capsicum annuum) and Tsw (a Tomato spotted wilt virus resistance gene in Capsicum chinense) via a genome-based approach using independent segregating populations. The genes both encode typical NLRs and are located at the same locus on pepper chromosome 10. Despite the fact that these two genes recognize completely different viral effectors, the genomic structures and coding sequences of the two genes are strikingly similar. Phylogenetic studies revealed that these two immune receptors diverged from a progenitor gene of a common ancestor. Our results suggest that sequence variations caused by gene duplication and neofunctionalization may underlie the evolution of the ability to specifically recognize different effectors. These findings thereby provide insight into the divergent evolution of plant immune receptors.
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Affiliation(s)
- Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Won-Hee Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Hoang Ngoc Huy
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Seon-In Yeom
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Jeong-Tak An
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Min-Young Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Hyun Jung Kim
- Department of Eco-Friendly Horticulture, Cheonan Yonam College, Cheonan, 331-709, Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Yeaseong Ha
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
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Jo YD, Ha Y, Lee JH, Park M, Bergsma AC, Choi HI, Goritschnig S, Kloosterman B, van Dijk PJ, Choi D, Kang BC. Fine mapping of Restorer-of-fertility in pepper (Capsicum annuum L.) identified a candidate gene encoding a pentatricopeptide repeat (PPR)-containing protein. Theor Appl Genet 2016; 129:2003-17. [PMID: 27470425 DOI: 10.1007/s00122-016-2755-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/15/2016] [Indexed: 05/24/2023]
Abstract
Using fine mapping techniques, the genomic region co-segregating with Restorer - of - fertility ( Rf ) in pepper was delimited to a region of 821 kb in length. A PPR gene in this region, CaPPR6 , was identified as a strong candidate for Rf based on expression pattern and characteristics of encoding sequence. Cytoplasmic-genic male sterility (CGMS) has been used for the efficient production of hybrid seeds in peppers (Capsicum annuum L.). Although the mitochondrial candidate genes that might be responsible for cytoplasmic male sterility (CMS) have been identified, the nuclear Restorer-of-fertility (Rf) gene has not been isolated. To identify the genomic region co-segregating with Rf in pepper, we performed fine mapping using an Rf-segregating population consisting of 1068 F2 individuals, based on BSA-AFLP and a comparative mapping approach. Through six cycles of chromosome walking, the co-segregating region harboring the Rf locus was delimited to be within 821 kb of sequence. Prediction of expressed genes in this region based on transcription analysis revealed four candidate genes. Among these, CaPPR6 encodes a pentatricopeptide repeat (PPR) protein with PPR motifs that are repeated 14 times. Characterization of the CaPPR6 protein sequence, based on alignment with other homologs, showed that CaPPR6 is a typical Rf-like (RFL) gene reported to have undergone diversifying selection during evolution. A marker developed from a sequence near CaPPR6 showed a higher prediction rate of the Rf phenotype than those of previously developed markers when applied to a panel of breeding lines of diverse origin. These results suggest that CaPPR6 is a strong candidate for the Rf gene in pepper.
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Affiliation(s)
- Yeong Deuk Jo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | - Yeaseong Ha
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea
| | - Minkyu Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea
| | | | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Republic of Korea
| | | | | | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro, Gwank-gu, Seoul, 151-921, Korea.
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Im SB, Kwon SJ, Ryu J, Jeong SW, Kim JB, Ahn JW, Kim SH, Jo YD, Choi HI, Kang SY. Development of a transposon-based marker system for mutation breeding in sorghum (Sorghum bicolor L.). Genet Mol Res 2016; 15:gmr8713. [PMID: 27706735 DOI: 10.4238/gmr.15038713] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Under certain circumstances, transposable elements (TE) can create or reverse mutations and alter the genome size of a cell. Sorghum (Sorghum bicolor L.) is promising for plant transposon tagging due to its small genome size and its low content of repetitive DNA. We developed a marker system based on targeted region amplification polymorphisms (TE-TRAP) that uses the terminal inverted repeats (TIRs) of transposons. A total of 3816 class 2 transposons belonging to the PIF/Harbinger family were identified from the whole sorghum genome that produced five primers, including eight types of TIRs. To define the applicability and utilization of TE-TRAP, we used 21 individuals that had been bred after ɤ-ray irradiation. In total, 31 TE-TRAP, 16 TD, and 21 AFLP primer combinations generated 1133, 223, and 555 amplicons, respectively. The percent polymorphic marker was 62.8, 51.1, and 59.3% for the TE-TRAP, TD, and AFLP markers, respectively. Phylogenetic and principal component analyses revealed that TE-TRAP divided the 21 individuals into three groups. Analysis of molecular variance suggested that TE-TRAP had a higher level of genetic diversity than the other two marker systems. After verifying the efficiency of TE-TRAP, 189 sorghum individuals were used to investigate the associations between the markers and the ɤ-ray doses. Two significant associations were found among the polymorphic markers. This TE-based method provides a useful marker resource for mutation breeding research.
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Affiliation(s)
- S B Im
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - S-J Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea .,Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Daejeon, Korea
| | - J Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - S W Jeong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - J B Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - J-W Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea.,Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Daejeon, Korea
| | - S H Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Y D Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - H-I Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - S-Y Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
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21
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Liu L, Venkatesh J, Jo YD, Koeda S, Hosokawa M, Kang JH, Goritschnig S, Kang BC. Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense). Theor Appl Genet 2016; 129:1541-56. [PMID: 27147070 DOI: 10.1007/s00122-016-2723-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/22/2016] [Indexed: 05/24/2023]
Abstract
The sy - 2 temperature-sensitive gene from Capsicum chinense was fine mapped to a 138.8-kb region at the distal portion of pepper chromosome 1. Based on expression analyses, two putative F-box genes were identified as sy - 2 candidate genes. Seychelles-2 ('sy-2') is a temperature-sensitive natural mutant of Capsicum chinense, which exhibits an abnormal leaf phenotype when grown at temperatures below 24 °C. We previously showed that the sy-2 phenotype is controlled by a single recessive gene, sy-2, located on pepper chromosome 1. In this study, a high-resolution genetic and physical map for the sy-2 locus was constructed using two individual F2 mapping populations derived from a cross between C. chinense mutant 'sy-2' and wild-type 'No. 3341'. The sy-2 gene was fine mapped to a 138.8-kb region between markers SNP 5-5 and SNP 3-8 at the distal portion of chromosome 1, based on comparative genomic analysis and genomic information from pepper. The sy-2 target region was predicted to contain 27 genes. Expression analysis of these predicted genes showed a differential expression pattern for ORF10 and ORF20 between mutant and wild-type plants; with both having significantly lower expression in 'sy-2' than in wild-type plants. In addition, the coding sequences of both ORF10 and ORF20 contained single nucleotide polymorphisms (SNPs) causing amino acid changes, which may have important functional consequences. ORF10 and ORF20 are predicted to encode F-box proteins, which are components of the SCF complex. Based on the differential expression pattern and the presence of nonsynonymous SNPs, we suggest that these two putative F-box genes are most likely responsible for the temperature-sensitive phenotypes in pepper. Further investigation of these genes may enable a better understanding of the molecular mechanisms of low temperature sensitivity in plants.
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Affiliation(s)
- Li Liu
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
| | - Jelli Venkatesh
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
| | - Yeong Deuk Jo
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
| | - Sota Koeda
- Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Munetaka Hosokawa
- Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Jin-Ho Kang
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Korea
| | | | - Byoung-Cheorl Kang
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea.
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22
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Ryu J, Kwon SJ, Jo YD, Jin CH, Nam BM, Lee SY, Jeong SW, Im SB, Oh SC, Cho L, Ha BK, Kang SY. Comparison of Phytochemicals and Antioxidant Activity in Blackberry (Rubus fruticosus L.) Fruits of Mutant Lines at the Different Harvest Time. ACTA ACUST UNITED AC 2016. [DOI: 10.9787/pbb.2016.4.2.242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Jo YD, Choi Y, Kim DH, Kim BD, Kang BC. Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing. BMC Genomics 2014; 15:561. [PMID: 24996600 PMCID: PMC4108787 DOI: 10.1186/1471-2164-15-561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/20/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. RESULTS We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. CONCLUSIONS Although large portion of sequence context was shared by mitochondrial genomes of CMS and male-fertile pepper lines, extensive genome rearrangements were detected. CMS candidate genes located on the edges of highly-rearranged CMS-specific DNA regions and near to repeat sequences. These characteristics were detected among CMS-associated genes in other species, implying a common mechanism might be involved in the evolution of CMS-associated genes.
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Affiliation(s)
- Yeong Deuk Jo
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
- />Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185 South Korea
| | - Yoomi Choi
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
| | - Dong-Hwan Kim
- />Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Byung-Dong Kim
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
| | - Byoung-Cheorl Kang
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
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24
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Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JKC, Sørensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 2014; 46:270-8. [PMID: 24441736 DOI: 10.1038/ng.2877] [Citation(s) in RCA: 534] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/30/2013] [Indexed: 12/12/2022]
Abstract
Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.
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Affiliation(s)
- Seungill Kim
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Minkyu Park
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Seon-In Yeom
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Yong-Min Kim
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Je Min Lee
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3]
| | - Hyun-Ah Lee
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Eunyoung Seo
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2]
| | - Jaeyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyeongchae Cheong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyongyong Jung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gir-Won Lee
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
| | - Sang-Keun Oh
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Chungyun Bae
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Saet-Byul Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hye-Young Lee
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Shin-Young Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Myung-Shin Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Byoung-Cheorl Kang
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3] Vegetable Breeding Research Center, Seoul National University, Seoul, Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hee-Bum Yang
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Hee-Jin Jeong
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Won-Hee Kang
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Jin-Kyung Kwon
- Vegetable Breeding Research Center, Seoul National University, Seoul, Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - June-Sik Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Byung-Dong Kim
- Department of Plant Science, Seoul National University, Seoul, Korea
| | - Oded Cohen
- Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel
| | - Ilan Paran
- Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
| | - Saet Buyl Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea
| | - Yeon-Ki Kim
- Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Korea
| | | | | | | | - Young Sam Seo
- Ginseng Resources Research Laboratory, Korea Ginseng Corporation, Daejeon, Korea
| | - Suk-Yoon Kwon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun A Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Jeong Mee Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea
| | - Paul W Bosland
- 1] Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA. [2] Chile Pepper Institute, New Mexico State University, Las Cruces, New Mexico, USA
| | - Gregory Reeves
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA
| | | | | | - Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hee-Seung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Min-Soo Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA
| | - Yang Do Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Beom-Seok Park
- Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea
| | - Allen van Deynze
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, Davis, California, USA
| | - Woo Taek Kim
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Hee Kyung Ahn
- Department of Systems Biology, Yonsei University, Seoul, Korea
| | - Inhwa Yeam
- Department of Horticulture and Breeding, Andong National University, Andong, Korea
| | - James J Giovannoni
- 1] US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, USA. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Sang-Jik Lee
- Biotechnology Institute, Nongwoo Bio, Yeoju, Korea
| | - Ryan W Kim
- Genome Center, University of California, Davis, Davis, California, USA
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Jong-Sung Lim
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Doil Choi
- 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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25
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Li J, Pandeya D, Jo YD, Liu WY, Kang BC. Reduced activity of ATP synthase in mitochondria causes cytoplasmic male sterility in chili pepper. Planta 2013; 237:1097-109. [PMID: 23274393 DOI: 10.1007/s00425-012-1824-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/22/2012] [Indexed: 05/05/2023]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait characterized by the inability to produce functional pollen. The CMS-associated protein Orf507 (reported as Orf456 in previous researches) was previously identified as a candidate gene for mediating male sterility in pepper. Here, we performed yeast two-hybrid analysis to screen for interacting proteins, and found that the ATP synthase 6 kDa subunit containing a mitochondrial signal peptide (MtATP6) specifically interacted with Orf507. In addition, the two proteins were found to be interacted in vivo using bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays. Further functional characterization of Orf507 revealed that the encoded protein is toxic to bacterial cells. Analysis of tissue-specific expression of ATP synthase 6 kDa showed that the transcription level was much lower in anthers of the CMS line than in their wild type counterparts. In CMS plants, ATP synthase activity and content were reduced by more than half compared to that of the normal plants. Taken together, it can be concluded that reduced ATP synthase activity and ATP content might have affected pollen development in CMS plants. Here, we hypothesize that Orf507 might cause MtATP6 to be nonfunctional by changing the latter's conformation or producing an inhibitor that prevents the normal functioning of MtATP6. Thus, further functional analysis of mitochondrial Orf507 will provide insights into the mechanisms underlying CMS in plants.
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Affiliation(s)
- Jinjie Li
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, Republic of Korea
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26
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Jo YD, Park J, Kim J, Song W, Hur CG, Lee YH, Kang BC. Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep 2011; 30:217-29. [PMID: 20978766 DOI: 10.1007/s00299-010-0929-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 09/18/2010] [Accepted: 10/01/2010] [Indexed: 05/06/2023]
Abstract
Plants in the family Solanaceae are used as model systems in comparative and evolutionary genomics. The complete chloroplast genomes of seven solanaceous species have been sequenced, including tobacco, potato and tomato, but not peppers. We analyzed the complete chloroplast genome sequence of the hot pepper, Capsicum annuum. The pepper chloroplast genome was 156,781 bp in length, including a pair of inverted repeats (IR) of 25,783 bp. The content and the order of 133 genes in the pepper chloroplast genome were identical to those of other solanaceous plastomes. To characterize pepper plastome sequence, we performed comparative analysis using complete plastome sequences of pepper and seven solanaceous plastomes. Frequency and contents of large indels and tandem repeat sequences and distribution pattern of genome-wide sequence variations were investigated. In addition, a phylogenetic analysis using concatenated alignments of coding sequences was performed to determine evolutionary position of pepper in Solanaceae. Our results revealed two distinct features of pepper plastome compared to other solanaceous plastomes. Firstly, large indels, including insertions on accD and rpl20 gene sequences, were predominantly detected in the pepper plastome compared to other solanaceous plastomes. Secondly, tandem repeat sequences were particularly frequent in the pepper plastome. Taken together, our study represents unique features of evolution of pepper plastome among solanaceous plastomes.
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Affiliation(s)
- Yeong Deuk Jo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, 599 Gwanak-ro Gwanak-gu, Seoul 151-921, Republic of Korea
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27
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Abstract
Single nucleotide polymorphisms (SNPs) derived from both nuclear and cytoplasmic DNA sequences were developed to identify distinct species of Capsicum . Species identification was achieved by detecting allelic variations of these type of markers via high resolution melting analysis (HRM). We used the HRM polymorphisms of COSII markers and the Waxy gene from the nuclear sequence, in addition to the intergenic spacer between trnL and trnF from cytoplasmic DNA as our SNP markers. A total of 31 accessions of Capsicum, representing six species, were analyzed using this method. As single markers were insufficient for identifying Capsicum species, combinations of all markers unambiguously identified all six. A phylogeny based on the SNP markers was consistent with the current taxonomy of Capsicum species. These observations demonstrate that the markers developed in this study are useful for rapid identification of new germplasm for management of Capsicum species.
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Affiliation(s)
- Hee-Jin Jeong
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Soung-Woo Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agricultural Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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28
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Kim DH, Han MS, Cho HW, Jo YD, Cho MC, Kim BD. Molecular cloning of a pepper gene that is homologous to SELF-PRUNING. Mol Cells 2006; 22:89-96. [PMID: 16951555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
"Determinate" and "indeterminate" inflorescences in plants are controlled by a single recessive gene, for example, SELF-PRUNING (SP) in Solanum lycopersicum, TERMINAL FLOWER1 in Arabidopsis, CENTRORADI-ALIS in Antirrhinum, and CENTRORADIALIS-like gene in tobacco. Pepper (Capsicum annuum L.) is an indeterminate species in which shoots grow indefinitely. In this study, we cloned and characterized the pepper SP-like gene (CaSP). RT-PCR revealed that the CaSP transcript accumulates to higher levels in floral buds than in other organs. Comparison of genomic DNA and cDNA sequences from indeterminate and determinate pepper plants revealed the insertion of a single base in the first exon of CaSP in the determinate pepper plants. CaSP is annotated in linkage group 8 (chromosome 6) of the SNU2 pepper genetic map and showed similar synteny to SP in tomato. Transgenic tobacco plants overexpressing CaSP displayed late-flowering phenotypes similar to the phenotypes caused by overexpression of CaSP orthologs in other plants. Collectively, these results suggest that pepper CaSP is an ortholog of SP in tomato.
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Affiliation(s)
- Dong Hwan Kim
- Center for Plant Molecular Genetics and Breeding Research, Seoul National University, Seoul 151-921, Korea
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