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

High-throughput genotyping has substantially advanced the quality and accuracy of single nucleotide polymorphism (SNP) discovery and provided an effective way to interpret phenotypic variations in a mapping population. High-resolution quantitative trait locus (QTL) mapping is important for understanding agricultural traits. However, constructing a high-resolution map without sufficient markers to detect QTLs/genes of agronomically important traits is laborious and time consuming. In this study, 160 recom-binant inbred lines (RILs) derived from a cross between Milyang23 and Gihobyeo were re-sequenced, and their SNPs were used for high-resolution QTL mapping of yield-related traits. A total of 1,850,671 high-quality SNPs from RILs were detected, and 3,563 bins were used as genetic markers to construct a high-resolution genetic map using the sliding window approach. The total genetic distance was 1,278.62 cM. Using the QTL analysis, we identified 35 QTLs controlling six yield traits, namely, culm length, panicle length, panicle number per plant, primary branch number per panicle, grain number per plant, and 100-grain weight. In addition, we detected major QTLs associated with culm length and grain number, and compared their physical distances using a conventional genetic map. These results showed that rapid, high-resolution QTL mapping using high-quality SNPs as bin markers is a powerful tool for fine-mapping and cloning important QTLs/genes.

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• Development of Molecular Markers for Flower Color Determination Based on Carotenoid Genes Using QTL Analysis in Chrysanthemum
  Ye-Ji Lee, So Youn Won, Jae-A Jung, Jung Sun Kim
  Korean Journal of Breeding Science.2025; 57(2): 91.     CrossRef
• Fine-Mapping of a Major Quantitative Trait Locusq2ID1for Rice Stem Diameter
  Ye-Ji Lee, Yeisoo Yu, Hyeonso Ji, Gang-Sub Lee, Nam-In Hyung, Keunpyo Lee, Tae-Ho Kim
  Plant Breeding and Biotechnology.2021; 9(4): 298.     CrossRef

Perilla species (Lamiaceae) have been used as a resource for oilseeds and vegetables, and medicinal purposes. Cytogenetic studies based on chromosomal composition are essential to understand the basic genome structure of a species and to provide vital information for crop improvements. However, only a few studies have assessed the cytogenetic aspects of Perilla species. Fluorescence in situ hybridization (FISH) karyotypes using 5S and 45S rDNA probes were analyzed for the wild and cultivated species of Perilla: P. citriodora and P. frutescens. Chromosome complements were diploid in P. citriodora and allotetraploid in P. frutescens. The chromosome length ranged from 3.07 to 4.92 μm and 2.41 to 5.73 μm in the diploid and allotetraploid variants, respectively. The karyotypic formula was 2n = 12m + 8sm (2 satellites) for P. citriodora and 2n = 20m + 20sm (2 satellites) for P. frutescens. A pair of 5S signals was detected in the telomeric region of chromosome pair 7, while a pair of 45S rDNA signals was detected in the telomeric region extending through the satellite region of chromosome 2 of P. citriodora. However, two pairs of 5S signals were detected from the interstitial to the telomeric regions of chromosome 7 and 17, and a pair of 45S rDNA signals was located on the satellite region of chromosome 20 of P. frutescens. This result will provide useful information to develop a breeding program and to construct the chromosomal backbone for the ongoing genome sequence assembly project.

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• Cytogenomic profiling of Panax ginseng cultivars and in vitro root cultures through multi-color PLOP-FISH and flow cytometry reveals somaclonal variations
  Eliazar A. Peniton Jr., Hong T. Nguyen, Nomar E. Waminal, Tae-Jin Yang, Hyun Hee Kim
  Journal of Ginseng Research.2026; 50(4): 101058.     CrossRef
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  Eliazar Alumbro Peniton, Hong Thi Nguyen, Nomar Espinosa Waminal, Tae-Jin Yang, Hyun Hee Kim
  Scientific Reports.2024;[Epub]     CrossRef
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  Hong Thi Nguyen, Soon Ju Park, Byung Yong Kang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2023; 64(5): 811.     CrossRef
• Comparative FISH analysis of Senna tora tandem repeats revealed insights into the chromosome dynamics in Senna
  Thanh Dat Ta, Nomar Espinosa Waminal, Thi Hong Nguyen, Remnyl Joyce Pellerin, Hyun Hee Kim
  Genes & Genomics.2021; 43(3): 237.     CrossRef
• Comparative triple-color FISH mapping in eleven Senna species using rDNA and telomeric repeat probes
  Thi Hong Nguyen, Nomar Espinosa Waminal, Do Sin Lee, Remnyl Joyce Pellerin, Thanh Dat Ta, Nicole Bon Campomayor, Byung Yong Kang, Hyun Hee Kim
  Horticulture, Environment, and Biotechnology.2021; 62(6): 927.     CrossRef
• FISH Karyotype Comparison ofPlatycodon grandiflorus(Jacq.) A. DC. ‘Jangbaek’ and Its Colchicine-Induced Tetraploid ‘Etteumbaek
  Eliazar Alumbro Peniton Jr., Yurry Um, Hyun Hee Kim
  Plant Breeding and Biotechnology.2020; 8(4): 389.     CrossRef

Perilla species belong to the Lamiaceae family of flowering plants and are widely grown in East Asia, for use in a traditional herbal medicine or functional food. To identify single nucleotide polymorphisms (SNPs) in Perilla species and conduct a phylogenomic analysis, we determined the complete sequences of the chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) of six cultivated and three wild Perilla species. The complete cp genome ranged in size from 152,588 bp to 152,656 bp and the length variation in cp genomes was 68 bp. The length of the 45S nrDNA ranged from 6,235 bp to 8,303 bp and the main variation of length differences was in the intergenic spacer (IGS) region. Comparative analysis of the cp genome sequences of nine Perilla species showed low genetic diversity at the intra- and inter-species level. Using SNP analysis, we detected 42 synonymous SNPs (sySNPs) from 27 genes and 37 non-synonymous SNPs (nsSNPs) from 15 genes. A comparison of the 45S nrDNA sequences revealed two SNPs in the 18S rRNA, five SNPs in the 26S rRNA, three SNPs and two InDels in the internal transcribed spacer (ITS) 1 region, and six SNPs in the ITS 2 region. Our phylogenomic analysis suggests that the tetraploidization of Perilla cultivars may have arisen from the P. citriodora genome. The genotyping data from this study may be used to develop molecular markers associated with useful traits for use in Perilla breeding.

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  Xiang Chen, Yi-Yang Liu, Fu-Shun Zheng, Guo-Xin Cheng, Meng Guo, Jian-She Li, Xiao-Min Wang
  Scientia Horticulturae.2025; 339: 113855.     CrossRef
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  Korean Journal of Breeding Science.2025; 57(4): 359.     CrossRef
• Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)
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  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
  Antoine Fort, Marcus McHale, Kevin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
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  Frontiers in Genetics.2021;[Epub]     CrossRef

Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean japonica rice varieties, Junam and Nampyeong. The sequencing yielded 16.6 × 10⁹ bps for Junam, and 15.1 × 10⁹ bps for Nampyeong. After quality trimming and read mapping onto the reference genome sequence of Nipponbare, 11.9 × 10⁹ bps from Junam and 10.6 × 10⁹ bps from Nampyeong were mapped onto the reference sequence. The final effective mapping depth was 31.98x for Junam and 28.41x for Nampyeong. This study found 398,123 DNA polymophisms between Junam and Nampyeong. These were classified into 352,478 SNPs (88.5%) and 45,645 InDels (11.5%) by polymorphism types, 338,485 homozygous (85%) and 59,638 (15%) heterozygous by zygosity, and 331,855 intergenic (83.4%) and 66,268 genic (16.6%) by genomic location. To see the availability of these results in DNA marker development, Cleaved Amplified Polymorphic Sequences (CAPS) markers were developed based on 22 SNPs lying in restriction enzyme sites. Among them, 17 CAPS markers showed polymorphisms between Junam and Nampyeong. It is expected that sufficient DNA markers for mapping genes/QTLs with progeny population from a cross between Junam and Nampyeong can be developed based on the results of the study.

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• Development of 454 New Kompetitive Allele-Specific PCR (KASP) Markers for Temperate japonica Rice Varieties
  Kyeong-Seong Cheon, Young-Min Jeong, Hyoja Oh, Jun Oh, Do-Yu Kang, Nyunhee Kim, Eungyeong Lee, Jeongho Baek, Song Lim Kim, Inchan Choi, In Sun Yoon, Kyung-Hwan Kim, Yong Jae Won, Young-il Cho, Jung-Heon Han, Hyeonso Ji
  Plants.2020; 9(11): 1531.     CrossRef
• QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing
  Kyeong-Seong Cheon, Yong Jae Won, Young-Min Jeong, Youn-Young Lee, Do-Yu Kang, Jun Oh, Hyoja Oh, Song Lim Kim, Nyunhee Kim, Eungyeong Lee, In Sun Yoon, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim, Hyun-Su Park, Hyeonso Ji
  Molecular Genetics and Genomics.2020; 295(5): 1129.     CrossRef
• Kompetitive Allele-Specific PCR Marker Development and Quantitative Trait Locus Mapping for Bakanae Disease Resistance in Korean Japonica Rice Varieties
  Kyeong-Seong Cheon, Young-Min Jeong, Youn-Young Lee, Jun Oh, Do-Yu Kang, Hyoja Oh, Song Lim Kim, Nyunhee Kim, Eungyeong Lee, Jeongho Baek, Inchan Choi, Kyung-Hwan Kim, Yong Jae Won, In Sun Yoon, Young-il Cho, Jung-Heon Han, Hyeonso Ji
  Plant Breeding and Biotechnology.2019; 7(3): 208.     CrossRef
• Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing
  Hyeonso Ji, Tae-Ho Kim, Gang-Seob Lee, Hyun-Ju Kang, Seung-Bum Lee, Seok Cheol Suh, Song Lim Kim, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim
  Molecular Genetics and Genomics.2018; 293(3): 579.     CrossRef
• Single Nucleotide Polymorphism (SNP) Discovery and Kompetitive Allele-Specific PCR (KASP) Marker Development with Korean Japonica Rice Varieties
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  Plant Breeding and Biotechnology.2018; 6(4): 391.     CrossRef