Gelatinization temperature (GT) is an important component of eating and cooking quality (ECQ) of rice. While direct measurement of GT is cumbersome, the alkali spreading value (ASV) test is a robust method commonly used to rapidly identify different GT types. In this study, we employed a modified ASV assay to screen a population of chemically-induced rice (cv. Kitaake) mutants (n = 405). Two mutant families, KDS-1623B and KDS-1824B, with significantly lower ASV (higher GT type) than wild type Kitaake (low GT type) were isolated. A nonsynonymous homozygous mutation in the isoamylase-type starch debranching enzyme gene ISA1 was identified in KDS-1623B. The mutation (G2709T) is predicted to change a valine at position 354 to a leucine in the α-amylase catalytic domain of ISA1. This result is consistent with the shrunken endosperm exhibited by KDS-1623B grains and the replacement of starch with phytoglycogen in isa1 (sugary-1) mutants. The altered ASV trait in KDS-1824B appears to be controlled by a single recessive mutation; however, the causal genetic lesion remains to be determined. These mutants will be useful resources for elucidating the complex nature of starch metabolism and its influence on ECQ of rice.

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• Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
  Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
  G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
• Efficient identification of palatability-related genes using QTL mapping in rice breeding
  Yoon-Hee Jang, Jae-Ryoung Park, Eun-Gyeong Kim, Rahmatullah Jan, Saleem Asif, Muhammad Farooq, Dan-Dan Zhao, Kyung-Min Kim
  Molecular Breeding.2023;[Epub]     CrossRef

Simple sequence repeat (SSR) markers were developed from Pinus densiflora, a species native to Asia, to investigate its genetic diversity and population structure in order to provide information for the management and breeding of this species. Using next-generation sequencing, a total of 1,008 putatively polymorphic SSR primer sets were designed. Seventeen polymorphic SSR markers in 121 individuals belonging to four natural populations of P. densiflora were identified and characterized, with three to seventeen alleles per locus. The expected heterozygosity ranged from 0.1844 to 0.8731 in four populations, and the average of the PIC values ranged from 0.2789 to 0.8488. Cross amplification of these markers was performed among the related species P. rigida, P. koraiensis, P. parviflora, and P. bungeana. The developed novel SSR markers are promising tools for studying the genetic diversity or population structure of P. densiflora and its related species.

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• Analysis of the genetic diversity and population structure of Lindera obtusiloba (Lauraceae), a dioecious tree in Korea
  Ho Bang Kim, Hye-Young Lee, Mi Sun Lee, Yi Lee, Youngtae Choi, Sung-Yeol Kim, Jaeyong Choi
  Journal of Plant Biotechnology.2023;[Epub]     CrossRef
• Genome-wide microsatellite characterization and marker development in Diospyros oleifera
  Yang Xu, Cuiyu Liu, Xu Yang, Kaiyun Wu, Bangchu Gong
  Industrial Crops and Products.2023; 203: 117182.     CrossRef
• Genetic Diversity and Structure of Pinus densiflora Siebold & Zucc. Populations in Republic of Korea Based on Microsatellite Markers
  Ji-Young Ahn, Jei-Wan Lee, Kyung-Nak Hong
  Forests.2021; 12(6): 750.     CrossRef

Miniature transposable elements (mTEs) such as miniature inverted-repeat transposable element (MITE), terminal repeat retrotransposon in miniature, and short interspersed element are exquisite sources for marker development. mTEs are short, non-autonomous and stably inherited. The high-copy members are widely distributed into the gene rich euchromatic regions. Here, we conducted a modified transposon display (TD) for a high-copy MITE family, BraSto-2 (Bs2). The Bs2-specific primers derived from conserved sequences of Bs2 members as well as MseI adapter primers were used for polymerase chain reaction (PCR) in two Brassica rapa accessions, ‘Chiifu’ and ‘Kenshin’. The pooled PCR products were sequenced by Illumina sequencing platform instead of high-resolution gel electrophoresis. Subsequent in silico-based insertion polymorphism (IP) analysis (next-generation sequencing [NGS]-based Bs2 transposon display) was conducted, which generated more than 99 putative polymorphic insertion sites between ‘Chiifu’ and ‘Kenshin’. Among 90 successful PCR amplification, 34 showed Bs2 IP (IP-Bs2) between ‘Chiifu’ and ‘Kenshin’ accessions, 27 and seven ‘Chiifu’- and ‘Kenshin’-unique insertions, respectively. When the 90 IP-Bs2 primer sets were applied to 10 Brassica accessions, including four additional B. rapa and B. oleracea accessions, 69 (76%) showed insertion olymorphism among accessions. The IP-Bs2 were evenly distributed through all the chromosomes and provide rich polymorphism among various B. rapa and B. oleracea accessions demonstrating the usefulness of these markers for various genetic diversity and molecular breeding studies in Brassica. In addition, NGS-based TD will be applicable to various high copy transposable elements family for high throughput and rapid polymorphic marker development which will be helpful for efficient plant genomics and breeding purposes.

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  Horticultural Plant Journal.2021; 7(6): 539.     CrossRef
• Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding
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  Molecular Biology Reports.2020; 47(4): 3155.     CrossRef

The pear (Pyrus spp.) is most important fruit crop in the world. The genus Pyrus belongs to the subfamily Maloideae in the Rosaceae family and contains at least 22 primary species; however, only a few species, including P. pyrifolia, P. ussuriensis, P. bretschneideri, and P. communis have been utilized for fruit production. In Korea, awareness of the importance of the fruit industry and fruit tree breeding is low, and there is little support for genetic and genomic studies of fruit trees. In foreign countries, studies have focused on obtaining genomic information of fruit crops and the development of important agronomic trait-related molecular markers, providing a genomic framework for fruit tree breeding. Although Korea does not actively participate in research on the genomics of fruit trees, it is not far behind other countries in terms of technology and is therefore still competitive in research and development. The resequencing of ‘Whangkeumbae’ and ‘Minibae’ pears has been performed using the Illumina Hiseq 2000 platform as a part of the Biogreen 21 project, offering novel, rapid methods for identification of molecular marker, such as single nucleotide polymorphisms, insertion-deletions, and simple sequence repeats, through next-generation sequencing (NGS) technology. These NGS-based molecular markers are useful for genetic studies of Asian pears, e.g., for construction of genetic linkage maps, mapping of quantitative trait loci, and marker-assisted selection.

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• Fruit Cracking in Pears: Its Cause and Management—A Review
  Ho-Jin Seo, Shailesh S. Sawant, Janghoon Song
  Agronomy.2022; 12(10): 2437.     CrossRef
• Construction of a Genetic Map using the SSR Markers Derived from “Wonwhang” of Pyrus pyrifolia
  Ji Yun Lee, Mi-Suk Seo, So Youn Won, Kyoung Ah Lim, Il Sheob Shin, Dongsu Choi, Jung Sun Kim
  Korean Journal of Breeding Science.2018; 50(4): 434.     CrossRef
• Researches of pear tree (Pyrus spp.) genomics
  Youngjae Oh, Hyunsuk Shin, Keumsun Kim, Hyeondae Han, Yoon-Kyeong Kim, Daeil Kim
  Journal of Plant Biotechnology.2015; 42(4): 290.     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
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  Plants.2020; 9(11): 1531.     CrossRef
• QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing
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  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
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  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
  Kyeong-Seong Cheon, Jeongho Baek, Young-il Cho, Young-Min Jeong, Youn-Young Lee, Jun Oh, Yong Jae Won, Do-Yu Kang, Hyoja Oh, Song Lim Kim, Inchan Choi, In Sun Yoon, Kyung-Hwan Kim, Jung-Heon Han, Hyeonso Ji
  Plant Breeding and Biotechnology.2018; 6(4): 391.     CrossRef