Pre-harvest sprouting is a major physiological problem in rice caused by prolonged rainfall and high humidity during the harvest period, and it is one of the most important targets in current rice breeding programs. In this study, the effect of cold and freezing storage on the pre-harvest sprouting rate was investigated using ten rice varieties under four different treatments. The result showed storage treatments of panicle samples used for germinate evaluation had no significant influence on the pre-harvest sprouting rate. These findings may enhance the efficiency of mass screening for pre-harvest sprouting and support the development of tolerant rice varieties.

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 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
• Comparative Analysis of Chloroplast Promoters for Optimized Production of Recombinant Proteins in Plants
  Juho Lee, Woo-Hyun Jeong, Seon-Kyeong Lee, Kyeong-Ryeol Lee, Sichul Lee, Beom-Gi Kim
  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)
  Ya-Ping Chen, Fei Zhao, Alan J. Paton, Purayidathkandy Sunojkumar, Lian-Ming Gao, Chun-Lei Xiang
  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
  Journal of Phycology.2021; 57(1): 219.     CrossRef
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  Jiahui Sun, Yiheng Wang, Thomas Avery Garran, Ping Qiao, Mengli Wang, Qingjun Yuan, Lanping Guo, Luqi Huang
  Frontiers in Genetics.2021;[Epub]     CrossRef