Pre-harvest sprouting (PHS) is one of the important traits that not only cause serious economic issues but also lead to reduction in grain quality and yield in rice (Oryza sativa L.). To analyze the quantitative trait loci (QTLs) for PHS tolerance, we evaluated PHS, seed dormancy (SD), and low-temperature germination (LTG) of 88 F_2:3 populations and their parental lines. Genotypic analysis was performed by using 441 single nucleotide polymorphisms (SNPs) detected from re-sequencing data. Seed dormancy (SD) and low-temperature germination (LTG) were identified to exhibit a positive correlation with PHS. Under the field condition, two major QTLs for PHS, qPHS1-1^FC and qPHS1-2^FC were identified on chromosome 1. Under the growth chamber condition, qPHS1-1^GC and qPHS1-2^GC had the same regions on chromosome 1. QTLs of SD and LTG (qSD1-1, qSD1-2, qLTG1-1, and qLTG1-2) had the same regions; these results suggested that candidate QTLs demonstrate pleiotropy about PHS, SD, and LTG. The major QTLs detected in this study are hypothesized to provide an important resource for molecular breeding and gain a better understanding of the genetics of traits in rice.

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• Integrated physiological, genetic, and environmental insights into pre-harvest sprouting in cereal for climate-resilient breeding
  Trung Quoc Nguyen, Gioi Huy Dong, Nguyen LV, Thao Duc Le, Nguyen Nguyen Chuong, Weiqiang Li, Ha Duc Chu, Cuong Ngoc Duong, Lam-Son Phan Tran
  Seed Biology.2026;[Epub]     CrossRef
• Mapping QTLs for PHS resistance and development of a deep learning model to measure PHS rate in japonica rice
  Soojin Jun, Mi Hyun Cho, Hyoja Oh, Younguk Kim, Dong Kyung Yoon, Myeongjin Kang, Hwayoung Kim, Seon‐Hwa Bae, Song Lim Kim, Jeongho Baek, HwangWeon Jeong, Jae Il Lyu, Gang‐Seob Lee, Changsoo Kim, Hyeonso Ji
  The Plant Genome.2025;[Epub]     CrossRef
• Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice
  Kelvin Dodzi Aloryi, Nnaemeka Emmanuel Okpala, Mawuli Korsi Amenyogbe, Daniel Bimpong, Benjamin Karikari, Hong Guo, Semiu Folaniyi Bello, Selorm Akaba, Akwasi Yeboah, Abdul Razak Ahmed, Patrick Maada Ngegba, Nabieu Kamara, Juliet Nkiruku Anyanwu, Danielle
  BMC Plant Biology.2025;[Epub]     CrossRef
• QTL Analysis for Pre-Harvest Sprouting and Low-Temperature Germinability Using Recombinant Inbred Lines Derived from a Cross between ‘Chamdongjin’ and ‘Younghojinmi’
  Hyun-Su Park, Jeonghwan Seo, Heyonso Ji, Gileung Lee, Chang-Min Lee, Jae-Ryoung Park, Songhee Park, Keon-Mi Lee, Mina Jin, O-Young Jeong
  Korean Journal of Breeding Science.2024; 56(2): 79.     CrossRef
• Discovery of Genomic Regions and Candidate Genes for Awn Length Using QTL-seq in Rice (Oryza sativa L.)
  Dongryung Lee, Hongjia Zhang, Yuting Zeng, Backki Kim, Soon-Wook Kwon
  Plant Breeding and Biotechnology.2023; 11(4): 271.     CrossRef
• Fine-Mapping Analysis of the Genes Associated with Pre-Harvest Sprouting Tolerance in Rice (Oryza sativa L.)
  Seong-Gyu Jang, Backki Kim, Insoo Choi, Joohyun Lee, Tae-Ho Ham, Soon-Wook Kwon
  Agronomy.2023; 13(3): 818.     CrossRef
• QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice
  Chang-Min Lee, Hyun-Su Park, Man-Kee Baek, O-Young Jeong, Jeonghwan Seo, Suk-Man Kim
  Frontiers in Plant Science.2023;[Epub]     CrossRef
• Application of CRISPR/Cas9 Genome Editing System to Reduce the Pre- and Post-Harvest Yield Losses in Cereals
  Thumadath Palayullaparambil Ajeesh Krishna, Theivanayagam Maharajan, Stanislaus Antony Ceasar
  The Open Biotechnology Journal.2022;[Epub]     CrossRef
• Seed Dormancy and Pre-Harvest Sprouting in Rice—An Updated Overview
  Soo-In Sohn, Subramani Pandian, Thamilarasan Senthil Kumar, Yedomon Ange Bovys Zoclanclounon, Pandiyan Muthuramalingam, Jayabalan Shilpha, Lakkakula Satish, Manikandan Ramesh
  International Journal of Molecular Sciences.2021; 22(21): 11804.     CrossRef

Spotted leaf mutants which produce necrotic lesions spontaneously are important sources to study programmed cell death in plant defense responses. A novel white-spotted leaf (wspl) mutant was induced from Ilpum, Korean japonica rice cultivar by the treatment of ethyl methane sulfonate (EMS). The phenotype of wspl mutant differed from that of other spotted leaf mutants in that not only brown spots but also white lesion mimic spots were observed on the tip of the leaves from the vegetative stage. Strong nitro blue tetrazolium (NBT) and 3, 3ʹ-diaminobenzidine (DAB) staining were observed on the older leaf of wspl mutant in microscopic reactive oxygen species (ROS) assay, and the chlorophyll content of wspl mutant maintained longer than wild-type in the old leaves. Genetic analysis revealed that the wspl mutant trait was controlled by a single recessive gene and the locus of wspl gene was mapped on the long arm of chromosome 5 between the flanking markers S05100 and S05112 (4.1 Mb). Through the combination of the genetic mapping and SNP analysis, two candidate genes for white-spotted leaf were identified in the genic region. A novel phenotype of white-spotted leaf mutant has not yet been reported, thus further study of the wspl mutant will contribute to understanding of the molecular mechanisms involved in lesion mimic phenotype in rice.

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• Next generation sequencing-based MutMap identifies genomic regions associated with strong culm in rice
  Pritam Kanti Guha, Anil A. Hake, Kalyani M. Barbadikar, Potupureddi Gopi, Nakul D. Magar, Vishalakshi Balija, C. G. Gokulan, Madhavilatha Kommana, Md Jamaloddin, Anjana Sharma, Raju Madanala, A. Chandra Sekhar, D. Vijaya Raghava Prasad, D. Vijaya Lakshmi,
  Journal of Crop Science and Biotechnology.2026;[Epub]     CrossRef
• Rice Lesion Mimic Mutants (LMM): The Current Understanding of Genetic Mutations in the Failure of ROS Scavenging during Lesion Formation
  Sang Gu Kang, Kyung Eun Lee, Mahendra Singh, Pradeep Kumar, Mohammad Nurul Matin
  Plants.2021; 10(8): 1598.     CrossRef

Sesame (Sesamum indicum L.) is the queen of oil seed crops and is cultivated widely in tropical and subtropical areas. The availability of the sesame genome sequence presents unprecedented opportunities for studying its genetics, genomics, and evolution. In this report, we conducted a genome resequencing-based identification of sesame orthologs; in total, 26,379 coding sequences (CDSs) were isolated. Using a reciprocal best hit, we ultimately identified a total of 639 orthologs sets after one-to-one orthologs extraction across seven Pentapetalae plant species. These orthologs were considered to be the most credible between the two species, and in sesame. Furthermore, we performed a branch model-based maximum likelihood estimation of dN/dS of the orthologs, resulting in the identification of 198 evolutionarily accelerated orthologs and 66 positively selected genes (P-value and FDR < 0.05). An enrichment analysis and protein interaction network suggested 19 genes with important functions of the orthologs specific in sesame development and domestication. The method we used here provides a case study for identifying orthologous genes between sesame and other plants species that are distributed in equilibrium phylogenetically, which can be used in other plants.

The
objective
of this study was to develop high-throughput SNP or SNP-based markers by re-sequencing of two peanut cultivars, ‘K-Ol’ and ‘Pungan’. The whole genome re-sequencing for the two cultivars was performed to produce sequences of 35.3 × 10⁹ bp with 350 × 10⁶ reads and 32.0 × 10⁹ bp with 318 × 10⁶ reads, respectively. As compared with the peanut reference genome, the distribution of homozygous and heterozygous SNPs on each chromosome showed very similar patterns between ‘K-Ol’ and ‘Pungan’, and most of them were in intergenic-region regardless of the peanut cultivars and reference genome type. The SNPs identified between the two peanut cultivars were evenly distributed across chromosomes of peanut diploid A and B reference genomes. It indicated that these SNPs could be available to construct a genetic map using the segregating population derived from a cross between ‘K-Ol’ and ‘Pungan’. Total 61 CAPS marker were developed and tested for their availability. Of the CAPS markers, 60 CAPS markers produced normal PCR products and 18 out of them presented polymorphism among 6 peanut varieties. Results of the present study could provide useful genetic resources to facilitate marker-assisted selection for breeding programs as well as germplasm screening for peanut.

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• Optimization of commercial SNP arrays and the generation of a high-efficiency GenoBaits Peanut 10K panel
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  Scientific Reports.2025;[Epub]     CrossRef
• Identification of QTL Associated With Luteolin Content in Peanut (Arachis hypogaea L.) Shells
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• Genome-wide association and RNA-seq analyses reveal genes linked to salt stress in peanut (Arachis hypogaea L.)
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  Theoretical and Applied Genetics.2024;[Epub]     CrossRef
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• Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)
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  Food Science and Biotechnology.2018; 27(5): 1275.     CrossRef