Rice culm is an important trait for determining rice lodging yield, and stem diameter has been suggested as a yield-related trait; however, studies for the genetic basis of its phenotypic variation are still required. In this study, we used 160 recombination inbred lines derived from a cross of two different rice varieties [‘Milyang23’ (Tongil rice) and ‘Giho’ (japonica)] for quantitative trait locus (QTL) mapping with nine stem traits. The analysis showed that QTLs for the diameters of the first, second, third and fourth internode traits were independently separated in the top of chromosome 1, whereas four lengths of internodes were estimated as being related to the semidwarf1 (sd1) gene. A major-effect QTL (q2ID1) was identified that the overlapped region of our previous mapping with a large genomic region. Therefore, we performed high-resolution genetic mapping for fine-mapping of q2ID1 to a ~140 kb region between Ind1_1 and Ind1_2 of genetic markers, with candidate genes predicted using a reference genome. We ultimately identified nine of the 15 candidate genes with specific gene functions and analyzed the sequence variations between two parents. These results offer valuable gene and/or genetic information on stem diameter to improve lodging resistance and yield.

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• Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.)
  Ognigamal Sowadan, Shanbin Xu, Yulong Li, Everlyne Mmbone Muleke, Hélder Manuel Sitoe, Xiaojing Dang, Jianhua Jiang, Hui Dong, Delin Hong
  Genes.2024; 15(1): 105.     CrossRef

Milk thistle (Silybum marianum Gaertn.) is a well-known medicinal plant which has been used for more than 2,000 years around the world. It produces silymarin, which cures the liver from hepatitis and toxin damages. In this study, a selfed and purified breeding line of the milk thistle from the Korean environment was used as a source of chloroplast genome construction. It showed high concentration of silybin B (3.50 mg/g) in its dried seeds. The complete chloroplast genome of S. marianum acc. ‘912036’ is 152,556 bp in length and G+C content is 37.69%. A total of 87 protein coding genes with 104 exons were annotated. Chloroplast genomes of five accessions from different countries were compared with that of ‘912036’, and no sequence polymorphism among them was identified. Thus, the chloroplast genome from this study can be used to develop S. marianum-specific DNA markers when compared with other diverse S. marianum accessions and Asteraceae species.

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• The genetics and genomics of milk thistle: unlocking its therapeutic potential through modern breeding and biotechnological innovations
  Priskila Tolangi, Jeehyoung Shim, Raña Mae Sumabat, Sunghan Kim, Hyun-Seung Park, Kyung Do Kim, Hyun Uk Kim, Sanghyun Lee, Joong Hyoun Chin
  Applied Biological Chemistry.2024;[Epub]     CrossRef
• Analysis of silybin A and silybin B in different accessions of Silybum marianum seeds
  Neil Patrick Uy, Jeehyoung Shim, Hak-Dong Lee, Jung Sook Sung, Eunae Yoo, Joong Hyoun Chin, Sanghyun Lee
  Journal of Applied Biological Chemistry.2024;[Epub]     CrossRef
• Agricultural phenotype and silymarin content variations of cultivated milk thistle in Korea
  Jeehyoung Shim, Hyejin Cho, Jung Sook Sung, Eunae Yoo, Joong Hyoun Chin, Sanghyun Lee
  Horticulture, Environment, and Biotechnology.2024; 65(5): 891.     CrossRef
• A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea
  Jeehyoung Shim, Su Young Hong, Jae-Hyuk Han, Yeisoo Yu, Eunae Yoo, Jungsook Sung, Joong Hyoun Chin, O New Lee
  Plants.2023; 12(14): 2702.     CrossRef
• The complete chloroplast genome of Elephantopus scaber L. (Vernonioideae, Asteraceae), a useful ethnomedicinal plant in asia
  Pham Anh Thi Nguyen, Do Tan Khang, Pham Thien Trang Nguyen, Hoang Dang Khoa Do
  Mitochondrial DNA Part B.2023; 8(9): 936.     CrossRef
• Assembly and Comparative Analysis of Complete Mitogenome of Silybum marianum (L.) Gaertner
  Jeongwoo Lee, Yedomon Ange Bovys Zoclanclounon, Hwajin Jung, Taeho Lee, Jeonggu Kim, Guhwang Park, Keunpyo Lee, Kwanghoon An, Jeehyoung Shim, Joonghyoun Chin, Suyoung Hong
  Korean Journal of Breeding Science.2022; 54(4): 294.     CrossRef

Seedling vigor in drought stress conditions is an important characteristic of the dry direct-seeded rice system. The drought stress in the seedling stage disrupts seed germination and delays the establishment of seedlings. However, little is known about the genetic mechanism of seedling vigor in drought conditions. The identification of quantitative trait loci (QTL) was conducted using 162 recombinant inbred lines (RILs) derived from a cross between two rice varieties—a Tongil-type Milyang23 and a temperate japonica Tong88-7. The seedling vigor of these RILs was characterized by measuring 10 morphological traits of the seedlings grown under drought conditions. The Tong88-7 seedlings showed significantly higher values than the Milyang23 seedlings for all traits. The genotyping-by-sequencing method was used to construct a map of 6140 single nucleotide polymorphisms. Six main-effect QTLs (M-QTLs) associated with seedling vigor traits under drought stress were identified on chromosomes 9 and 11. In particular, five out of these six QTLs were located on chromosome 11, explaining the phenotypic variances of 4.3% through 10.1%. In addition, 21 epistatic QTLs (E-QTLs) were detected, and the 27 loci involved in this interaction were distributed on 11 chromosomes. Both M-QTLs and E-QTLs detected in this study would be useful in breeding programs to develop elite rice varieties especially adapted to dry direct-seeded rice system.

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• Analysis of Seed Vigor and Grain Quality Traits under Accelerated Aging Treatment in japonica Rice
  Kyeongmin Kang, Seung Young Lee, Su-Kyung Ha, Gileung Lee, Jae-Ryoung Park, Mina Jin, Jung-Pil Suh, Youngjun Mo, Hyun-Sook Lee
  Korean Journal of Breeding Science.2025; 57(3): 217.     CrossRef
• The resilience of rice under water stress will be driven by better roots: Evidence from root phenotyping, physiological, and yield experiments
  Sadiah Shafi, Insha Shafi, Aaqif Zaffar, Sajad Majeed Zargar, Asif B. Shikari, Anuj Ranjan, P.V. Vara Prasad, Parvaze A. Sofi
  Plant Stress.2023; 10: 100211.     CrossRef
• Hydraulic conductance and xylem vessel diameter of young maize roots subjected to sustained water‐deficit
  Nahid Jafarikouhini, Thomas R. Sinclair
  Crop Science.2023; 63(4): 2458.     CrossRef
• Shaping the root system architecture in plants for adaptation to drought stress
  Alok Ranjan, Ragini Sinha, Sneh L. Singla‐Pareek, Ashwani Pareek, Anil Kumar Singh
  Physiologia Plantarum.2022;[Epub]     CrossRef
• Genetics and genomics of root system variation in adaptation to drought stress in cereal crops
  Md Nurealam Siddiqui, Jens Léon, Ali A Naz, Agim Ballvora, Miriam Gifford
  Journal of Experimental Botany.2021; 72(4): 1007.     CrossRef
• Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?
  Paulo Henrique Ramos Guimarães, Isabela Pereira de Lima, Adriano Pereira de Castro, Anna Cristina Lanna, Patrícia Guimarães Santos Melo, Marcel de Raïssac
  Rice.2020;[Epub]     CrossRef

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

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• Complete plastid and 45S rDNA sequences allow authentication of Liriope platyphylla and Ophiopogon japonicus
  Yeonjeong Lee, Hyun-Seung Park, Jae-Hyeon Jeon, Jee Young Park, Seung Hyun Kim, Jungmoo Huh, Sunmin Woo, Do-Won Jeong, Tae-Jin Yang
  Current Plant Biology.2022; 30: 100244.     CrossRef
• De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species
  Hakjoon Choi, Wan Seok Kang, Jin Seok Kim, Chang-Su Na, Sunoh Kim
  Current Issues in Molecular Biology.2021; 43(3): 2177.     CrossRef