Capsicum chinense is one of the five domesticated pepper species belonging to the Solanaceae family. Capsicum sp. have been used as model systems in comparative and evolutionary genomics because their superior availability of chloroplast genome in the solanaceae family. Similarly, molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. So far however, only partial taxonomic and phylogenetic analyses have been carried out for the genus. Thus, the complete chloroplast genome sequence of a cultivated pepper (C. chinense) has been reported here. The total length of the chloroplast genome is 156,936 bp, with 37.7% overall GC content. A pair of inverted repeats (IRs) of 25,847 bp was separated by a small single copy (SSC) region of 17,912 bp and a large single copy (LSC) region of 87,330 bp. The chloroplast genome harbors 113 known genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA (tRNA) genes. In all, 21 of these genes are duplicated in the inverted repeat regions, 15 genes and six tRNA genes contain a single intron, while two genes have two introns. Analysis revealed 117 simple sequence repeat (SSR) loci, which are mostly located in the intergenic regions. The complete chloroplast genome reported here enriches our knowledge of the genetic complement of C. chinense, and contributes to our understanding of the genetic relationships within the genus Capsicum.

Citations

Citations to this article as recorded by  

• Characterization of the complete chloroplast genome of the rare medicinal plant: Mandragora caulescens (Solanaceae)
  Heqin Ma, Erdong Zhang, Yajing An, Yuqing Wei, Lei Zhang
  Mitochondrial DNA Part B.2024; 9(6): 812.     CrossRef
• Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae)
  Shuilian He, Yinqi Siman, Gengyun Li, Junheng Lv, Kai Zhao, Minghua Deng
  BMC Genomics.2024;[Epub]     CrossRef
• Monograph of wild and cultivated chili peppers (Capsicum L., Solanaceae)
  Gloria E. Barboza, Carolina Carrizo García, Luciano de Bem Bianchetti, María V. Romero, Marisel Scaldaferro
  PhytoKeys.2022; 200: 1.     CrossRef
• Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
  Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Heba Hassan, Bihong Feng, Nathan Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
  Horticulture Research.2019;[Epub]     CrossRef
• Development of the ovule and seed of Habanero chili pepper (Capsicum chinense Jacq.): Anatomical characterization and immunocytochemical patterns of pectin methyl-esterification
  Jacobo Pérez-Pastrana, Ignacio Islas-Flores, Ivett Bárány, Dulce Álvarez-López, Adriana Canto-Flick, Blondy Canto-Canché, Laura Peña-Yam, Liliana Muñoz-Ramírez, Susana Avilés-Viñas, Pilar S. Testillano, Nancy Santana-Buzzy
  Journal of Plant Physiology.2018; 230: 1.     CrossRef
• The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution
  Nunzio D’Agostino, Rachele Tamburino, Concita Cantarella, Valentina De Carluccio, Lorenza Sannino, Salvatore Cozzolino, Teodoro Cardi, Nunzia Scotti
  Genes.2018; 9(10): 503.     CrossRef

Production of spring wheat, the major crop in Mongolia, accounts for 98% of the cultivated area. Understanding genetic variability in existing gene bank accessions is critical for collection, conservation and use of wheat germplasms. To determine genetic diversity and population structure among a representative collection of Mongolian local wheat cultivars and lines, 200 wheat accessions were analyzed with 15 SSR markers distributed throughout the wheat genome. A total of 85 alleles were detected, with three to five alleles per locus and a mean genetic richness of 5.66. Average genetic diversity index was 0.69, with values ranging from 0.37–0.80. The 200 Mongolian wheat accessions were mainly divided into two subgroups based on structure and phylogenetic analyses, and some phenotypes were divergent by the subgroups. Results from this study will provide valuable information for conservation and sustainable use of Mongolian wheat genetic resources.

Citations

Citations to this article as recorded by  

• The Genetic Diversity of Tunisian Sea Barley (Hordeum marinum ssp. marinum): Insights from Cross-species SSRs
  Warda Saoudi, Wael Taamalli, Mounawer Badri, António Martin, Chedly Abdelly
  Plant Molecular Biology Reporter.2026;[Epub]     CrossRef
• Harnessing genetic potentials for drought tolerance in wheat (Triticum aestivum L.) using tolerance indices and molecular markers
  Mst. Anamika Amzad, Md. Arifuzzaman, Md. Ashraful Alam
  Gene Reports.2025; 40: 102230.     CrossRef
• Morphological characterization and molecular diversity assessment of rust resistant genetic stocks of wheat
  Sneha Adhikari, S. C. Bhardwaj, O. P. Gangwar, Pramod Prasad, Charu Lata, Subodh Kumar, Gulab Chand
  Tropical Plant Pathology.2024; 49(4): 525.     CrossRef
• Structure and genetic diversity of macauba [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] approached by SNP markers to assist breeding strategies
  Bruno Galvêas Laviola, Adriano dos Santos, Erina Vitório Rodrigues, Larissa Pereira Ribeiro Teodoro, Paulo Eduardo Teodoro, Tatiana Barbosa Rosado, Cíntia Gonçalves Guimarães, Léo Duc Haa Carson Schwartzhaupt da Conceição
  Genetic Resources and Crop Evolution.2022; 69(3): 1179.     CrossRef
• Genetic diversity, population structure and relationship of Ethiopian barley (Hordeum vulgare L.) landraces as revealed by SSR markers
  Allo A. Dido, M. S. R. Krishna, Ermias Assefa, Dawit T. Degefu, B. J. K. Singh, Kassahun Tesfaye
  Journal of Genetics.2022;[Epub]     CrossRef
• Genetic diversity and population structure in Jatropha (Jatropha curcas L.) based on molecular markers
  Adriana de Souza Carneiro, Adriano dos Santos, Bruno Galvêas Laviola, Larissa Pereira Ribeiro Teodoro, Paulo Eduardo Teodoro, Erina Vitório Rodrigues
  Genetic Resources and Crop Evolution.2022; 69(1): 245.     CrossRef
• Association analysis for agronomic traits in wheat under terminal heat stress
  Adeel Khan, Munir Ahmad, Mukhtar Ahmed, Kulvinder Singh Gill, Zahid Akram
  Saudi Journal of Biological Sciences.2021; 28(12): 7404.     CrossRef
• Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)
  Kunyan Zou, Ki-Seung Kim, Kipoong Kim, Dongwoo Kang, Yu-Hyeon Park, Hokeun Sun, Bo-Keun Ha, Jungmin Ha, Tae-Hwan Jun
  Genes.2020; 12(1): 2.     CrossRef
• Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
  Kamal Khadka, Davoud Torkamaneh, Mina Kaviani, Francois Belzile, Manish N. Raizada, Alireza Navabi
  BMC Plant Biology.2020;[Epub]     CrossRef
• Development of genomic simple sequence repeat markers for Glycyrrhiza lepidota and cross-amplification of other Glycyrrhiza species
  Jun Hyoung Bang, Chi Eun Hong, Sebastin Raveendar, Kyong Hwan Bang, Kyung Ho Ma, Soon Wook Kwon, Hojin Ryu, Ick Hyun Jo, Jong-Wook Chung
  PeerJ.2019; 7: e7479.     CrossRef
• Genome-Wide Genetic Diversity and Population Structure of Tunisian Durum Wheat Landraces Based on DArTseq Technology
  Cyrine Robbana, Zakaria Kehel, M’barek Ben Naceur, Carolina Sansaloni, Filippo Bassi, Ahmed Amri
  International Journal of Molecular Sciences.2019; 20(6): 1352.     CrossRef
• Melatonin Mitigates Salt Stress in Wheat Seedlings by Modulating Polyamine Metabolism
  Qingbo Ke, Jun Ye, Bomei Wang, Jianhong Ren, Lina Yin, Xiping Deng, Shiwen Wang
  Frontiers in Plant Science.2018;[Epub]     CrossRef

Finger millet (Eleusine coracana L. Gaertn.) is an important cereal crop in eastern Africa and southern India with excellent grain storage capacity and the unique ability to thrive in extreme environmental conditions. In this study, we analyzed the genetic diversity and population structure of finger millet using 12 developed microsatellites. By sequencing 815 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in finger millet accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 76 finger millet accessions in Asia, Africa, and unknown origins. The number of alleles ranged from 2 to 9, with an average of 3.3 alleles. The mean values of observed heterozygosity and expected heterozygosity were 0.27 and 0.35, respectively. The average polymorphism information content was 0.301 in all 76 finger millet accessions. AMOVA analysis showed that the percentage of molecular variance among the populations was 1%, that among individuals was 5%, and that within individuals was 94%. In STRUCTURE analysis, the 76 finger millet accessions were divided into two subpopulations which had an admixture of alleles. There was a correspondence among PCoA, AMOVA, and population structure. This study may form the basis for a finger millet breeding and improvement program.

Citations

Citations to this article as recorded by  

• Integrating path analysis and molecular markers to understand genetic diversity in finger millet, Eleusine coracana (L.) Gaertn.
  Mihir A. Hansalia, Vikas Pali, Amar A. Sakure, Sushil Kumar, Dinesh J. Parmar, Mihir M. Pandya, Dinesh Joshi
  The Nucleus.2026;[Epub]     CrossRef
• Development of iron and zinc transporter based genic SSR markers in foxtail millet and their cross- genera transferability in little millet
  Kumari Anjani, Kaushal Kumar, V. K. Sharma
  Cereal Research Communications.2026; 54(2): 875.     CrossRef
• Unlocking Climate Resilience Through Omics in Underutilized Small Millets
  S Muruganantham, Kannabiran Sakthivel, Chockalingam Vanniarajan, Paramasiwam Jeyaprakash, Subramaniam Geethanjali, Mathivanan Sivaji, Thanakkan Ramesh, Sadayandi Geethanjali, Selvavinayagam Monika, Lakshmanan Vigneshwari
  Tropical Plant Biology.2025;[Epub]     CrossRef
• Finger millet (Eleusine coracana) improvement: Challenges and prospects—A review
  Adane Gebreyohannes, Hussein Shimelis, Jacob Mashilo, Damaris A. Odeny, Taye Tadesse, Chris O. Ojiewo
  Plant Breeding.2024; 143(3): 350.     CrossRef
• Cross transferability of finger millet SSR markers to little millet (Panicum sumatrense Roth. Ex Roem & Schult.)
  Komal G. Lakhani, Kirankumar Suthar, Diwakar Singh, Sumankumar Jha, Harshal Patil, Rehana Niyaria
  Ecological Genetics and Genomics.2024; 32: 100281.     CrossRef
• Profiling of foxtail millet (Setaria italica L.) germplasm using in vitro drought screening and SSR markers
  N. S. Ahmad, M. A. Abid, A. A. Al-Assie
  Plant Genetic Resources: Characterization and Utilization.2022; 20(4): 277.     CrossRef
• Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank
  C. Backiyalakshmi, Mani Vetriventhan, Santosh Deshpande, C. Babu, V. Allan, D. Naresh, Rajeev Gupta, Vania C. R. Azevedo
  Frontiers in Plant Science.2021;[Epub]     CrossRef

The present study aimed to determine the contents of five flavonols and two glycoalkaloids as well as the antioxidant activities of leaf ethanol extracts of 50 tomato accessions. The antioxidant activity was assessed using different tests: 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), 2,2-diphenyl-1-picryl hydrazyl (DPPH), nitric oxide (NO), and total polyphenol content (TPC). Flavonols and glycoalkaloids contents were determined using a high performance liquid chromatography-diode array detector system. Among five flavonols and two glycoalkaloids, naringenin and tomatine were detected in tomato leaves at high concentrations. Of the 50 tomato accessions, IT 229711, IT2365203, and IT 207224 were found to have the highest contents of quercetin, kaempferol, and tomatine, respectively. Leaf extract of IT189949 exhibited the highest relative antioxidant capacity index (RACI). Among the five flavonols, myricetin showed positive correlations with DPPH, ABTS, and NO, while isorhamnetin had positive correlation with DPPH. These results will expand the chemical constitution database and provide information on tomato leaves. They are valuable for the development of functional foods or feed-additives.

Citations

Citations to this article as recorded by  

• Protective role of α-tomatine against oxidative stress induced reactive oxygen species: In vitro radical scavenging assays
  
  International Journal of Biosciences (IJB).2025; : 123.     CrossRef
• Genetic Response of Solanum lycopersicum L. (Tomato) to Phytophthora infestans and Aspergillus niger
  Tavershima Moses Anakaa, Odunayo Joseph Olawuyi, Segun Gbolagade Jonathan
  International Journal of Plant Biology.2025; 16(1): 35.     CrossRef
• Extracts of tomatoes and potatoes as biopesticides: a review
  Joshua Ibukun Adebomi, Jianfeng Guo, Catherine Hui Niu
  Discover Agriculture.2025;[Epub]     CrossRef
• Solanaceae Leaves as are Sources of Antioxidants and Vitamin D
  Ekaterina Borodina, Oksana Kozlova, Veronika Boger, Larisa Proskuryakova, Vladimir Yustratov
  Food Processing: Techniques and Technology.2025; 55(1): 197.     CrossRef
• Bioformulation development via valorizing silica-rich spent mushroom substrate with Trichoderma asperellum for plant nutrient and disease management
  Garima Singh, Abhay Tiwari, Akansha Gupta, Ashwani Kumar, P. Hariprasad, Satyawati Sharma
  Journal of Environmental Management.2021; 297: 113278.     CrossRef
• Acute and Subacute Toxicity Profiles of the Methanol Extract of Lycopersicon esculentum L. Leaves (Tomato), a Botanical with Promising In Vitro Anticancer Potential
  Gaëlle S. Nguenang, Arsène S. M. Ntyam, Victor Kuete, Armando Zarrelli
  Evidence-Based Complementary and Alternative Medicine.2020;[Epub]     CrossRef

Sixty-nine Rubus accessions were analyzed to determine the genetic relationships using simple sequence repeat (SSR) markers. Twenty-three SSR markers generated a total of 351 alleles from all accessions, with an average of 15.3 alleles per locus. The average value of polymorphism information content was 0.76, ranging from 0.52 to 0.91. As a result of population structure analysis, 69 Rubus accessions of six Rubus species were subdivided into six subpopulations. Four subpopulations included distinct Rubus species accessions; pop2 (Rubus crataegifolius var. subcuneatus, 2 accessions), pop3 (R. crataegifolius Bunge., 18 accessions), pop4 (R. fruticosus L., 3 accessions) and pop6 (R. coreanus Miq., 36 accessions) while The pop1 and pop5 mainly included R. idaeus L. and R. parvifolius L., respectively. In cluster analysis, 69 Rubus accessions were divided into three groups. Group I contained 35 Rubus accessions, which consisted of six Rubus species. Groups II and III had 30 and 4 Rubus accessions, respectively. They consisted of only R. coreanus. The uncertain diversity of species and artificial groups of the Rubus genus has created confusion with respect to the correct classification of the species at both commercial and scientific levels. The results of the present study will provide basic information for phylogeny, taxonomy and breeding programs of Rubus species.

Citations

Citations to this article as recorded by  

• Genetic diversity and population structure of some blackberry genotypes collected from different parts of Türkiye using inter simple sequence repeat (ISSR) markers
  Fatma Alan, Aydın Uzun, Hasan Pınar
  Genetic Resources and Crop Evolution.2025; 72(7): 9001.     CrossRef
• Cross-transferability of Rubus ellipticus EST–SSR markers for genetic diversity analysis of peach (Prunus persica)
  Samriti Sharma, Rajinder Kaur, Krishan Kumar, Heerendra Sagar
  Genetic Resources and Crop Evolution.2024; 71(4): 1615.     CrossRef
• Genetic diversity and population relationships in wild Korean black raspberry (Rubus coreanus Miq.) based on microsatellite markers: establishing a fruit tree breeding strategy
  Sung-Kyung Han, Hanna Shin, Jei-Wan Lee, Kyung-Nak Hong, Ji-Young Ahn
  Horticulture, Environment, and Biotechnology.2024; 65(2): 293.     CrossRef
• Genetic differentiation between Czech and Norwegian raspberry populations: new options for breeding
  Jiří Sedlák, Leona Leišová-Svobodová, Inger Martinussen, Vojtěch Holubec
  Euphytica.2022;[Epub]     CrossRef
• Genetic variability in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers
  Samriti Sharma, Rajinder Kaur, Krishan Kumar, Dinesh Kumar, Amol Kumar U. Solanke
  Journal of Plant Biochemistry and Biotechnology.2021; 30(1): 37.     CrossRef
• Evaluación de marcadores microsatélites (SSRs) heterólogos en Rubus niveus para estudios de diversidad genética en las Islas Galápagos
  Pablo Alarcón Bolaños, María de Lourdes Torres, Gabriela Pozo, María Paula Erazo, Mayra Ortega, Estefanía Rojas, Noelia Barriga, Antonio Leon Reyes
  ACI Avances en Ciencias e Ingenierías.2021; 13(2): 20.     CrossRef
• Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops
  Hilde Nybom, Gunārs Lācis
  Plants.2021; 10(2): 415.     CrossRef
• MODERN WAYS OF RASPBERRY BREEDING
  L. V. FROLOVA, T. A. HASHENKO, O. A. HASHENKO
  Fruit-Growing.2021; 33: 211.     CrossRef
• Genetic diversity of the Andean blackberry (Rubus glaucusBenth.) in Ecuador assessed by AFLP markers
  Patricia Garrido, Eduardo Morillo, Wilson Vásquez-Castillo
  Plant Genetic Resources: Characterization and Utilization.2020; 18(4): 243.     CrossRef
• Molecular markers in the genetic diversity studies of representatives of the genus Rubus L. and prospects of their application in breeding
  A. M. Kamnev, O. Yu. Antonova, S. E. Dunaeva, T. A. Gavrilenko, I. G. Chukhina
  Vavilov Journal of Genetics and Breeding.2020; 24(1): 20.     CrossRef
• Genetic and genomic resources for Rubus breeding: a roadmap for the future
  Toshi M. Foster, Nahla V. Bassil, Michael Dossett, Margaret Leigh Worthington, Julie Graham
  Horticulture Research.2019;[Epub]     CrossRef

Tomato (Solanum lycopersicum L.) is one of the most economically important plants in the family Solanaceae. Understanding its genetic diversity of accessions is vital for additional collection of tomato germplasms. The
objective
of this study was to determine the genetic diversity and population structure of 355 tomato accessions from Asia using 18 simple-sequence repeats (SSRs). A total of 176 alleles were detected at an average of ten alleles per SSR locus. The average major allele frequency and polymorphic information content were 0.69 and 0.39, respectively. Model-based structure analysis revealed two subpopulations (88%), including admixtures (11%) in the 355 Asian tomato accessions, consistent with clustering results based on genetic distance. The overall F_ST value was 0.135, indicating a moderate differentiation between the inferred subpopulations. Analysis of molecular variance showed that the genetic variance among geographical groups was less than 6%, in contrast to 86% of genetic variance among individuals. The results from this study will provide important information for future germplasm conservation and improvement programs for tomato.

Citations

Citations to this article as recorded by  

• Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato
  Pasquale Tripodi
  Computational and Structural Biotechnology Journal.2022; 20: 6250.     CrossRef
• Genetic diversity, population structure and validation of SSR markers linked to Sw-5 and I-2 genes in tomato germplasm
  Saidaiah Pidigam, Vishnukiran Thuraga, Suchandranath Babu Munnam, Geetha Amarapalli, Gopal Kuraba, Someswara Rao Pandravada, Srinivas Nimmarajula, Hari Kishan Sudini
  Physiology and Molecular Biology of Plants.2021; 27(8): 1695.     CrossRef

In order to estimate genetic diversity of Korean rice landraces, rice characters and SSR markers of 76 rice germplasms were analyzed. Of 12 rice characters, amylose content (AC) showed as largest variance (4.9 to 28.9%), whereas grain length (GL) showed as the lowest variance (4.4 to 5.9 mm). In principal component analyses (PCA), the first principal component explained 60.3% of total variance, in which culm length (CL) and growth period (GP) showed as positive variance and AC showed as negative variance. The second principal component explained an additional 22.4% of the total variance, in which GP and AC showed highly positive variables and CL showed a negative variable. Forty nine SSR markers produced a total of 473 alleles with an average of 9.65 alleles. Polymorphism information content (PIC) was in the range of 0.11 to 0.93. Average observed heterozygosity ranged from 0.12 to 0.39, with an average value of 0.61. As a result of STRUCTURE analysis, 76 Korean rice landraces showed two subpopulations. In clustering analysis, rice characters and SSR markers were clustered into four groups and three groups, respectively. However, they were not significant different from each other. These results provided insight into the characteristics of Korean rice landraces, thus improving our knowledge on rice breeding.

Citations

Citations to this article as recorded by  

• Genome-Wide Association Study to identify Bakanae disease resistance-related QTLs carrying novel candidate genes in rice (Oryza sativa L.)
  Yuting Zeng, Fang-Yuan Cao, Ah-Rim Lee, Dongryung Lee, Backki Kim, Soon-Wook Kwon
  npj Science of Plants.2025;[Epub]     CrossRef
• Physio-biochemical and molecular characterization for drought tolerance in rice genotypes at early seedling stage
  Al-Ashkar IM, Zaazaa EI, EL Sabagh A, Barutçular C
  Journal of Experimental Biology and Agricultural Sciences.2016; 4(6): 675.     CrossRef

DNA barcoding is the use of short DNA sequences of the genome for large scale species identification. The Consortium for the Barcode of Life (CBOL) plant-working group recommended a 2-locus combination as the standard plant barcode. The evolutions of the chloroplast regions combined with nuclear gens are sufficiently rapid to allow discrimination between closely related species. We evaluated the efficacy of the proposed plant barcoding loci, matK, along with ITS2 for barcoding the Vigna species. To assess the discriminatory ability of barcoding loci for identifying the Vigna species, we sampled 52 of the taxonomically best known groups in the genus. Topologies of the phylogenetic trees based on ITS2 and matK analyses were similar but a few accessions were placed into distant phylogenetic groups. Neither ITS2 nor matK analyses were able to discriminate some closely related Vigna species. Thus, we used concatenated data to increase the resolving power of ITS2 and used matK as an additional tool for phylogenetic analysis in Vigna because characterization of the nucleotide sequences of the matK region was easier and more cost-effective than that of the ITS region.

Citations

Citations to this article as recorded by  

• Genetic Diversity of Asian Vigna Species (Subgenus Ceratotropis; Genus Vigna) in India Based on ITS2 Sequences Data
  Suraj D. Umdale, Nikhil B. Gaikwad, Shaila Kadam, Mahendra L. Ahire, Pankaj S. Mundada, Kangila V. Bhat
  Plant Molecular Biology Reporter.2023; 41(3): 454.     CrossRef
• Identification of Apiaceae using ITS, ITS2 and psba-trnH barcodes
  Zhehui Jiang, Meiqi Zhang, Lingyang Kong, Yihong Bao, Weichao Ren, Hongyuan Li, Xiubo Liu, Zhen Wang, Wei Ma
  Molecular Biology Reports.2023; 50(1): 245.     CrossRef
• Molecular characterization and phylogenetic relationships in Asiatic Vigna using ITS and cpDNA loci
  Ruchi Vir, Tabassum Jehan, K. V. Bhat, Suman Lakhanpaul
  Vegetos.2022; 36(4): 1397.     CrossRef
• Comparative Genetic Analysis between the Jeju ‘Inchangkyool’ and Chinese ‘Ichangensis’ (Citrus ichangensis) using Internal Chloroplast trnL-trnF Intergenic Spacers and Transcribed Spacer Sequence Regions
  Min Ju Kim, Mi Sun Kim, Kihye Shin, Sukman Park, Cheolwoo Choi, Su Hyun Yun, Seong Beom Jin
  Korean Journal of Breeding Science.2021; 53(1): 16.     CrossRef
• Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions
  Yu Takahashi, Prakit Somta, Chiaki Muto, Kohtaro Iseki, Ken Naito, Muthaiyan Pandiyan, Senthil Natesan, Norihiko Tomooka, Vijai Gupta
  PLOS ONE.2016; 11(1): e0147568.     CrossRef

Chloroplast DNA sequences are a versatile tool for species identification and phylogenetic reconstruction of land plants. Different chloroplast loci have been utilized for phylogenetic classification of plant species. However, there is no report for a short DNA sequence that can distinguish all plant species from each other. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Thus, the complete chloroplast genome sequence of Korean landrace “Subicho” pepper (Capsicum annuum var. annuum) has been determined here. The total length of the chloroplast genome is 156,878 bp, with 37.7% overall GC content. A pair of IRs (inverted repeats) of 25,801 bp was separated by a small single copy (SSC) region of 17,929 bp and a large single copy (LSC) region of 87,347 bp. The chloroplast genome harbors 132 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of seven of these genes are duplicated in the inverted repeat regions, nine genes and six tRNA genes contain one intron, while two genes and a ycf have two introns. Analysis revealed 144 simple sequence repeat (SSR) loci and 96 variants, mostly located in the intergenic regions. The types and abundances of repeat units in Capsicum species were relatively conserved and these loci will be useful for developing C. annuum cp genome vectors.

Citations

Citations to this article as recorded by  

• Ripening‐related metabolic changes in different chili pepper cultivars revealed by nuclear magnetic resonance spectroscopy
  Gi‐Un Seong, Dae‐Yong Yun, Jeong‐Seok Cho, Seul‐Ki Park, Gyu Seok Lee, Jeong Hee Choi, Kee‐Jai Park, Jeong‐Ho Lim
  Journal of the Science of Food and Agriculture.2025; 105(11): 6084.     CrossRef
• NMR-Based Metabolomic Analysis of Biotic Stress Responses in the Traditional Korean Landrace Red Pepper (Capsicum annuum var. annuum, cv. Subicho)
  Gi-Un Seong, Dae-Yong Yun, Dong-Hyeok Shin, Jeong-Seok Cho, Seul-Ki Park, Jeong Hee Choi, Kee-Jai Park, Jeong-Ho Lim
  International Journal of Molecular Sciences.2024; 25(18): 9903.     CrossRef
• Comparative 1H NMR-Based Metabolomics of Traditional Landrace and Disease-Resistant Chili Peppers (Capsicum annuum L.)
  Gi-Un Seong, Dae-Yong Yun, Dong-Hyeok Shin, Jeong-Seok Cho, Gyuseok Lee, Jeong Hee Choi, Kee-Jai Park, Kyung-Hyung Ku, Jeong-Ho Lim
  Foods.2024; 13(13): 1966.     CrossRef
• Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f)
  P Maheswari, C Kunhikannan, R Yasodha
  Journal of Biosciences.2021;[Epub]     CrossRef
• Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
  Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Heba Hassan, Bihong Feng, Nathan Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
  Horticulture Research.2019;[Epub]     CrossRef
• Next generation sequencing technologies for the development of molecular markers and the analysis of genome diversity in Capsicum spp.
  T. Cardi, N. D’Agostino, C. Cantarella, V. Colonna, B. Greco, R. Tamburino, F. Taranto, N. Scotti, P. Tripodi
  Acta Horticulturae.2019; (1242): 831.     CrossRef
• The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution
  Nunzio D’Agostino, Rachele Tamburino, Concita Cantarella, Valentina De Carluccio, Lorenza Sannino, Salvatore Cozzolino, Teodoro Cardi, Nunzia Scotti
  Genes.2018; 9(10): 503.     CrossRef
• The complete chloroplast genome of Capsicum frutescens (Solanaceae)
  Donghwan Shim, Sebastin Raveendar, Jung‐Ro Lee, Gi‐An Lee, Na‐Young Ro, Young‐Ah Jeon, Gyu‐Taek Cho, Ho‐Sun Lee, Kyung‐Ho Ma, Jong‐Wook Chung
  Applications in Plant Sciences.2016;[Epub]     CrossRef
• Complete chloroplast genome sequence of Capsicum baccatum var. baccatum
  Tae-Sung Kim, Jung-Ro Lee, Sebastin Raveendar, Gi-An Lee, Young-Ah Jeon, Ho-Sun Lee, Kyung-Ho Ma, Sok-Young Lee, Jong-Wook Chung
  Molecular Breeding.2016;[Epub]     CrossRef
• The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing
  Sebastin Raveendar, Young-Wang Na, Jung-Ro Lee, Donghwan Shim, Kyung-Ho Ma, Sok-Young Lee, Jong-Wook Chung
  Molecules.2015; 20(7): 13080.     CrossRef

We investigated the species discriminatory efficiency of the proposed plant barcoding loci ITS2 and matK in Vicia species. In 2011, China Plant BOL Group proposed the addition of nuclear ITS2 to matK be accepted as a 2-locus DNA barcode to classify plant species. The matK region was chosen as a DNA barcode because of its effective species discriminating power, high quality sequence recovery, and easy experimental analysis. Integration of matK sequences into Vicia phylogeny could improve phylogenetic reconstruction of this species. To assess the ability of barcoding loci to resolve Vicia species, we sampled 36 of the taxonomically best known groups in the genus. Topologies of the phylogenetic trees based on ITS2 and matK analyses were similar but a few accessions were placed into distant phylogenetic groups. Neither ITS2 nor matK analyses alone could discriminate some closely related Vicia species. Thus, we have proposed a concatenated data approach to increase the resolving power of ITS2 and used matK as an additional tool for phylogenetic analysis in Vicia because characterization of the nucleotide sequences of the matK region was easier to recover and more cost-effective than those of the ITS region.

Citations

Citations to this article as recorded by  

• Deep learning for Fabaceae identification by integrating molecular and morphological data and a solution for barcode selection
  Kawtar Lhayani, Karim Rabeh, Leila Medraoui
  Journal of Systematics and Evolution.2026; 64(2): 229.     CrossRef
• Rapid Specific PCR Detection Based on THCAS and CBDAS for the Prediction of Cannabis sativa Chemotypes: Drug, Fiber, and Intermediate
  Patwira Boonjing, Worakorn Wiwatcharakornkul, Chayapol Tungphatthong, Taksina Chuanasa, Somchai Keawwangchai, Tae-Jin Yang, Wanchai De-Eknamkul, Suchada Sukrong
  International Journal of Molecular Sciences.2025; 26(11): 5077.     CrossRef
• DNA-Based Identification of Eurasian Vicia Species Using Chloroplast and Nuclear DNA Barcodes
  Irene Bosmali, Georgios Lagiotis, Nadia Haider, Maslin Osathanunkul, Costas Biliaderis, Panagiotis Madesis
  Plants.2022; 11(7): 947.     CrossRef
• Interspecific variation of seed morphological and micro‐morphological traits in the genus Vicia (Fabaceae)
  Seahee Han, Raveendar Sebastin, Kyung Jun Lee, XiaoHan Wang, Myoung‐Jae Shin, Seong‐Hoon Kim, Sookyeong Lee, Jung‐Ro Lee, Gyu‐Taek Cho, Do Yoon Hyun, Jong‐Wook Chung
  Microscopy Research and Technique.2021; 84(2): 337.     CrossRef
• Identification of Vicia Species Native to South Korea Using Molecular and Morphological Characteristics
  Seahee Han, Raveendar Sebastin, XiaoHan Wang, Kyung Jun Lee, Gyu-Taek Cho, Do Yoon Hyun, Jong-Wook Chung
  Frontiers in Plant Science.2021;[Epub]     CrossRef
• Comparative Genetic Analysis between the Jeju ‘Inchangkyool’ and Chinese ‘Ichangensis’ (Citrus ichangensis) using Internal Chloroplast trnL-trnF Intergenic Spacers and Transcribed Spacer Sequence Regions
  Min Ju Kim, Mi Sun Kim, Kihye Shin, Sukman Park, Cheolwoo Choi, Su Hyun Yun, Seong Beom Jin
  Korean Journal of Breeding Science.2021; 53(1): 16.     CrossRef
• Recent advances of novel technologies for quality consistency assessment of natural herbal medicines and preparations
  Xi-Chuan Wei, Bo Cao, Chuan-Hong Luo, Hao-Zhou Huang, Peng Tan, Xiao-Rong Xu, Run-Chun Xu, Ming Yang, Yi Zhang, Li Han, Ding-Kun Zhang
  Chinese Medicine.2020;[Epub]     CrossRef
• Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species
  Sebastin Raveendar, Jung-Ro Lee, Donghwan Shim, Gi-An Lee, Young-Ah Jeon, Gyu-Taek Cho, Kyung-Ho Ma, Sok-Young Lee, Gi-Ho Sung, Jong-Wook Chung
  Plant Genetic Resources.2017; 15(4): 286.     CrossRef
• Editorial: Food Legume Diversity and Legume Research Policies
  Matthew W. Blair, Jing Wu, Shumin Wang
  The Crop Journal.2016; 4(5): 339.     CrossRef

Eggplant (Solanum melongena L.) is an excellent source of vitamins A and C and of flavonoid compounds, which are important antioxidant components believed to reduce the risk of various diseases. We investigated the antioxidant activity and flavonoid content in eggplant leaves and fruits to identify genetic resources with high antioxidant capacity for use in food or as feed additives, and also determined the influence of days to flowering, leaf blade colors, and latitudes of origin on the antioxidant activity and flavonoid content in eggplant leaves. The accessions originating from 45°N showed the highest flavonoid contents (AVG. = 15.4 μg mg⁻¹) followed by accessions from 30°~45°N (AVG. = 13.0 μg mg⁻¹), 15°~30°N (AVG. = 11.0 μg mg⁻¹), and 0°~15°N (AVG. = 9.5 μg mg⁻¹). The same pattern was also found in 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 1,1-diphenyl-2-picryl-hydrazil (DPPH) antioxidant activities. High ABTS and DPPH activity and flavonoid content were found in the early-flowering accessions. All flavonoids of the greenish violet leaves were significantly higher than those of green leaves. The flavonoid concentration in eggplant leaves was 10 to 20 fold greater, at an average of 15.6 μg mg⁻¹, than that of the fruit (AVG. = 0.9 μg mg⁻¹). Taken together, eggplant leaves represent a potential source of natural antioxidants due to their high flavonoid content.

Citations

Citations to this article as recorded by  

• Valorization of Solanum melongena L. crop by-products: Phenolic composition and in vitro antioxidant, antidiabetic, anti-inflammatory, cytotoxic, and antimicrobial properties
  Mikel Añibarro-Ortega, Maria Inês Dias, Jovana Petrović, Sonia Núñez, Ricardo C. Calhelha, Eduardo M. Costa, M. Machado, Manuela Pintado, Marina Soković, Víctor López, Lillian Barros, José Pinela
  Process Biochemistry.2025; 153: 315.     CrossRef
• Exploration of natural colourant of ( Solanum melongena L.) brinjal plant residues for fabric dyeing: a novel approach towards textile processing
  Fatima Batool, Naeem Iqbal, Shahid Adeel, Muhammad Azeem, Sahar Mumtaz, Muhammad Hussaan
  Natural Product Research.2025; 39(7): 1834.     CrossRef
• Effect of Solanum melongena on Components and Kidney Damage of Fructose-Induced Metabolic Syndrome in Rats
  Elizabeth Guzmán Hernández, Maria del Rosario González Valle, José Carmelo Benítez Flores, Maria Eugenia Garian Aguilar, Rubén San Miguel Chávez, Maria Dolores Hernández Martínez, Leonardo del Valle Mondragón, David Segura Cobos, Gil Alfonso Magos Guerrer
  Iranian Journal of Pharmaceutical Research.2024;[Epub]     CrossRef
• Characterization of Flavonoid, Free Amino Acid, Volatiles Components of ‘Minihyang’ Fruit, a New Cultivar Citrus reticulata
  Sang Suk Kim, YoSup Park, Seung-Gab Han
  Korean Journal of Breeding Science.2023; 55(3): 244.     CrossRef
• Metabolomic Analysis of Phytochemical Compounds from Agricultural Residues of Eggplant (Solanum melongena L.)
  Laura Aracely Contreras-Angulo, Aldo Moreno-Ulloa, Rommel A. Carballo-Castañeda, Josefina León-Felix, José Geovanni Romero-Quintana, Maribel Aguilar-Medina, Rosalío Ramos-Payán, J. Basilio Heredia
  Molecules.2022; 27(20): 7013.     CrossRef
• Assessing Physicochemical Parameters, Bioactive Profile and Antioxidant Status of Different Fruit Parts of Greek Eggplant Germplasm
  Kalliopi I. Kadoglidou, Konstantinos Krommydas, Parthenopi Ralli, Ifigeneia Mellidou, Apostolos Kalyvas, Maria Irakli
  Horticulturae.2022; 8(12): 1113.     CrossRef
• Biochemical Composition of Eggplant Fruits: A Review
  Meenakshi Sharma, Prashant Kaushik
  Applied Sciences.2021; 11(15): 7078.     CrossRef
• Bioactive compounds and enzymatic activity in minimally processed eggplant packedunderactive modified atmosphere
  Flávia Aparecida de Carvalho Mariano-Nasser, Cristine Vanz Borges, Juliana Arruda Ramos, Maurício Dominguez Nasser, Giovanna Alencar Lundgren, Karina Aparecida Furlaneto, Tânia Regina Kovalski, Rogério Lopes Vieites
  Semina: Ciências Agrárias.2019; 40(1): 139.     CrossRef
• Health benefits and bioactive compounds of eggplant
  Nergiz Gürbüz, Selman Uluişik, Anne Frary, Amy Frary, Sami Doğanlar
  Food Chemistry.2018; 268: 602.     CrossRef
• A Polyphenol Rich Extract from Solanum melongena L. DR2 Peel Exhibits Antioxidant Properties and Anti-Herpes Simplex Virus Type 1 Activity In Vitro
  Antonella Di Sotto, Silvia Di Giacomo, Donatella Amatore, Marcello Locatelli, Annabella Vitalone, Chiara Toniolo, Giuseppe Leonardo Rotino, Roberto Lo Scalzo, Anna Teresa Palamara, Maria Elena Marcocci, Lucia Nencioni
  Molecules.2018; 23(8): 2066.     CrossRef

Rice (Oryza sativa L.) germplasms with an amylose content above 30% were identified by screening 9481 accessions from the Rural Development Administration (RDA) gene bank. The total set of accessions came from 65 countries, including Korea, China, Japan, the Philippines, India, Taiwan, the United States, and Russia. High-throughput near infrared reflectance (NIR) spectroscopy equipped with a fiberoptic probe (700~2500 nm) was used to estimate the amylose content. The amylose contents ranged from 5 to 40% based on NIR spectroscopy; divided into 5% increments, the amylose content of 2820 accessions was found to be between 15 and 20%. To select rice accessions high in amylose, 239 accessions with an amylose content of 30% or greater were selected based on NIR spectroscopy data and cultivated in the field for final selection. Among the 239 accessions selected and cultivated, 151 were deemed agronomically satisfactory. Among the 151 accessions, based on laboratory analysis, 14 had an amylose content higher than 30% and 33 had an amylose content between 28 and 30%. The amylose contents of the reference cultivars Hopum-byeo and Sobi-byeo were 20.7% and 19.9%, respectively. Finally, successful selection of accessions with high amylose content from the large RDA gene bank collection was achieved based on a combination of NIR spectroscopy and laboratory data.

Citations

Citations to this article as recorded by  

• New Source of Rice with a Low Amylose Content and Slow In Vitro Digestion for Improved Health Benefits
  Pichayaporn Srinang, Sirimaporn Khotasena, Jirawat Sanitchon, Sompong Chankaew, Sanun Jogloy, Tidarat Monkham
  Agronomy.2023; 13(10): 2622.     CrossRef
• Quality Characteristics of Rice-Based Ice Creams with Different Amylose Contents
  Gi-Un Seong, Ji-Yoon Kim, Jung-Soo Kim, Sae-Ul Jeong, Jun-Hyeon Cho, Ji-Yoon Lee, Sais-Beul Lee, Nkulu-Rolly Kabange, Dong-Soo Park, Kwang-Deog Moon, Ju-Won Kang
  Foods.2023; 12(7): 1518.     CrossRef

The present study investigated the isolation and characterization of 34 polymorphic microsatellite markers developed from Actinidia arguta (Sieb. and Zucc.) Planch. ex Miq. var arguta. These markers produced 349 alleles in eight Actinidia species, with an average of 10.3 alleles per locus. Observed heterozygosity ranged from 0.50 to 0.87 (mean = 0.72), and polymorphism information content ranged from 0.37 to 0.88 (mean = 0.69). The phylogenetic relationship obtained using microsatellite markers showed minor clustering and population differences among species while 38 A. arguta accessions fell into two subgroups. These newly developed polymorphic microsatellite markers will be very useful in sustainable genetic conservation, marker-assisted breeding, and classification of the Actinidia genus.

Citations

Citations to this article as recorded by  

• Scientific and breeding value of wild Actinidia Sect. Leiocarpae
  X.-M. Lu, J. Wang, Z.-Z. Li, Y.-C. Wang
  Acta Horticulturae.2025; (1431): 193.     CrossRef
• Structural analysis of Actinidia arguta natural populations and preliminary application in association mapping of fruit traits
  Xue-Mei Lu, Yu-Ping Man, Rui Lei, Yongbo Liu, Jin-Hu Wu, Yan-Chang Wang
  Scientia Horticulturae.2022; 304: 111306.     CrossRef
• Ploidy levels and genetic diversity of Actinidia arguta (Siebold & Zucc.) Planch. ex Miq., A. kolomikta (Rupr. & Maxim.) Maxim., A. callosa Lindl., and A. melanandra Franch., accessions
  Sigita Bogačiovienė, Laima Česonienė, Sezai Ercisli, Andrius Valatavičius, Baltramiejus Jakštys, Saulius Šatkauskas, Algimantas Paulauskas
  Genetic Resources and Crop Evolution.2019; 66(5): 1107.     CrossRef
• Development and validation of polymorphic EST-SSR markers for genetic diversity analysis in Actinidia arguta
  Haiyue Sun, Jiahui Wang, Li Chen, Jian Xu, Yadong Li
  Fruits.2019; 74(1): 25.     CrossRef
• Genetic diversity of kiwifruit (Actinidia spp.), including Korean native A. arguta, using single nucleotide polymorphisms derived from genotyping-by-sequencing
  Sewon Oh, Mockhee Lee, Keumsun Kim, Hyeondae Han, Kyungho Won, Yong-Bum Kwack, Hyunsuk Shin, Daeil Kim
  Horticulture, Environment, and Biotechnology.2019; 60(1): 105.     CrossRef
• Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops
  Gi-An Lee, Sok-Young Lee, Ho-Sun Lee, Kyung-Ho Ma, Jae-Gyun Gwag, Yeon-Gyu Kim, Jung-Ro Lee
  Plant Genetic Resources.2014; 12(S1): S125.     CrossRef