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Ro N, Lee GA, Ko HC, Oh H, Lee S, Haile M, Lee J. Exploring Disease Resistance in Pepper ( Capsicum spp.) Germplasm Collection Using Fluidigm SNP Genotyping. PLANTS (BASEL, SWITZERLAND) 2024; 13:1344. [PMID: 38794415 PMCID: PMC11125113 DOI: 10.3390/plants13101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Ho-Cheol Ko
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Hyeonseok Oh
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Sukyeung Lee
- International Technology Cooperation Center, Rural Development Administration, Jeonju 54875, Republic of Korea;
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Jundae Lee
- Department of Horticulture, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Han D, Ma X, Zhang L, Zhang S, Sun Q, Li P, Shu J, Zhao Y. Serial-Omics and Molecular Function Study Provide Novel Insight into Cucumber Variety Improvement. PLANTS 2022; 11:plants11121609. [PMID: 35736760 PMCID: PMC9228134 DOI: 10.3390/plants11121609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Cucumbers are rich in vitamins and minerals. The cucumber has recently become one of China’s main vegetable crops. More specifically, the adjustment of the Chinese agricultural industry’s structure and rapid economic development have resulted in increases in the planting area allocated to Chinese cucumber varieties and in the number of Chinese cucumber varieties. After complete sequencing of the “Chinese long” genome, the transcriptome, proteome, and metabolome were obtained. Cucumber has a small genome and short growing cycle, and these traits are conducive to the application of molecular breeding techniques for improving fruit quality. Here, we review the developments and applications of molecular markers and genetic maps for cucumber breeding and introduce the functions of gene families from the perspective of genomics, including fruit development and quality, hormone response, resistance to abiotic stress, epitomizing the development of other omics, and relationships among functions.
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Affiliation(s)
- Danni Han
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Xiaojun Ma
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Lei Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271018, China; (L.Z.); (S.Z.); (Q.S.)
| | - Pan Li
- School of Pharmacy, Liaocheng University, Liaocheng 252000, China;
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
- Correspondence: (J.S.); (Y.Z.)
| | - Yanting Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
- Correspondence: (J.S.); (Y.Z.)
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Jo HE, Son SY, Lee CH. Comparison of Metabolome and Functional Properties of Three Korean Cucumber Cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:882120. [PMID: 35498687 PMCID: PMC9051474 DOI: 10.3389/fpls.2022.882120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/29/2022] [Indexed: 05/17/2023]
Abstract
Cucumber (Cucumis sativus L.) is consumed worldwide and various cultivars have been developed to enhance fruit quality. However, few studies have comprehensively evaluated the quality of various cultivars. We carried out a metabolomics approach to study the three different cucumber cultivars (Chuichung, White Dadagi, and Mini) and their parts (peel and flesh) coupled with antioxidant activities. The amino acids, sugars, flavonoids, carotenoids, and chlorophylls were upregulated in Mini flesh; however, in the case of peel, they were highly expressed in Chuichung. The highest antioxidant activity was observed in the peel of Chuichung and flesh of Mini. Through correlation analysis between metabolites and antioxidant activity, apigenin and quercetin derivatives, chlorophyll a, chlorophyll b, lutein, α-carotene, and β-carotene were found to be significantly positively correlated with antioxidant activity. To understand the metabolism of these compounds, we performed a comprehensive pathway analysis using a metabolomics approach and analysis of associated gene expression. In secondary metabolism, the expression levels of carotenoid-related genes (15-cis-phytoene synthase and ζ-carotene desaturase) and chlorophyll-related genes (protochlorophyllide reductase and glutamyl-tRNA reductase) were consistent with the metabolome analysis data. Collectively, carotenoid and chlorophyll metabolism were upregulated in Chuichung peel and Mini flesh, which had the highest antioxidant activity in each part. These bioactive compounds can be used as biomarkers of commercial cucumber fruit quality. Accordingly, this study offers integrative insights into the quality of different cucumber cultivars and explores valuable metabolites and genes that are helpful in improving quality with functional properties.
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Affiliation(s)
- Hyo Eun Jo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Su Young Son
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea
- Research Institute for Bioactive-Metabolome Network, Konkuk University, Seoul, South Korea
- *Correspondence: Choong Hwan Lee,
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Park JS, Kang MY, Shim EJ, Oh J, Seo KI, Kim KS, Sim SC, Chung SM, Park Y, Lee GP, Lee WS, Kim M, Jung JK. Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce ( Lactuca sativa L.). HORTICULTURE RESEARCH 2022; 9:uhac119. [PMID: 35928401 PMCID: PMC9343917 DOI: 10.1093/hr/uhac119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/04/2022] [Indexed: 05/08/2023]
Abstract
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation analyses based on the selected SNPs classified the lettuce cultivars into three main groups. Core sets of 192, 96, 48, and 24 markers were further selected and validated using the Fluidigm platform. Phylogenetic analyses based on all core sets of SNPs successfully discriminated individual cultivars that have been currently recognized. These core sets of SNP markers will support the construction of a DNA database of lettuce that can be useful for cultivar identification and purity testing, as well as DUS testing in the plant variety protection system. Additionally, this work will facilitate genetic research to improve breeding in lettuce.
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Affiliation(s)
- Jee-Soo Park
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Min-Young Kang
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Eun-Jo Shim
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - JongHee Oh
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyoung-In Seo
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames IA 50011, USA
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Min Chung
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Ansung 17546, South Korea
| | - Won-Sik Lee
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Minkyung Kim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
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Song K, Shin Y, Jung M, Subramaniyam S, Lee KP, Oh EA, Jeong JH, Kim JG. Chromosome-Scale Genome Assemblies of Two Korean Cucumber Inbred Lines. Front Genet 2021; 12:733188. [PMID: 34868208 PMCID: PMC8640492 DOI: 10.3389/fgene.2021.733188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023] Open
Affiliation(s)
- Kihwan Song
- Department of Bioresources Engineering, Sejong University, Seoul, South Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc., Gyeonggi-do, South Korea
| | - Myunghee Jung
- Research and Development Center, Insilicogen Inc., Gyeonggi-do, South Korea
| | | | - Keun Pyo Lee
- Genomics Division, National Institute of Agricultural Sciences, Nongsaengmyeong, Jeonju, South Korea
| | - Eun-A Oh
- Genomics Division, National Institute of Agricultural Sciences, Nongsaengmyeong, Jeonju, South Korea
| | - Jin Ho Jeong
- Genomics Division, National Institute of Agricultural Sciences, Nongsaengmyeong, Jeonju, South Korea
| | - Jeong-Gu Kim
- Genomics Division, National Institute of Agricultural Sciences, Nongsaengmyeong, Jeonju, South Korea
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