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.

Quantitative trait locus (QTL) analysis is a powerful approach for identifying variants associated with the phenotypic variation of complex traits. However, selecting optimal methods and pre-processing steps require considerable time and effort. In this study, we demonstrated applicability and replicability of machine learning (ML) models in QTL analysis by evaluating their performance in comparison with conventional QTL analysis methods using 142 recombinant inbred lines derived from two japonica rice cultivars, Koshihikari and Baegilmi. Random forest and gradient boosting models showed the highest predictive accuracy, and consistently identified three QTLs associated with heading date: qDTH3, qDTH6, and qDTH7. Moreover, ML-based QTL analysis detected minor-effect qDTH10, where Koshihikari allele promoted heading date when combined with Koshihikari alleles of qDTH6 and qDTH7. These results demonstrate the applicability of ML models in QTL analysis on bi-parental mapping population in rice.

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• Machine Learning Method to Select Single Nucleotide Polymorphism Markers for Protein Content, Grain Filling Rate, Height, and Panicle Length in Korean Rice
  Jeong-Gu Kim, Minwoo Kim, Gyu-Hwang Park, Jinhyun Kim, Jinho Jung, Tae-Ho Lee
  Korean Journal of Breeding Science.2025; 57(4): 403.     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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• Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines
  Sampath Perumal, Nomar Espinosa Waminal, Jonghoon Lee, Hyun-Jin Koo, Boem-soon Choi, Jee Young Park, Kyounggu Ahn, Tae-Jin Yang
  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
  Venkatesh, B. Nandini
  Molecular Biology Reports.2020; 47(4): 3155.     CrossRef