• Molecules and Cells
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• v.21 no.3
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• pp.360-366
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• 2006

Up to 35% of the rice genome consists of various kinds of transposons, and CACTA and MITE are two of the major class 2 DNA transposons in the genome. We have employed the consensus sequences of Rim2/Hipa CACTA, Stowaway MITE Pangrangja, and Tourist MITE Ditto for transposon display (TD) analysis to locate them on a genetic map, with 58 SSR markers used to anchor them. The TD analysis produced a high profile of the polymorphisms between the parental lines, Oryza sativa var. Gihobyeo/O. sativa var. Milyang, in intraspecific $F_{15}$ RIL lines, locating 368 markers of Rim2/Hipa CACTA, 78 markers of Tourist MITE Ditto, and 22 markers of Stowaway MITE Pangrangja. In the segregation analysis, non-parental segregating bands and segregation distortion bands were observed. The recombinant genetic map spans 3023.9 cM, with 5.7 cM the average distance between markers. The TD markers were distributed unequally on the chromosomes because many TD markers were located in pericentric chromosomal regions except in the cases of chromosomes 2, 3, 6 and 9. Although the number of transposon markers was not sufficient to include all rice class 2 transposons, the current map of CACTA and MITE transposons should provide new insight into the genome organization of rice since no previous DNA transposon map is available.

• Molecules and Cells
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• v.45 no.5
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• pp.273-283
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• 2022

During meiosis, homologous chromosomes (homologs) pair and undergo genetic recombination via assembly and disassembly of the synaptonemal complex. Meiotic recombination is initiated by excess formation of DNA double-strand breaks (DSBs), among which a subset are repaired by reciprocal genetic exchange, called crossovers (COs). COs generate genetic variations across generations, profoundly affecting genetic diversity and breeding. At least one CO between homologs is essential for the first meiotic chromosome segregation, but generally only one and fewer than three inter-homolog COs occur in plants. CO frequency and distribution are biased along chromosomes, suppressed in centromeres, and controlled by pro-CO, anti-CO, and epigenetic factors. Accurate and high-throughput detection of COs is important for our understanding of CO formation and chromosome behavior. Here, we review advanced approaches that enable precise measurement of the location, frequency, and genomic landscapes of COs in plants, with a focus on Arabidopsis thaliana.

• Childhood Kidney Diseases
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• v.28 no.1
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• pp.8-15
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• 2024

With the rapid evolution of diagnostic tools, particularly next-generation sequencing, the identification of genetic diseases, predominantly those with pediatric-onset, has significantly advanced. However, this progress presents challenges that span from selecting appropriate tests to the final interpretation of results. This review examines various genetic testing methodologies, each with specific indications and characteristics, emphasizing the importance of selecting the appropriate genetic test in clinical practice, taking into account factors like detection range, cost, turnaround time, and specificity of the clinical diagnosis. Interpretation of variants has become more challenging, often requiring further validation and significant resource allocation. Laboratories primarily classify variants based on the American College of Medical Genetics and Genomics and the Association for Clinical Genomic Science guidelines, however, this process has limitations. This review underscores the critical role of clinicians in matching patient phenotypes with reported genes/variants and considering additional factors such as variable expressivity, disease pleiotropy, and incomplete penetrance. These considerations should be aligned with specific gene-disease characteristics and segregation results based on an extended pedigree. In conclusion, this review aims to enhance understanding of the complexities of clinical genetic testing, advocating for a multidisciplinary approach to ensure accurate diagnosis and effective management of rare genetic diseases.

• Mycobiology
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• v.49 no.3
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• pp.235-248
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• 2021

This study aimed to understand whether the geo-ecological segregation of native plant species affects the root-associated fungal community. Rhizoplane (RP) and rhizosphere (RS) fungal microbiota of Sedum takesimense native to three geographically segregated coastal regions (volcanic ocean islands) were analyzed using culture-independent methods: 568,507 quality sequences, 1399 operational taxonomic units, five phyla, and 181 genera were obtained. Across all regions, significant differences in the phyla distribution and ratio were confirmed. The Chao's richness value was greater for RS than for RP, and this variance coincided with the number of genera. In contrast, the dominance of specific genera in the RS (Simpson value) was lower than the RP at all sites. The taxonomic identity of most fungal species (95%) closely interacting with the common host plant was different. Meanwhile, a considerable number of RP only residing fungal genera were thought to have close interdependency on their host halophyte. Among these, Metarhizium was the sole genus common to all sites. These suggest that the relationship between potential symbiotic fungi and their host halophyte species evolved with a regional dependency, in the same halophyte species, and of the same natural habitat (volcanic islands); further, the fungal community differenced in distinct geographical regions. Importantly, geographical segregation should be accounted for in national culture collections, based on taxonomical uniqueness.

• Journal of Sericultural and Entomological Science
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• v.39 no.2
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• pp.134-139
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• 1997

To elucidate genetical and biochemical characters of the white egg strains preserved in National Sericultural and Entomology Research Institute(NSERI), RDA of Korea, the genetic segregation ratios in egg colours were investigated by crossing test, and egg pigment precursors were also analyzed by paper chromatography and UV-spectrophotometer scanning. The result obtained by crossing test between the white egg strains and normal one illustrated that the most of white egg strains showed typical segregation ratio of white egg-2(w-2), while maternal inheritance which can be seen in white egg-1(w-1) was not found in any white egg strains. Paper chromatographic analysis showed that egg extracts of all the white egg strains contained 3OH-kynurenine, while kynurenine which is known to existed in white egg-1(w-1) could not be detected at all. From the results of these experiments, it was found that all the white egg strains preserved in NSERI were classified as the white egg-2(w-2) strain.

• Journal of Plant Biology
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• v.39 no.3
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• pp.185-188
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• 1996

Randomly amplified polymorphic DNAs were employed to study the genetic variation and gene introgression in potato dihaploids (2n=24) which were generated after interspecific pollination of tetraploid cultivars (2n=4X=48, Solanum tuberosum cv Irish Cobbler, Superior and Dejima) by haploid inducer clones (2n=2X=24, Solanum phureja 1.22, Hes-5 and Hes-6). Genetic variation and DNA marker segregation among dihaploids were observed. Most dihaploids contain S. tuberosum specific RAPD markers but haploid inducer-specific RAPD markers were also found in some dihaploids. Of six different arbitrary 10-mer oligonucletide primers which showed polymorphism betwen tetraploid cultivars and haploid inducers used, three generated amplification products which seemed to be derived from the S. phureja parent. Our results indicate that chromosomes of dihaploids may not be pure S. tuberosum and the dihaploids may not be produced by parthenogenesis.

• Korean Journal of Breeding Science
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• v.43 no.4
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• pp.260-264
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• 2011

Leaf structure is one of the important agronomic traits. A rolled leaf mutant was induced from an ethyl methane sulfonate (EMS)-treated japonica rice, 'Koshihikari'. The rolled leaf mutant showed phenotypes of reduced leaf width and leaf rolling. In addition, several abnormal morphological characteristics were observed, including dwarfism, defected panicle, delayed germination, and lower seed-setting. Microscopic analysis revealed that the number of small veins was decreased and the sizes of adaxial bulliform cells were reduced in the mutant leaves. The genetic study with two $F_2$ populations from the crosses of the rolled leaf mutant with 'Koshihikari' and Milyang23 suggested that the mutant phenotype might be controlled by a single dominant gene.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.56 no.1
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• pp.14-17
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• 2011

Dwarfuess and Kunitz trypsin inhibitor (KTI) protein in soybean is useful traits for basic studies. df2 and ti gene control dwarfness and the expression of Kunitz trypsin inhibitor (KTI) protein in soybean, respectively. The objective of this research was to verify genetic linkage or independent inheritance of df2 and ti loci in soybean. The $F_2$ population was made by cross combination between "Gaechuck#2" (Df2Df2titi genotype, KTI protein absence and a normal growth type) and T210 (df2df2TiTi genotype, a dwarf growth type and KTI protein present). A total of 258 $F_2$ seeds were analyzed for the segregation of KTI protein using SDS-PAGE. And so, 198 $F_2$ plants were recorded for the segregation of dwarfness. The segregation ratio of 3 : 1 for Ti locus (201 Ti_ : 57 titi) and Df2 locus (143 Df2_ : 55 df2df2) was observed. Segregation ratio of 9 : 3 : 3 : 1 (116 Ti_Df2_: 44 Ti_df2df2: 27 titiDf2_: 11 titidf2df2) between df2 gene and ti gene was observed ($x^2$=3.53, P = 0.223). These results showed that df2 gene was inherited independently with the ti gene in soybean.

• Molecules and Cells
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• v.20 no.2
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• pp.201-209
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• 2005

We have constructed an AFLP-based linkage map of Japanese red pine (Pinus densiflora Siebold et Zucc.) using haploid DNA samples of 96 megagametophytes from a single maternal tree, selection clone Kyungbuk 4. Twenty-eight primer pairs generated a total of 5,780 AFLP fragments. Five hundreds and thirteen fragments were verified as genetic markers with two alleles by their Mendelian segregation. At the linkage criteria LOD 4.0 and maximum recombination fraction 0.25(${\theta}$), a total of 152 markers constituted 25 framework maps for 19 major linkage groups. The maps spanned a total length of 2,341 cM with an average framework marker spacing of 18.4 cM. The estimated genome size was 2,662 cM. With an assumption of equal marker density, 82.2% of the estimated genome would be within 10 cM of one of the 230 linked markers, and 68.1% would be within 10 cM of one of the 152 framework markers. We evaluated map completeness in terms of LOD value, marker density, genome length, and map coverage. The resulting map will provide crucial information for future genomic studies of the Japanese red pine, in particular for QTL mapping of economically important breeding target traits.

• The Korean Journal of Mycology
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• v.49 no.4
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• pp.487-495
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• 2021

Lentinula edodes is a tetrapolar basidiomycete and its mating type is determined by two unlinked genetic loci, A and B. Theoretically, one dikaryotic strain could produce basidiospores with four different mating types in a 1:1:1:1 ratio. Previous studies have described the skewed segregation ratio of mating types among basidiospores of L. edodes. However, they were based only on morphological characteristics, such as clamp connection, to determine mating types. To clarify whether the segregation distortion of mating types is a general phenomenon in L. edodes, we analyzed the mating types of basidiospores obtained from three cultivars of L. edodes using recently developed DNA markers. We found that the skewed segregation of mating types was strain-specific, as reported previously. Among the three cultivars, one cultivar showed balanced segregation, while the other two displayed distorted segregation. We also examined the relationship between mating type and mycelial growth rate of monokaryons derived from each basidiospore. It was found that the monokaryotic mycelial growth rate was related to the A mating type but not to the B mating type. Therefore, homeodomain transcription factor genes that reside on the A locus or other genes linked to the A locus affect the growth rate of monokaryotic mycelia. Considering the importance of mating types in mushroom breeding, this study is informative for establishing an efficient breeding strategy as well as for understanding the mechanism of monokaryotic mycelial growth.