Tomato (Solanum lycopersicum) is a premier global crop, celebrated not only for its economic importance but also as a fundamental “well-being food” that provides essential vitamins, minerals, and potent antioxidants. This review highlights the transformative impact of CRISPR/Cas9 and next-generation precision tools, such as base and prime editing, on modern tomato breeding. Beyond functional genomics, we focus on the strategic engineering of tomato to maximize productivity through fruit size optimization and the biofortification of high-value metabolites (e.g., GABA, lycopene, and vitamins). Furthermore, we examine recent advances in developing multi-stress resilience against both biotic and abiotic challenges. A significant emphasis is placed on re-designing plant architecture and developmental traits to tailor tomato varieties for future agricultural systems, particularly indoor and vertical farming. By advanced delivery methods, CRISPR technologies offer unprecedented potential to accelerate the development of “smart” tomato, ensuring sustainable agriculture and global food security in a changing climate.

Amylopectin branch-chain length distribution is a key determinant of rice starch functionality and eating quality, yet the genetic basis underlying specific chain fractions remains incompletely understood in diverse germplasm. In this study, amylopectin fine structure was quantified in 137 accessions of the Korean Rice Core Selection (KRICE_Core) using HPAEC-PAD, and genome-wide association studies were conducted with 2.1 million high-quality SNPs under the FarmCPU model. The short-chain distribution (SCD, DP 6-12) varied from 26.85% to 37.20%, whereas the intermediate-chain distribution (ICD, DP 12-24) ranged from 52.57% to 61.04%, and the two fractions showed a strong inverse correlation. GWAS identified two major loci on chromosomes 4 and 6, with the chromosome 6 region showing exceptionally strong association signals and co-localizing with Os06g0229800 (SSIIa). Haplotype analysis of SSIIa detected five non-synonymous SNPs defining five haplotypes. Hap1 and Hap5 were associated with increased SCD and reduced ICD, whereas indica-related haplotypes (Hap2-Hap4) showed the opposite trend, indicating that SSIIa allelic variation quantitatively shifts the balance between short and intermediate chain fractions. In a panel of 113 Korean-bred cultivars, Hap1 and Hap5 together accounted for > 99% of genotypes, suggesting strong directional selection for japonica-type SSIIa alleles during Korean breeding. These findings provide robust molecular targets for designing rice varieties with tailored starch architecture and cooking qualities.

The GeBP gene family, known for its GLABROUS1 enhancer-binding proteins, represents a standard transcription factor characterized by an unconventional leucine-zipper motif. The constituents of this family possess a core DNA-affinity domain. This protein is crucial for controlling plant growth and development. GeBP genes have been analyzed and defined only in some Gramineae crops, Arabidopsis, rice and soybean. However, a comprehensive examination of the role of the GeBP genes in Brassica rapa has yet to be conducted. This study used genome-wide characterization to identify twenty BrGeBP genes and accessible RNA sequencing data to evaluate each gene's expression. Based on phylogenetic research, we grouped 114 GeBP proteins from five different plant species into six groups. Generally, groupings of BrGeBP genes with comparable motifs and exon-intron distribution were conserved. The twenty BrGeBP genes were found on six of the ten B. rapa chromosomes, and one paralog showed segmental duplication. The varied protein motifs and gene structures showed that the GeBP genes had various roles in plants. The functions of BrGeBP genes are numerous and include expressions responsive to specific tissues, stress, and hormones according to cis-elements analysis. Furthermore, expression analysis using RNA sequencing revealed that the genes BrGeBP3, BrGeBP9, and BrGeBP20 showed substantially increased expression in different organs. These findings will aid in elucidating the possible roles and traits of BrGeBP genes in the B. rapa biological cycle and related species.

Rice yield is severely affected by phosphorus (P) deficiency, and plants have evolved various strategies to cope with this limitation. While some rice genotypes are adapted to low phosphate (Pi) availability, others remain sensitive to Pi deficiency. In this study, we conducted a genome-wide association study (GWAS) using a hydroponically cultivated population of 190 North Korean (NK) rice plants to identify genes associated with phosphorus use efficiency (PUE) and Pi deficiency tolerance. The rice plants were grown in Yoshida nutrient media with either full (10 mg/L) or low-P (1 mg/L) concentrations for 40 days. The phenotypic response to Pi deficiency was assessed at the seedling stage, followed by an evaluation of eight agricultural traits: chlorophyll content (SPAD), shoot length (SL), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), root dry weight (RDW), and tiller number (TN). The GWAS analysis revealed a total of 166 significant lead SNPs, with six located near known genes for Pi deficiency tolerance: OsTre6P and OsPT3 for RL, OsGH3.12 for SPAD, OsCPK30 for SL, OsWRKY74 for RSL, and OsPT10 for RSL and RRFW. An additional six lead SNPs were identified as novel genes. The haplotypes of 12 candidate genes showed significant differences in the phenotypic values of the corresponding traits. In conclusion, both known and novel genes identified in this GWAS have significant impacts on Pi deficiency tolerance in the NK rice population.

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• Transcription factors in phosphorus utilization: enhancing crop productivity and stress resilience
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• Genetic Exploration of β-glucan and Cellulose Synthesis in Barley
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• RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice
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  Briefings in Bioinformatics.2024;[Epub]     CrossRef

Gene introgression that involves the transfer of favorable allelic diversity for broadening the genetic base of breeding materials is a powerful 'toolkit' for creating novel allelic combinations during plant sexual reproduction. It is a key factor playing an important role in plant breeding schemes by reintroducing genetic variation at selective sweeps or introgression of desirable traits required for the development of new varieties. Meiosis is a specialized cell division not only enables sexually reproducing organisms to reduce their genomic constituent by half, also provides indefinitely novel combinations of allelic diversity by reshuffling the parental genetic makeup. Crossing over that takes place during prophase-I facilitates the meiotically exchange of genetic materials between homolog pairs as well as their accurate segregations. It is tightly modulated and many intrinsic factors and extrinsic agents are associated with regulation of the process, however, the modulation of meiosis is possible. Although, advanced approaches such as CRIPR/Cas and Virus-Induced gene Silencing (VIGS) have opened new horizons for manipulation of meiotic recombination, distant hybridization could effectively influence the frequency and distribution of homologous (HR) and particularly homoeologous recombination (HeR). In this review, we provide a brief overview of the recent advances in the plant mechanisms for manipulation of HR and HeR employing distant hybridization.

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Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (qSUB3), 4 (qSUB4), 6 (qSUB6-1 and qSUB6-2), 11 (qSUB11-1, qSUB11-2 and qSUB11-3), and 12 (qSUB12-1 and qSUB12-2). Two candidate genes (Os03g0679300 and Os11g0517800) in the two QTL regions associated with submergence tolerance were detected. The results of this study provide associated SNPs in candidate genes for submergence condition and strategies for developing submergence condition in breeding programs.

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• Comprehensive Evaluation of Cold and Anaerobic Tolerance in Rice Oryza sativa L. and Screening of Multistress‐Resistant Germplasm
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• Identification of Candidate Genes for Hypoxia Tolerance in Rice by Genome-Wide Association Analysis and Transcriptome Sequencing
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  Rice.2025;[Epub]     CrossRef
• Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1
  Md Ibrahim Khalil, Md Mahmudul Hassan, Swadesh Chandra Samanta, Abul Kashem Chowdhury, Md Zahid Hassan, Nasar Uddin Ahmed, Uzzal Somaddar, Sharmistha Ghosal, Arif Hasan Khan Robin, Ujjal Kumar Nath, Mohammad Golam Mostofa, David J. Burritt, Chien Van Ha,
  Plant Physiology and Biochemistry.2024; 206: 108224.     CrossRef
• Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)
  Sushma Naithani, Bijayalaxmi Mohanty, Justin Elser, Peter D’Eustachio, Pankaj Jaiswal
  Plants.2023; 12(11): 2146.     CrossRef

Plant Growth Promoting Rhizobacteria (PGPR) were used in many previous studies for increasing plant growth and productivity. Some mechanisms were used to enhance the soil productivity such as mineral phosphate solubilization, siderophore production, biological nitrogen fixation, induced systemic resistance and indole acetic acid (IAA) production. Some of the related researches adopted the phosphate solubilization in organisms which was repressed in the presence of succinate resembling the phenomenon of catabolite repression. In addition, the sugar utilization pattern (monosaccharide, disaccharide, and trisaccharide), organisms showed the characteristics like slow and fast-growing rhizobia respectively. Whole-genome sequencing has been used for identifying unique genes in Fast-growing Rhizobia. Existing literature in PGPR studies has been considered and mechanisms for increasing plant growth and productivity have been identified. The review tries to analyse the mechanism of phosphate solubilization and sugar utilization in fast growing Rhizobia. On the contrary, repression due to various carbon sources such as succinate has been reported, leading to succinate mediated catabolite repression.

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  Current Issues in Molecular Biology.2024; 46(6): 5194.     CrossRef

Targeted genome editing using CRISPR/Cas nucleases has become the standard approach for creating mutant plants. Significant progress has been made to enhance the editing efficiencies through optimizing CRISPR/Cas expression, including applying heat stress. In this study, we used heat stress to enhance the Potato virus X (PVX)-mediated CRISPR/Cas9 mutagenesis in Nicotiana benthamiana. We show that heat stress at 4-5 days after PVX inoculation effectively increases the mutagenesis efficiency of Cas9 nuclease. We observed up to a 5-8% increase in mutation efficiency depending on the sgRNA construct when heat stress is applied to the pPVX-Cas9::sgRNA infiltrated samples. Furthermore, analysis of the effect of the heat stress on the pattern of mutation types in the target gene regions showed no obvious changes in CRISPR/Cas9 induced mutagenesis pattern between heat stress treated and no heat stress treated samples. Overall, our experiments demonstrate that heat stress treatment at the optimal time after viral inoculation is most effective in increasing the PVX-mediated CRISPR/Cas9 editing efficiency in plants.

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  Sunjeet Kumar, Rui Yu, Yang Liu, Yi Liu, Mohammad Nauman Khan, Yonghua Liu, Mengzhao Wang, Guopeng Zhu
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• Broadening the Nicotiana benthamiana research toolbox through the generation of dicer-like mutants using CRISPR/Cas9 approaches
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  Horticulture Research.2024;[Epub]     CrossRef
• Considerations in engineering viral vectors for genome editing in plants
  Xiaoyun Wu, Ying Zhang, Xue Jiang, Tingshuai Ma, Yating Guo, Xiaoxia Wu, Yushuang Guo, Xiaofei Cheng
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• CRISPR/Cas9-gene editing approaches in plant breeding
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  GM Crops & Food.2023; 14(1): 1.     CrossRef

Cultivation of the medicinal herb Panax ginseng Meyer began by domesticating wild mountain ginsengs several hundred years ago in Korea. Elucidating the diversity of the maternally inherited plastid genome (plastome) in diverse ginseng collections including wild ginsengs would provide valuable information on ginseng breeding and cultivation history. We sequenced and compared the plastomes of 44 ginseng accessions collected from various Northeast Asian countries. The plastomes revealed 18 polymorphic sites, including 11 SNPs and 7 InDels, which portrayed less diversity than in the most closely related species, P. quinquefolius. We developed 10 kompetitive allele-specific PCR (KASP) markers and utilized them along with four previously developed InDel markers to characterize the genotypes of 203 ginseng accessions. Digital genotyping based on the developed KASP markers classified the accessions into 10 main and 2 branching haplotypes. Four InDel markers derived from different copy numbers of tandem repeats showed dynamic subgrouping within the haplotypes due to the occurrence of multi-alleles and reversible mutations. The digital haplotype genotyping (haplotyping) revealed that haplotype A, representing 60.1% of the accessions, might be the original plastome form without any SNP occurrence. Accumulation patterns of the variations suggest that nine main haplotypes (B-J) diverged independently by new SNP occurrences from the original plastome, and branching haplotypes may have derived from the first mutant lineage by additional SNP deposition. The digital haplotyping system based on plastome diversity deepens understanding of ginseng evolution and serves as a useful molecular breeding tool.

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• PCR-Based Molecular Authentication Method for Sources of Agrimoniae Herba via Comparative Analyses of Complete Chloroplast Genomes
  Woojong Jang, Sae Hyun Lee, Wook Jin Kim, Sungyu Yang, Byeong Cheol Moon
  International Journal of Molecular Sciences.2025; 26(22): 11189.     CrossRef
• Development and authentication of Panax ginseng cv. Sunhong with high yield and multiple tolerance to heat damage, rusty roots and lodging
  Jiho Seo, Joon-Soo Lee, Sung-Lye Shim, Jun-Gyo In, Chol-Soo Park, Yong-Jae Lee, Hee-Jun Ahn
  Horticulture, Environment, and Biotechnology.2023; 64(5): 753.     CrossRef
• The current research progress of ginseng species: The cultivation and application
  Kaimei Zhang, Shengai Zhang, Atsushi Ebihara, Xiaoqi Zhou, Likun Fan, Pengfei Li, Zhuqi Zhang, Yuyan Wang, Yu Shen
  Cogent Food & Agriculture.2023;[Epub]     CrossRef
• In Vitro Cultivation and Ginsenosides Accumulation in Panax ginseng: A Review
  Fengjiao Xu, Anjali Kariyarath Valappil, Ramya Mathiyalagan, Thi Ngoc Anh Tran, Zelika Mega Ramadhania, Muhammad Awais, Deok Chun Yang
  Plants.2023; 12(17): 3165.     CrossRef

At the reproductive development stage of rice (Oryza sativa L.), temperature stress can decrease spikelet fertility, ultimately resulting in a yield loss. In this study, a total of 98 rice varieties were used in genome-wide association study (GWAS) to understand spikelet fertility under a high temperature (SFHT). GWAS results revealed that two lead SNPs were significantly associated with SFHT. Candidate genes located within ± 250 kb of the corresponding SNP position were discovered, resulting in a total of 21 candidate genes on chromosome 10 and 18 candidate genes on chromosome 11. Based on previously reported function and haplotype analysis, Os10g0177200 (EF-HAND 2domain containing protein) as one candidate gene showed significant differences among groups of haplotypes. This candidate gene will be further evaluated for its function to determine whether it is useful for improving molecular breeding studies and developing new high temperature tolerant rice varieties.

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  Abel Sefasi, Mvuyeni Nyasulu, Rowland Maganizo Kamanga, Louis Yalaukani, Samson Pilanazo Katengeza, Maurice Monjerezi, Charles Malidadi, Kingsley Masamba
  BMC Plant Biology.2025;[Epub]     CrossRef
• Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers
  Muhammad Ashfaq, Abdul Rasheed, Renshan Zhu, Muhammad Ali, Muhammad Arshad Javed, Alia Anwar, Javaria Tabassum, Shabnum Shaheen, Xianting Wu
  Genes.2023; 14(5): 1089.     CrossRef
• An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice)
  Muhammad Abu Bakar Zia, Muhammad Farhan Yousaf, Arslan Asim, Muhammad Naeem
  Molecular Biology Reports.2022; 49(12): 12077.     CrossRef

Brassica oleracea contains various morphotypes within the species, but genomic signatures differentiating each morphotype have been poorly understood of. Here, we utilized whole genome sequence data of 44 B. oleracea collections including those of seven different morphotypes such as cabbage, broccoli, cauliflower, kailan, kale, brussels sprout, and kohlrabi to elucidate the genomic signature of B. oleracea morphotypes. Molecular structure analysis divided the 44 B. oleracea lines into two groups: group I represents broccoli, cauliflower, kailan; group II represents other B. oleracea subspecies. Kohlrabi has admixed genomic structure through genetic admixture analysis. Based on the population stratification result, we have investigated genetic signatures that offer the possible evolutionary processes for the kohlrabi morphotype. Several statistical analyses were implemented to identify selective regions and explore 45 candidate loci that may contribute to stem swollen in kohlrabi. Above all, we identified two kohlrabi-unique genes, LOC106333915 and LOC106308097, showing kohlrabi-unique non-synonymous mutations, which might be candidate genes for stem swollen in kohlrabi.

Milk thistle (Silybum marianum Gaertn.) is a well-known medicinal plant which has been used for more than 2,000 years around the world. It produces silymarin, which cures the liver from hepatitis and toxin damages. In this study, a selfed and purified breeding line of the milk thistle from the Korean environment was used as a source of chloroplast genome construction. It showed high concentration of silybin B (3.50 mg/g) in its dried seeds. The complete chloroplast genome of S. marianum acc. ‘912036’ is 152,556 bp in length and G+C content is 37.69%. A total of 87 protein coding genes with 104 exons were annotated. Chloroplast genomes of five accessions from different countries were compared with that of ‘912036’, and no sequence polymorphism among them was identified. Thus, the chloroplast genome from this study can be used to develop S. marianum-specific DNA markers when compared with other diverse S. marianum accessions and Asteraceae species.

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• The genetics and genomics of milk thistle: unlocking its therapeutic potential through modern breeding and biotechnological innovations
  Priskila Tolangi, Jeehyoung Shim, Raña Mae Sumabat, Sunghan Kim, Hyun-Seung Park, Kyung Do Kim, Hyun Uk Kim, Sanghyun Lee, Joong Hyoun Chin
  Applied Biological Chemistry.2024;[Epub]     CrossRef
• Analysis of silybin A and silybin B in different accessions of Silybum marianum seeds
  Neil Patrick Uy, Jeehyoung Shim, Hak-Dong Lee, Jung Sook Sung, Eunae Yoo, Joong Hyoun Chin, Sanghyun Lee
  Journal of Applied Biological Chemistry.2024;[Epub]     CrossRef
• Agricultural phenotype and silymarin content variations of cultivated milk thistle in Korea
  Jeehyoung Shim, Hyejin Cho, Jung Sook Sung, Eunae Yoo, Joong Hyoun Chin, Sanghyun Lee
  Horticulture, Environment, and Biotechnology.2024; 65(5): 891.     CrossRef
• A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea
  Jeehyoung Shim, Su Young Hong, Jae-Hyuk Han, Yeisoo Yu, Eunae Yoo, Jungsook Sung, Joong Hyoun Chin, O New Lee
  Plants.2023; 12(14): 2702.     CrossRef
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  Pham Anh Thi Nguyen, Do Tan Khang, Pham Thien Trang Nguyen, Hoang Dang Khoa Do
  Mitochondrial DNA Part B.2023; 8(9): 936.     CrossRef
• Assembly and Comparative Analysis of Complete Mitogenome of Silybum marianum (L.) Gaertner
  Jeongwoo Lee, Yedomon Ange Bovys Zoclanclounon, Hwajin Jung, Taeho Lee, Jeonggu Kim, Guhwang Park, Keunpyo Lee, Kwanghoon An, Jeehyoung Shim, Joonghyoun Chin, Suyoung Hong
  Korean Journal of Breeding Science.2022; 54(4): 294.     CrossRef

Salinity stress is one of the important abiotic stresses in crops. In this study, ten different concentrations of NaCl solutions were tested to determine the optimal level of NaCl concentration for salinity tolerance test at the germination stage in peanut, and 0.6% NaC1 was suitable for the test. A total of 249 peanut accessions were tested with 0.6% NaC1 and radical root lengths of the accessions were measured. The results showed that there were significant genetic variations on the tolerance to salinity stress among the tested accessions. Through a Genome-Wide Association Study (GWAS) using the Axiom_Arachis array with 58K SNPs, three putative SNPs with significant relation to radicle root length were identified on chromosomes Aradu.A03, Araip.B01, and Araip.B05.

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• Physiological and biochemical mechanisms underlying the role of anthocyanin in acquired tolerance to salt stress in peanut (Arachis hypogaea L.)
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  Frontiers in Plant Science.2024;[Epub]     CrossRef
• Designing future peanut: the power of genomics-assisted breeding
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  Theoretical and Applied Genetics.2024;[Epub]     CrossRef
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  Sunil S. Gangurde, Janila Pasupuleti, Sejal Parmar, Murali T. Variath, Deekshitha Bomireddy, Surendra S. Manohar, Rajeev K. Varshney, Prashant Singam, Baozhu Guo, Manish K. Pandey
  Frontiers in Genetics.2023;[Epub]     CrossRef
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  Frontiers in Plant Science.2023;[Epub]     CrossRef

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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  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
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  BMC Plant Biology.2025;[Epub]     CrossRef
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  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

Perilla species belong to the Lamiaceae family of flowering plants and are widely grown in East Asia, for use in a traditional herbal medicine or functional food. To identify single nucleotide polymorphisms (SNPs) in Perilla species and conduct a phylogenomic analysis, we determined the complete sequences of the chloroplast (cp) genome and 45S nuclear ribosomal DNA (45S nrDNA) of six cultivated and three wild Perilla species. The complete cp genome ranged in size from 152,588 bp to 152,656 bp and the length variation in cp genomes was 68 bp. The length of the 45S nrDNA ranged from 6,235 bp to 8,303 bp and the main variation of length differences was in the intergenic spacer (IGS) region. Comparative analysis of the cp genome sequences of nine Perilla species showed low genetic diversity at the intra- and inter-species level. Using SNP analysis, we detected 42 synonymous SNPs (sySNPs) from 27 genes and 37 non-synonymous SNPs (nsSNPs) from 15 genes. A comparison of the 45S nrDNA sequences revealed two SNPs in the 18S rRNA, five SNPs in the 26S rRNA, three SNPs and two InDels in the internal transcribed spacer (ITS) 1 region, and six SNPs in the ITS 2 region. Our phylogenomic analysis suggests that the tetraploidization of Perilla cultivars may have arisen from the P. citriodora genome. The genotyping data from this study may be used to develop molecular markers associated with useful traits for use in Perilla breeding.

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• Construction of a core collection of tomato (Solanum lycopersicum) germplasm based on phenotypic traits and SNP markers
  Xiang Chen, Yi-Yang Liu, Fu-Shun Zheng, Guo-Xin Cheng, Meng Guo, Jian-She Li, Xiao-Min Wang
  Scientia Horticulturae.2025; 339: 113855.     CrossRef
• Comparative Analysis of Chloroplast Promoters for Optimized Production of Recombinant Proteins in Plants
  Juho Lee, Woo-Hyun Jeong, Seon-Kyeong Lee, Kyeong-Ryeol Lee, Sichul Lee, Beom-Gi Kim
  Korean Journal of Breeding Science.2025; 57(4): 359.     CrossRef
• Plastome sequences fail to resolve shallow level relationships within the rapidly radiated genus Isodon (Lamiaceae)
  Ya-Ping Chen, Fei Zhao, Alan J. Paton, Purayidathkandy Sunojkumar, Lian-Ming Gao, Chun-Lei Xiang
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
  Antoine Fort, Marcus McHale, Kevin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
  Journal of Phycology.2021; 57(1): 219.     CrossRef
• Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources
  Jiahui Sun, Yiheng Wang, Thomas Avery Garran, Ping Qiao, Mengli Wang, Qingjun Yuan, Lanping Guo, Luqi Huang
  Frontiers in Genetics.2021;[Epub]     CrossRef

Rhus chinensis is a shrub widely distributed in Asia. It has been used for traditional medicine and ecological restoration. Here, we report the complete chloroplast genome sequence of two R. chinensis genotypes collected from China and Korea. The assembled chloroplast genome of Chinese R. chinensis is 149,094 bp long, consisting of a large single copy (97,246 bp), a small single copy (18,644 bp) and a pair of inverted repeats (16,602 bp). Gene annotation revealed 77 protein coding genes, 30 tRNA genes, and 4 rRNA genes. A phylogenomic analysis of the chloroplast genomes with 11 known complete chloroplast genomes clarified the relationship of R. chinensis with the other plant species in the Sapindales order. A comparative chloroplast genome analysis identified 170 SNPs and 85 InDels at intra-species level of R. chinensis between Chinese and Korean collections. Based on the sequence diversity between Korea and Chinese R. chinensis plants, we developed three DNA markers useful for genetic diversity and authentication system. The chloroplast genome information obtained in this study will contribute to enriching genetic resources and conservation of endemic Rhus species.

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• Complete plastid and 45S rDNA sequences allow authentication of Liriope platyphylla and Ophiopogon japonicus
  Yeonjeong Lee, Hyun-Seung Park, Jae-Hyeon Jeon, Jee Young Park, Seung Hyun Kim, Jungmoo Huh, Sunmin Woo, Do-Won Jeong, Tae-Jin Yang
  Current Plant Biology.2022; 30: 100244.     CrossRef
• Variation among the Complete Chloroplast Genomes of the Sumac Species Rhus chinensis: Reannotation and Comparative Analysis
  Yujie Xu, Jun Wen, Xu Su, Zhumei Ren
  Genes.2022; 13(11): 1936.     CrossRef
• Phytochemical, Antioxidant, Anti-Microbial, and Pharmaceutical Properties of Sumac (Rhus coriaria L.) and Its Genetic Diversity
  Anna Perrone, Sanaz Yousefi, Boris Basile, Giandomenico Corrado, Antonio Giovino, Seyed Alireza Salami, Alessio Papini, Federico Martinelli
  Horticulturae.2022; 8(12): 1168.     CrossRef
• Authentication of Rubus coreanus and Related Species via DNA Barcoding and HPLC Approaches
  Young Sang Park, Young Jun Kim, Tae Jin Yang, Ji Yeon Kim
  Korean Journal of Medicinal Crop Science.2021; 29(6): 425.     CrossRef
• Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.
  Craig F. Barrett
  PeerJ.2020; 8: e9315.     CrossRef

Chloroplast genome sequencing has served as valuable source for developing DNA markers, including the authentication of plant material used for health supplement from its fraudulent materials. We sequenced and analyzed the chloroplast genome of Allium victorialis, a medicinal plant, to discover potential marker regions for the authentication from Veratrum patulum, an inedible toxic plant. Although we examined conventional barcode marker loci in chloroplast, matK and rbcL, there was a difficulty in aligning coding regions and determining PCR primer sequences in these two loci between A. victorialis and V. patulum, possibly due to the distant evolutionary relationship. Instead, we identified potential DNA markers that carry Insertion/Deletion (InDels) that are able to discriminate these two species around clpP, petB, petD, rpl22, and ycf2 loci. In this analysis, we demonstrated the possibility of developing potential DNA markers in the chloroplast genome other than conventional barcode markers, such as matK and rbcL. The potential DNA markers identified in this analysis will serve as useful tools for future authentication of Allium and Veratrum species.

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• Complete plastome sequence of Narcissus pseudonarcissus L., one of the most iconic European plants
  Martino Adamo, Valeria Fochi, Marco Mucciarelli
  Mitochondrial DNA Part B.2024; 9(8): 1132.     CrossRef
• Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA
  Minyoung Lee, Hyo Young Lee, Jong-Soo Kang, Hyeji Lee, Ki-Jin Park, Jee Young Park, Tae-Jin Yang, Yanbin Yin
  PLOS ONE.2023; 18(11): e0294457.     CrossRef
• Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum
  Yanan Jin, Ting Zhang, Binke Liu, Chengzhong Zheng, Hongyan Huo, Jixing Zhang
  Scientific Reports.2022;[Epub]     CrossRef
• Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
  Junpei Chen, Dengfeng Xie, Xingjin He, Yi Yang, Xufeng Li
  Genes.2022; 13(7): 1279.     CrossRef
• A Review of Genetic Understanding and Amelioration of EdibleAlliumSpecies
  Geetika Malik, Ajmer Singh Dhatt, Ajaz Ahmed Malik
  Food Reviews International.2021; 37(4): 415.     CrossRef
• Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
  Victoria A. Scobeyeva, Ilya V. Artyushin, Anastasiya A. Krinitsina, Pavel A. Nikitin, Maxim I. Antipin, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Evgenii A. Konorov, Andrey E. Samoilov, Anna S. Speranskaya
  Frontiers in Genetics.2021;[Epub]     CrossRef
• Omics approaches inAlliumresearch: Progress and way ahead
  Kiran Khandagale, Ram Krishna, Praveen Roylawar, Avinash B. Ade, Ashwini Benke, Bharat Shinde, Major Singh, Suresh J. Gawande, Ashutosh Rai
  PeerJ.2020; 8: e9824.     CrossRef
• Complete plastome sequencing of Allium paradoxum reveals unusual rearrangements and the loss of the ndh genes as compared to Allium ursinum and other onions
  Denis O. Omelchenko, Anastasia A. Krinitsina, Maxim S. Belenikin, Evgenii A. Konorov, Sergey V. Kuptsov, Maria D. Logacheva, Anna S. Speranskaya
  Gene.2020; 726: 144154.     CrossRef
• Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences
  Deng-Feng Xie, Jin-Bo Tan, Yan Yu, Lin-Jian Gui, Dan-Mei Su, Song-Dong Zhou, Xing-Jin He
  Annals of Botany.2020; 125(7): 1039.     CrossRef
• Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
  Xin Yang, Deng-Feng Xie, Jun-Pei Chen, Song-Dong Zhou, Yan Yu, Xing-Jin He, Marcelo A. Soares
  BioMed Research International.2020;[Epub]     CrossRef
• Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing
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  Molecular Phylogenetics and Evolution.2020; 146: 106737.     CrossRef
• Development of the chloroplast genome-based InDel markers in Niitaka (Pyrus pyrifolia) and its application
  Ho Yong Chung, So Youn Won, Yoon-Kyung Kim, Jung Sun Kim
  Plant Biotechnology Reports.2019; 13(1): 51.     CrossRef
• Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome
  Deng-Feng Xie, Huan-Xi Yu, Megan Price, Chuan Xie, Yi-Qi Deng, Jun-Pei Chen, Yan Yu, Song-Dong Zhou, Xing-Jin He
  Frontiers in Plant Science.2019;[Epub]     CrossRef

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

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• Complete plastid and 45S rDNA sequences allow authentication of Liriope platyphylla and Ophiopogon japonicus
  Yeonjeong Lee, Hyun-Seung Park, Jae-Hyeon Jeon, Jee Young Park, Seung Hyun Kim, Jungmoo Huh, Sunmin Woo, Do-Won Jeong, Tae-Jin Yang
  Current Plant Biology.2022; 30: 100244.     CrossRef
• De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species
  Hakjoon Choi, Wan Seok Kang, Jin Seok Kim, Chang-Su Na, Sunoh Kim
  Current Issues in Molecular Biology.2021; 43(3): 2177.     CrossRef

The genus Brassica is an important resource for major agricultural products such as oils, vegetable and fodder. The Brassiceae tribe-specific whole-genome triplication that occurred ~15.9 million years ago influenced the speciation and morphological diversification that has been exploited in agriculture, making Brassica an excellent model system for studying polyploidization-mediated evolution. Genome sequencing and comparative genome analysis have revealed conserved structures and uncovered the genome evolution of Brassica species. While chromosome shuffling and asymmetric subgenome gene retention are widely reported in Brassica species, limited information is available about the dynamics of repetitive elements (REs), which are central to epigenetic mechanisms and thus play a pivotal role in plant genome adaptation and evolution. The assembled reference genome sequences of B. rapa (AA) and B. oleracea (CC), and their derived allotetraploid, B. napus (AACC), cover 58%, 86%, and 75% of their respective estimated genome sizes. The remaining non-assembled genome portions vary between these three genome sequences, and the major components remain hidden in each genome. Here, we review the dynamics of the major Brassica repeats that have played roles in speciation of the AA, CC, and AACC genomes. We show that 10 major Brassica repeats appear to occupy more than 50% of each respective unassembled genome sequence, yet represent less than 1% of assembled reference genome sequences. We have estimated their genome proportions using whole-genome Illumina reads and cytogenetic analyses in an attempt to understand the role of these repeats in genome evolution.

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• Construction and evaluation of Brassica rapa orphan genes overexpression library
  Mingliang Jiang, Zongxiang Zhan, Xiaonan Li, Zhongyun Piao
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• Fluorescence in situ Hybridization Analysis of Oligonucleotide 5S Ribosomal DNA, 45S Ribosomal DNA, and (TTTAGGG)3 Locations in Gloriosa superba L.
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• Exploring the mechanism of blindness physiopathy in Brassica oleracea var italica L. by comprehensive transcriptomics and metabolomics analysis
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• Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis
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  Ana Gabriela Damasceno, Marco Túlio Mendes Ferreira, Isadora Cardoso Soares, Sanzio Carvalho Lima Barrios, Cacilda Borges Do Valle, Vânia Helena Techio
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• Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy
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• Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines
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• Subgenome Discrimination in Brassica and Raphanus Allopolyploids Using Microsatellites
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• BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa
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• Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa
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• Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution
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The rise of whole genome sequences of different plants provided more understanding about the gene regulation and genome evolution in further studying plants. More and more pathways and networks are identified by novel gene discoveries. Therefore, the Plant and Animal Genome Conference (PAG XXIV) provides a good venue to share the recent progress in the area of plant research genome sequencing technologies in various plants. However, this information can make a powerful system for developing improved crop varieties. By the way, the genome annotation and assembly is an essential key for breeding of stress-tolerant plants. PAG XXIV demonstrated different works about the extensive use of genomic databases accompanied by bioinformatics tools to accelerate breeding methods, discovery of new approaches to genomics, further increasing biomass of bioenergy crops, and explaining the genetic mechanisms in plant growth and defense. This review article summarizes some of the researches in various plants of rice, corn, wheat, cottonwood, switchgrasses, Thinopyrum, wheatgrass and Arabidopsis presented in PAG XXIV with the focus on genome technologies and their applications in plant breeding.

Crop improvement is essential to attaining world food security and enhancing nutrition for human beings. Both conventional breeding and modern molecular breeding have contributed to increased crop production and quality. However, the time and resources for breeding practices have been limited. It takes a long time to bring a novel improved crop to the market, and the genetic sources from wild species cannot be always available for crops of our interests. Genome editing technology implemented molecular breeding can overcome those limitations of time and resource by facilitating the specific editing of plant genomes. However, there is a long-lasting argument about the safety of genetically modified organisms (GMOs). In this review, we briefly summarize the principle of genome editing tools, focusing on the CRISPR/Cas9 system and the application of these tools to plants in the service of crop engineering.

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• Research Advances in Wheat Breeding and Genetics for Powdery Mildew Resistance
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Functional stay-green (FSG) delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green (NFSG) retains only leaf greenness without sustaining photosynthetic activity. Retention of chlorophylls and photosynthetic capacity is important for increasing crop yield. We determined the main-effect quantitative trait loci (QTLs) for FSG traits in the japonica rice SNU-SG1 and isolated candidate genes. To identify QTLs influencing FSG, we analyzed eight traits: (1) 1 day after heading-degree of chlorophyll content of flag leaf, (2) 1 day after heading-degree of chlorophyll content of second leaf, (3) 1 day after heading-degree of chlorophyll content of flag and second leaves, (4) 50 day after heading-degree of chlorophyll content of flag leaf, (5) 50 day after heading-degree of chlorophyll content of second leaf, (6) 50 day after heading-degree of chlorophyll content of flag and second leaves, (7) relative decline degree of chlorophyll content of flag and second leaves, and (8) flowering time. We carried out QTL analysis with F₇ RIL from a cross of japonica rice ‘SNU-SG1’ and indica rice ‘Milyang23 (M23)’. Using 131 molecular markers, we identified 18 QTLs for the eight traits with a threshold LOD value > 2.8. Sequence analysis identified 16 candidate genes for 10 main-effect QTLs. Of these, we have chosen seven strong candidate genes for the 10 main-effect QTLs. These genetic resources will be useful for breeding high-yielding rice cultivars.

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