In-Jung Kim

Citrus breeding is challenged by seedlessness, polyembryony, and high heterozygosity, making it difficult to evaluate genetic variation and phenotypic diversity across lines. Jedae-unshiu is a γ-irradiation–derived mutant known for its unique peel morphology and fruit-quality traits. Although previous genomic studies have characterized its SNP and InDel variation, an integrated phenotype–genotype comparison across multiple citrus lines has not yet been performed. In this study, we analyzed phenotypic traits and whole-genome SNP variation from seven citrus lines, including Jedae-unshiu, to investigate line-level relationships. Phenotypic measurements collected from 2022 to 2024—covering size, color, peel thickness, sugar content, acidity, and hardness—were normalized to remove annual effects. Principal component analysis and clustering (hierarchical and k-means) revealed three major phenotype-driven clusters. PCA loadings indicated that color traits (L, a, b), acidity, and hardness were the primary factors driving the cluster containing Jedae-unshiu, Araunshiu, and 6b4-16, with sugar content contributing more weakly. Genotype analysis was performed using a pre-filtered SNP set (~660k variants) and IUPAC-encoded genotypes. IBS distances calculated with Jedae-unshiu as the reference showed that Araunshiu, 6b4-16, and Satsuma were relatively close genetically, reflecting a pattern broadly consistent with phenotype-based clustering. These findings demonstrate that phenotypic similarity and genomic proximity converge to reveal underlying structure among citrus lines. The agreement between trait-driven clusters and IBS-based distances suggests that some of the 160 Jedae-unshiu–specific SNP markers may be associated with key fruit-quality traits such as acidity, sugar content, or color characteristics. This integrated framework provides a foundation for identifying candidate markers and supporting data-driven citrus breeding strategies.

Yein-early is a gamma-irradiated mutant of Citrus unshiu that exhibits two stable traits distinct from the wild type (WT): a deeper red peel color and narrow, curled leaves. Fruit quality analysis showed that Yein-early has higher firmness and sugar content, while fruit size, acidity, and peel thickness were comparable to the WT. To uncover the genetic basis of these traits, we conducted whole-genome sequencing. The WT sequence data were sourced from our previous work (NCBI: PRJNA745525). Reads were mapped to the C. unshiu Marc. Miyagawa-wase reference genome (CUMW_v1.0; 359.7 Mb), producing 55,897 Mbp and 56,418 Mbp of clean reads for Yein-early and WT, with mapping rates of 84.8% and 86.9%, respectively. Comparative genomic analysis revealed extensive polymorphisms in Yein-early: 650,257 SNPs and 105,817 InDels, including 72,155 homozygous SNPs and 4,683 homozygous InDels. Most variants occurred in gene regions (26,339 genes for SNPs; 14,889 for InDels), indicating broad genomic perturbation. SNP polymorphisms were markedly more abundant than InDels, and Yein-early displayed a large number of fixed mutations, suggesting radiation-induced genomic restructuring. Transcriptome profiling of immature fruit identified differentially expressed genes. Up-regulated genes were associated with metabolism, transport, and photosynthetic processes, while genes linked to ribosomal function and redox balance were down-regulated. These multi-omic data connect phenotype, genomic variation, and transcriptional regulation, providing insight into the mechanisms underlying the peel pigmentation and altered leaf morphology of Yein-early.

Mushrooms are considered as health boosting medicinal fungi for hundred years that contains β -glucans mainly β-D-glucose, a bioactive components presents on the cell wall of fungi. β-glucans are not synthesized de novo but has important role in terms of immunomodulatory, anti-tumor, anti-inflammatory, anti-aging and reducers of glycemic and lipidemic indexes. Edible and medicinal mushroom β-glucans have great contribution in many areas of the biotechnological development such as pharmaceuticals, nutraceutical products, and functional foods for human and animals. Mushroom β-glucans are reported to be pharmacologically safe, efficient and non-toxic even at higher doses. Mushroom β-glucans can act as a prebiotics which may have great effects on gut microbiota, improve gastrointestinal health and metabolic disorders. However, the efficacy of β-glucans depends on its structural differences, bioavailability, solubility, molecular weight and species of mushrooms. This review encompasses the pharmacological effect of β–glucans sourced from mushroom in terms of managing obesity, diabetes and cardiovascular disease (CVD), immunomodulating effects, gut microbial shifting, management of inflammatory bowel disease (IBD) and Crohn’s disease or colitis, different cancer treatments, emerging diseases like COVID-19 as well as animal health management. This review also tried to find out research gaps in mushroom β-glucans and future directions for nanobiotechnological development of mushroom β-glucans for human and animal welfare.

This study conducts a rigorous comparative analysis between two cutting-edge instance segmentation methods, Mask R-CNN and YOLOv8, focusing on stomata pore analysis. A novel dataset specifically tailored for stomata pore instance segmentation, named PhenomicsStomata, was introduced. This dataset posed challenges such as low resolution and image imperfections, prompting the application of advanced preprocessing techniques, including image enhancement using the Lucy-Richardson Algorithm. The models underwent comprehensive evaluation, considering accuracy, precision, and recall as key parameters. Notably, YOLOv8 demonstrated superior performance over Mask R-CNN, particularly in accurately calculating stomata pore dimensions. Beyond this comparative study, the implications of our findings extend across diverse biological research, providing a robust foundation for advancing our understanding of plant physiology. Furthermore, the preprocessing enhancements offer valuable insights for refining image analysis techniques, showcasing the potential for broader applications in scientific domains. This research marks a significant stride in unraveling the complexities of plant structures, offering both theoretical insights and practical applications in scientific research.

Citrus unshiu Marc. cv. Miyagawa-wase is one of the most widely cultivated citrus varieties on Jeju Island in Republic of Korea. Mutation breeding is a useful tool for inducing genetic diversity by causing genomic mutations in a short period of time. We previously conducted mutation breeding using gamma irradiation to develop new varieties of C. unshiu. Here, we describe one of these varieties, Yein-early, which has a redder peel, greater hardness, and higher sugar content compared with the wild type (WT). Yein-early leaves also showed a unique phenotype compared with the WT, characterized by longer longitudinal length, shorter transverse length, stronger curling, and longer petiole length. Genome resequencing of Yein-early and the WT uncovered significant single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). These variations were crucial in identifying molecular markers unique to Yein-early. In addition, we developed an allele-specific PCR marker specifically targeting a homozygous SNP in Yein-early that distinguishes it from the WT and other citrus varieties. This study contributes to the understanding of pigment synthesis in fruits and provides a valuable tool for selection of the novel Yein-early variety in citrus breeding programs.

Gamma-ray irradiation is one of the most widely used mutagens worldwide. We previously conducted mutation breeding using gamma irradiation to develop new Citrus unshiu varieties. Among these mutants, Gwonje-early had an ovate shape, a protrusion of the upper part of the fruit, and a large fruit size compared with wild-type (WT) fruits. We investigated the external/internal morphological characteristics and fruit sugar/acid content of Gwonje-early. Additionally, we investigated genome-wide single-nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variants in Gwonje-early using whole-genome re-sequencing. Functional annotation by Gene Ontology analysis confirmed that InDels were more commonly annotated than SNPs. To identify specific molecular markers for Gwonje-early, allele-specific PCR was performed using homozygous SNPs detected via Gwonje-early genome re-sequencing. The GJ-SNP1 and GJ-SNP4 primer sets were effectively able to distinguish Gwonje-early from the WT and other commercial citrus varieties, demonstrating their use as specific molecular markers for Gwonje-early. These findings also have important implications in terms of intellectual property rights and the variety protection of Gwonje-early. Our results may provide insights into the understanding of morphological traits and the molecular breeding mechanisms of citrus species.

‘Miyagawa-wase’ mandarin (Citrus unshiu Marc. cv. Miyagawa-wase early) is one of the most widely cultivated citrus varieties on Jeju Island in Korea. Mutation breeding is a useful tool for the induction of genetic diversity for the rapid creation of new plant variants. We previously reported the use of gamma irradiation for the development of new citrus varieties. Here, we report a new mutant, Ara-unshiu, with a unique late fruit ripening phenotype. We investigated the fruit morphological characteristics including weight, vertical/transverse diameter, peel thickness, hardness, and color difference, as well as sugar and acid contents of the Ara-unshiu compared to wild-type controls. We then used whole genome re-sequencing and functional annotation by gene ontology to identify and characterize single nucleotide polymorphism (SNP) and insertion/deletion (InDel) variants in the Ara-unshiu, finding a greater abundance of annotated genes containing InDels compared to SNPs. Finally, we used allele-specific PCR to identify molecular markers among the homozygous SNPs detected from the Ara-unshiu genome sequencing. We report a primer set that effectively distinguishes the Ara-unshiu from the wild-type control and other citrus varieties. Our findings provide insights into the mechanisms controlling the timing of fruit ripening and tools for the molecular breeding of citrus varieties.