In most garlic producing countries, the yield of local garlic varieties is low due to small size bulbs and limited production area. Garlic in vitro culture can be induced in Basal Dunstan Short (BDS) or Murashige and Skoog medium (MS) medium supplemented with 2,4-D and Kinetin or with 2,4-D (2,4-dichlorophenoxyacetic acid) and BAP (Benzylaminopurine) for better callus production, cell and shoot proliferation from callus. This review aimed to describe the effect of growth hormones, colchicine concentration, and immersion time for increasing ploidy level of garlic varieties for genetic variability. Colchicine is effective to induce the meristematic basal discs of garlic plants at a concentration of 0.25-0.5% and immersion time at 24, 36, and 48 hours in vitro. High concentration and longer duration of colchicine could reduce the survival rate, whereas low concentration with a longer duration of colchicine treatment results in a higher polyploidy induction rate. A high percentage of polyploidy induction occurs in high colchicine concentration and longest time duration, but it leads to a high percentage of dead plants. Ploidy induction of diploid garlic genome can be induced by treating garlic stem discs up to 0.75% colchicine. The application of colchicine at 0.5% treatment improved the genetic potential of garlic varieties in vitro, but a lower duplication rate at 0.75% due to higher toxicity. The application of colchicine increased the ploidy level and an increase in ploidy is expected to have a larger bulb size. Larger tuber size is expected to increase the overall tuber weight and total garlic production.

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The anaerobic germination 1 (AG1) locus, which confers tolerance to the anaerobic germination of rice seed, has been previously identified and a gel-based InDel DNA marker developed for marker-assisted selection (MAS). However, there is a need for marker development for high-throughput genotyping in order to increase the breeding efficiency. Single nucleotide polymorphisms (SNPs)-based Kompetitive Allele Specific PCR (KASP) markers enable high-accuracy and high-throughput analyses for the genotyping of AG1 locus. In the present study, we developed one AG1 InDel-specific and four flanking KASP markers, which can be used as the foreground and recombination markers, respectively, for the AG1 locus. Of those, three KASP markers developed were validated with Dasan-AG1 (BC₃F₂) segregating lines; the AG1 InDel-specific KASP marker was 100% consistent with the existing AG1 gel-based marker, while the two flanking markers showed 70.3 and 66.7 percent consistency to the AG1 gel-based marker, respectively. In addition, the five KASP markers developed were further used to genotype 78 Korean and 95 foreign rice varieties. The genotyping results with 172 varieties revealed that most of the Korean varieties possessed the AG1 locus; however, a wide variation was observed in the foreign varieties for AG1 locus. Hence, the KASP markers developed for AG1 locus show promise as useful tools for expediting the breeding of varieties tolerant to anaerobic germination stress via high-throughput genotyping.

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• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
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• Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean
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• KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)
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Gene editing technologies such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems have been developed to create targeted DNA mutagenesis in many crop plants. This report describes application of the TALEN system to generate bialaphos resistance (bar)-knockout null segregants in herbicide-tolerant rice (Ba15) and microarray analysis on transcriptome changes of mutated lines, to identify unexpected effects resulting from off-targets. We generated 41 T₀ plants and identified TALEN-mediated bar sequence mutations in 14 of them. Non-target site single nucleotide polymorphisms (SNPs) and small insertion/deletions (InDels) accounted for a large proportion of the mutations. Segregations of phosphinothricin acetyltransferase (PAT) protein expression levels were observed in T₁ generations of two lines, R6 and R9. In addition, most T₁ offspring harbored the TALE-R expression cassette and acquired some de novo mutations that were not inherited from their T₀ parents. Three bar-knockout T₁ lines were tested for PAT protein expression in progeny seedlings, and their T₂ plants possessed inactive bar. We selected three bar-knockout T₂ plants that were TALE-DNA-free for microarray analysis, aiming to understand the transcriptome differences between mutated null segregants and their recipient line. Only 31 differentially expressed genes (DEGs) were identified in the bar-knockout rice lines, possibly resulting from somaclonal variations from the in vitro cell culture process. Taken together, TALEN-mediated bar mutations have little effect on the whole transcriptome profile of rice. We believe our results will be helpful to study unexpected consequences in gene-edited crops.

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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.

The plants of the Papaveraceae family are used for ornamental purposes because of their varicolored flowers, and are known as medicinal crops. Some species of poppy are used in foods such as salads or sorbets, utilizing the seeds, leaves, pedicels, and petals. There are several morphological similarities among the species of this family, which make it difficult to distinguish the seeds of different species or identify opium poppies. The family is known to contain about 100 species. The leaves of Iceland poppy (Papaver nudicaule) cultivars with five different flower colors (white, yellow, pink, orange, and scarlet) were sequenced to obtain transcriptome data. Sequencing was done on plants in three different developmental growth stages (leaf rosette, branching and elongation of internodes, and blossom and seed formation). Systematic bioinformatics analysis was conducted to identify single nucleotide polymorphisms (SNPs) unique to the five Papaver nudicaule cultivars and two other Papaver species (Papaver rhoeas and Papaver somniferum). A 739-Mb reference transcriptome (94.6% BUSCO completeness score) from a 566-Gb RNA-sequencing (RNA-Seq) dataset was obtained. Likewise, 18 significant SNPs were identified to authenticate the three species and five cultivars of Papaver. This study will facilitate future Papaver research, including evaluation of the results for more detailed characterization.

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• Developing benzylisoquinoline alkaloid-enriched opium poppy via CRISPR-directed genome editing: A review
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Several environmental and genetic factors affect the isoflavone and anthocyanin contents in soybeans. This study aimed to assess the influences of cotyledon color and harvest period on the contents of five major isoflavones and three major anthocyanins in 323 black soybean landraces grown in Korea. In all the soybeans, malonylgenistin, malonyldaidzin and cyanidin-3-O-glucoside were the foremost components. The total isoflavone (TIC) and total anthocyanin (TAC) contents were in the ranges of 491.29-1998.39 µg/g and 452.60-2789.37 mg/100 g on dry weight basis, respectively. Both the average TIC and TAC were higher in green cotyledon soybeans (1493.93 µg/g and 1656.05 mg/100 g, respectively) than in yellow cotyledon soybeans (1423.09 µg/g and 1489.30 mg/100 g, respectively). With respect to the harvest period, the average TIC was in the order of Late-October (1517.31 µg/g) > Mid-October (1454.54 µg/g) > Early-October (1340.95 mg/g). Moreover, the average TAC decreased in the order of Late-October (1765.76 mg/100 g) > Mid-October (1503.93 mg/100 g) > Early-October (1350.91 mg/100 g). In general, cotyledon color appeared to cause a significant variation on TAC (P < 0.05) but not on TIC, whereas the harvest period appeared to cause significant variations on both the TAC and TIC. Among the 323 landraces, 20 were identified to contain high TIC (> 1800 mg/g) and TAC (> 2000 mg/100 g) in their seeds and hence, could be considered as important sources of dietary isoflavones and anthocyanins. Besides, they possibly provide a wide spectrum of options if considered during the development of improved soybean genotypes.

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In this study, in order to understand the differentiation process of Perilla crop and related weedy types collected from South Korea, morphological variation between accessions of cultivated var. frutescens and related weedy types of var. frutescens and var. crispa was investigated by principal component analysis (PCA) using morphological characteristics, especially including seed traits such as seed size, seed hardness, seed color and seed germination rate. The first and second principal components accounted for 54.1% and 17.9% of the total variance, respectively. In the PCA analysis, most of the qualitative and quantitative traits contributed significantly to the positive or negative direction on the first axis. Thus, the first axis could be used mainly to distinguish between accessions of cultivated var. frutescens and weedy var. frutescens, and also between accessions of cultivated and weedy types of var. frutescens and weedy var. crispa. However, for several accessions it was not possible to discriminate clearly between accessions of cultivated and weedy types of var. frutescens and also between accessions of the two weedy types of var. frutescens and var. crispa. The results of the PCA analysis are thought to provide useful information for understanding the cultivation process of Perilla crop and the differentiation process of Perilla crop and related weedy types. Also, this study demonstrates the efficacy and utility of PCA analysis using morphological traits, including seed traits such as seed size, seed hardness, seed color and seed germination rate, in the study of morphological variation of Perilla crop and related weedy types.

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