Peanut variety identification is essential for protecting the intellectual property rights of researchers, ensuring quality management for producers, and safeguarding the interests of seed production stakeholders. In this research, we developed a molecular marker set for peanut variety identification using single nucleotide polymorphism (SNP) markers. We used genotyping data and selection procedures, including decision tree and optimal combination selection, to identify a minimal set of informative SNP sites. These SNPs were then converted into Kompetitive allele-specific PCR (KASP) markers. We selected a subset of 14 informative SNPs from a pool of 22 candidate markers, representing the minimum number of combinations required to distinguish cultivars. SNPs obtained from the microarrays were converted to KASP markers and then evaluated across 51 peanut varieties. The developed marker set, which consists of a minimal number of markers, is expected to be a rapid and cost-effective tool for peanut variety identification.

Flowering time is a very important agronomic trait in Brassica crops and regulation of the time is one of major factor in the breeding program. To understand the control of flowering time in Brassica rapa, we have carried out Br300K microarray with two contrasting Brassica inbred lines, Rapid Cycling B. rapa (RCBr) as rapid cycling type and B. rapa ssp. pekinensis inbred line Chiifu as slow flowering phenotype. Reproductive process-related genes were specifically expressed in RCBr, whereas environmental stimuli-responsive genes in Chiifu. Flowering stimulating genes, such as BrFT and BrSOC1, were preferentially expressed in RCBr, while flowering repressing genes, such as BrFLC and BrMAF4, expressed in Chiifu. Several paralogues present in B. rapa, BrFLCs and BrCOLs, were expressed with paralog-specific pattern depending on flowering phenotypes: i.e., BrFLC1 and BrFLC2, major floral repressors, were expressed in Chiifu, BrFLCL/BrFLC5 in RCBr and BrFLC3 in both plants. The expression of several flowering repressing genes was gradually decreased in RCBr growth, but increased in Chiifu growth. However, the expression of genes involved in photoperiodic flowering was no difference between these two plants under LD and SD conditions, indicating photoperiodic pathway is not major factor to distinguish fast vs. slow flowering in B. rapa. The mechanism underlined in the rapid or fast flowering of RCBr would be further elucidated in association with the controlling mechanism of its short life span.

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• Homeologs of Brassica SOC1, a central regulator of flowering time, are differentially regulated due to partitioning of evolutionarily conserved transcription factor binding sites in promoters
  Tanu Sri, Bharat Gupta, Shikha Tyagi, Anandita Singh
  Molecular Phylogenetics and Evolution.2020; 147: 106777.     CrossRef
• Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa
  Soo In Lee, Muthusamy Muthusamy, Muhammad Amjad Nawaz, Joon Ki Hong, Myung-Ho Lim, Jin A. Kim, Mi-Jeong Jeong
  Molecular Genetics and Genomics.2019; 294(6): 1403.     CrossRef
• Genome-wide identification of flowering time genes associated with vernalization and the regulatory flowering networks in Chinese cabbage
  Won Yong Jung, Areum Lee, Jae Sun Moon, Youn-Sung Kim, Hye Sun Cho
  Plant Biotechnology Reports.2018; 12(5): 347.     CrossRef
• Genome-wide analysis of gene expression to distinguish photoperiod-dependent and -independent flowering in Brassicaceae
  Hayoung Song, Hankuil Yi, Changhee Do, Ching-Tack Han, Ill-Sup Nou, Yoonkang Hur
  Genes & Genomics.2017; 39(2): 207.     CrossRef

Grafting has widely used in the agriculture of fruit-bearing crops and trees because rootstocks have a profound influence on many aspects of scion development and scion responses to the environmental changes including biotic and abiotic stress tolerance. These effects appear to result from the change of gene expression on scion, but only limited numbers of papers have been published demonstrating it. To identify altered expression of genes in Chinese cabbage, Chiifu(Brassica rapa ssp. pekinensis, inbred line) shoot was grafted on three Brassica rootstocks: mustard, turnip and broccoli. After head formation, Br300K microarray experiment was conducted using total RNAs from scion leaves collected in two different seasons, spring (June) and fall (October). A large number of differentially expressed genes (DEGs) were identified both in two seasonal samples, but DEGs were more notable in June sample than in October sample. However, the number of DEGs by three rootstocks were high in October with respect to up-regulation, but high in June for down-regulation. Categories of DEGs included metal ion binding, response to hormonal stimuli, response to endogenous stimuli, regulation of transcription, oxidation reduction and response to stress. Up-regulated genes in both June and October samples were similar in mustard and turnip rootstocks, but different in broccoli rootstock. Two genes were found to respond to all experimental conditions: Brapa_ESTC049008 (hypothetical protein) as an up-regulated gene and Brapa_ESTC016027 (CNGC12) as a down-regulated gene. Together with the previous reports, these results suggest that grafting-induced gene expression depends on the species involved.

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• Transcriptome analysis reveals the effects of grafting on sweetpotato scions during the full blooming stages
  Changhe Wei, Ming Li, Jia Qin, Yunfan Xu, Yizheng Zhang, Haiyan Wang
  Genes & Genomics.2019; 41(8): 895.     CrossRef
• Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis
  Thomas K. Uthup, Rekha Karumamkandathil, Minimol Ravindran, Thakurdas Saha
  Planta.2018; 248(3): 579.     CrossRef

Soft rot disease caused by Pectobacterium carotovorum subsp. carotovorum (Pcc), is one of the most devastating diseases affecting the cruciferous plants industry worldwide. In our previous study, the soft rot-resistant transgenic Chinese cabbage (Brassica rapa L.) plants were produced via constitutively overexpressing a human cathelicidin antimicrobial peptide (hCAP18/LL-37). To unravel the molecular mechanisms underlying Pcc resistance of the transgenic plants, this study compares the global transcriptional profile of untransformed line (WT) and the transgenic lines (TG23, TG34) through hybridization with KBGP-24K, Chinese cabbage GeneChip. In total, 1,415 differentially expressed genes (DEGs) were identified, 910 of which were up-regulated, while 505 were down-regulated. The DEGs were classified into 31 categories after Gene ontology (GO) annotation, in which 68 genes are in response to stimulus and are involved in immune system process, 12 genes are related to cell wall, and 13 genes belong to transcription factors. These genes and those related to toxin and terpenoid metabolism, glutathione metabolism, biosynthesis of phenylpropanoids, and plant hormones were hypothesized to play major roles in the soft rot resistance of transgenic lines (TG23, TG34). Semiquantitative RT-PCR analysis showed that the transcript levels of several candidate genes in TG23 and TG34 were significantly higher than in WT both before and after Pcc inoculation, indicating their potential association with soft rot disease.

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• Enhanced resistance to bacterial pathogen in transgenic tomato plants expressing cathelicidin antimicrobial peptide
  Yu-Jin Jung
  Biotechnology and Bioprocess Engineering.2013; 18(3): 615.     CrossRef