Search

A leaf of Chinese cabbage (Brassica rapa ssp. pekinensis) is composed of a photosynthetic blade and a non-photosynthetic large midrib; thus each leaf contains both source and sink tissues. This structure suggests that, unlike in other plants, source-sink metabolism is present in a single leaf of Chinese cabbage. This study was designed to identify the transport route of photosynthetic carbon and to determine whether both source and sink tissues were present in a leaf. Plant samples were collected diurnally. Their carbohydrate contents were measured, and a genome-wide transcriptome analysis was performed using the Br300K microarray. Expression profiles of selected genes were validated using qRT-PCR analysis. The presence of two contrasting tissues (blade as source and midrib as sink) in a leaf was demonstrated by (1) diurnal distribution patterns of starch and sucrose content; (2) Gene Ontology (GO) enrichment analysis of microarray data; (3) expression profiles of photosynthetic and sucrose biosynthetic genes; and (4) expression patterns of a variety of sugar transporter genes. Source and sink tissues were both present in Chinese cabbage leaves, but the midrib functioned as a sink tissue as well as a site exporting to roots and other sink tissues. Function of most genes discriminating between source and sink tissue appeared to be regulated largely at the post-transcriptional level, not at the transcriptional level.

Glucoraphasatin (GRH) is a specific aliphatic glucosinolate (GSL) that is only abundant in radish (Raphanus sativus L.). The gene expression regulating GRH biosynthesis in radish is still poorly understood. We employed a total of 59 radish accessions to analyze GSL profiles and showed that GRH was specific and predominant among the aliphatic GSLs in radish roots. We selected five accessions roots with high, moderate and low GSL biosynthesis, respectively, to conduct a comparative transcriptome analysis and the qRT-PCR of the biosynthesis genes for aliphatic GSLs. In this study, among all the accessions tested, roots with the accession RA157-74 had a high GRH content and showed a significant expression of the aliphatic GSL biosynthesis genes. We defined the genes involved in the GRH biosynthesis process and found that they were regulated by a transcription factor (RSG00789) at the MYB29 locus in radish roots. We found 13 aliphatic GSL biosynthesis genes regulated by the RSG00789 gene in the GRH biosynthesis pathway.

Strawberry (Fragaria × ananassa) is a globallycultivated and popular fruit crop, prized for its flavor and nutritional value. Sweetness, a key determinant of fruit quality, depends on the sugar composition and concentration. We selected eight strawberry cultivars based on the fruit soluble solids content to represent high and low sugar content groups. The average soluble solid content was 13.6 °Brix (Okmae, Geumsil, Aram, and Maehyang) and 2.9 °Brix (Missionary, Camino Real, Portola, and Gilgyung53), for the high and low sugar content groups, respectively. Sucrose was the main sugar in the cultivars with high sugar content, whereas fructose was the main component in the low sugar content cultivars. Fruit starch concentration ranged from 3.247±0.056 to 3.850±0.055 g/100g, with a 12% higher concentration in the high sugar content cultivars. Additionally, we identified 41 sugar metabolism-related genes in Fragaria × ananassa and analyzed the relationship between their transcripts and the sugar accumulation in fruit. FaGPT1, FaTMT1, FaHXK1, FaPHS1, FaINVA-3, and FacxINV2-1 were highly expressed in the high sugar content cultivars, while FapGlcT, FaTMT2-1, FaPHS2-1, FaSUSY1-1, and FaSUSY1-2 were highly expressed in the low sugar content cultivars. In general, a greater number of genes encoding sugar transporters or involved in sugar synthesis were highly expressed in the high sugar content cultivars. Contrarily, genes involved in sugar degradation were preferentially transcribed in the low sugar content cultivars. Although gene expression was not perfectly proportional to sugar content or concentration, our analysis of the genes involved in sugar metabolism and accumulation in strawberries provides a framework for further studies and for the subsequent engineering of sugar metabolism to enhance fruit quality.

Background Water-soluble anthocyanin pigments are important ingredients in health-improving supplements and valuable for the food industry. Although great attention has been paid to the breeding and production of crops containing high levels of anthocyanin, genetic variation in red or purple cabbages (Brassica oleracea var. capitata F. rubra) has not yet been characterized at the molecular level. In this study, we identified the mechanism responsible for the establishment of purple color in cabbages. Results BoMYBL2–1 is one of the regulatory genes in the anthocyanin biosynthesis pathway in cabbages. It is a repressor whose expression is inversely correlated to anthocyanin synthesis and is not detectable in purple cabbages. Sequence analysis of purple cabbages revealed that most lacked BoMYBL2–1 coding sequences, although a few had a substitution in the region of the promoter 347 bp upstream of the gene that was associated with an absence of BoMYBL2–1 expression. Lack of transcriptional activity of the substitution-containing promoter was confirmed using transgenic Arabidopsis plants transformed with promoter::GUS fusion constructs. The finding that the defect in BoMYBL2–1 expression was solely responsible for purple coloration in cabbages was further demonstrated using genomic PCR and RT-PCR analyses of many other structural and regulatory genes in anthocyanin biosynthesis. Molecular markers for purple cabbages were developed and validated using 69 cabbage lines. Conclusion Expression of BoMYBL2–1 was inversely correlated to anthocyanin content, and purple color in cabbages resulted from a loss of BoMYBL2–1 expression, caused by either the promoter substitution or deletion of the gene. This is the first report of molecular markers that distinguish purple cabbages. Such markers will be useful for the production of intraspecific and interspecific hybrids for functional foods, and for industrial purposes requiring high anthocyanin content. Electronic supplementary material The online version of this article (10.1186/s12870-018-1290-9) contains supplementary material, which is available to authorized users.

Heterosis or hybrid vigor describes a phenomenon that superior phenotypes compared to the two parents are observed in the heterozygous F1-hybrid plants. Identification and characterization of heterosis-related genes (HRGs) will facilitate hybrid breeding in crops. To identify HRGs in Brassica rapa, we analyzed transcriptome profiling using a Br300K microarray in non-heading Chinese cabbage at three developmental stages. A large number of genes were differentially expressed in F1 hybrids and non-additive expression was prominent. Genes that are expressed specifically for F1 hybrid at all three stages were Brassica-specific uncharacterized genes and several defense-related genes. Expression of several photosynthesis- and stress-related genes were also F1 hybrid-specific. Thirteen NBS-LRR class genes showed high and specific expression in F1 hybrid Shulu: some of them were characterized as defense genes in Arabidopsis, but most have not been. Further characterization of these defense-related genes in Brassica species and its application will be helpful for understanding the role of defense responses in heterosis. In addition, results obtained in this study will be valuable to develop molecular markers for heterosis and disease resistance in B. rapa.

The objective of this study was to evaluate the performance of 3 environmentally friendly fertilizers and their effect on the growth of Chinese cabbage and its contents of bioactive compounds. The following fertilizers were applied: purslane extract, 5% sulfur, and 15% phosphoric acid with 5% calcium. A total of 9, 9, and 11 components were detected for fatty acids, carotenoids, and glucosinolates, respectively. The contents of cis-7 hexadecenoic acid, linoleic acid (C18:2n6c+t), and linolenic acid (C183n3) were generally increased, and also carotenoid amounts of violaxanthin, antheraxanthin, lutein, 13-cis-ß-carotene, α-carotene, ß-carotene, and 9-cis-ß-carotene were significantly increased by fertilizer treatments. All fertilization treatments decreased the amounts of progoitrin, a strong goitrogenic, by 20.9% (H fertilization) to 53.8% (HJ fertilization). Expression analysis of fatty acid, carotenoid, and glucosinolate biosynthesis genes showed that fertilizer treatments affected the accumulation of bioactive components by changing gene expression levels. These environmentally friendly fertilizers can add value to Chinese cabbage by increasing its yield and nutritional value.

In 2006 and 2007, a new bacterial disease was observed in field-cultivated soybeans in Boeun District and Munkyung City of Korea. The disease caused severe blighting of soybean (Glycine max) leaves. Soybean leaves in fields showed yellowish spots with brown centers. Brown and dead areas of variable size and shape were surrounded by wide, yellow haloes with distinct margins. Spots might coalesce and affected leaves fell readily. Seven bacterial strains were isolated from chlorotic areas of soybean leaves and all produced white colonies on trypticase soy agar. With the Biolog Microbial Identification System, version 4.2, (Biolog Inc., Hayward, CA) all strains and Pseudomonas syringae pv. tabaci CFBP2106T were identified as P. syringae pv. tabaci with a Biolog similarity index of 0.28 to 0.52 and 0.48 after 24 h. Pathogenicity of the strains (three plants per strain) on soybean leaves at the V5 stage (cv. Hwanggeum) was confirmed by rub inoculation with bacterial suspensions (1 × 108 CFU/ml) in sterile distilled water on the lesions cut 1 cm long on the upper side of the leaves with razor blades and by pinprick on 3-week-old leaves of tobacco (Nicotiana tabacum cv. Samsun) in the greenhouse. Wildfire symptoms on the soybean leaves and faint halos on tobacco leaves were observed 4 days after inoculation. The identification of reisolated bacterial strains was confirmed with the metabolic fingerprintings on Biolog. LOPAT tests (1) and phenotypic characteristics (3) of the strains were similar to those of the CFBP2106T. Colonies were levan positive, oxidase negative, potato soft rot negative, arginine dihydrase negative, and tobacco hypersensitivity negative. All strains were gram-negative, aerobic rods with a polar flagellum. Strains were negative for esculin hydrolysis, gelatin liquefaction, urea production, accumulation of poly-β-hydroxy butyrate, starch hydrolysis, ornithine dihydrolase, lysine dihydrolase, growth at 37°C, utilization of geraniol, benzoate, cellobiose, sorbitol, trehalose, l-rhamnose, and adonitol. Positive reactions were catalase and arbutin hydrolysis, utilization of sorbitol, d-arabinose, and dl-serine. The strains were variable in utilization of mannitol, sucrose, and d-arabinose. The 1,472-bp PCR fragments of strains, BC2366 (GenBank Accession No. FJ755788) and BC2367 (No. FJ755789) was sequenced using 16S rDNA universal primers (2). The sequences shared 100% identity with the analogous sequences of P. syringae pv. glycenea (GenBank Accession No. AB001443) available in NCBI databases. Based on the phenotypic, genetic, and pathological characteristics, all strains were identified as P. syringae pv. tabaci. To our knowledge, this is the first report of P. syringae pv. tabaci causing wildfire on soybean in Korea. References: (1) R. A. Lelliott et al. J. Appl. Bacteriol. 29:470, 1966. (2) I.-S. Myung et al. Plant Dis. 92:1472, 2008. (3) N. W. Schaad et al., eds. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2001.

Farfugium japonicum (L.) Kitam (common name: Leopard plant) is known as a medical herb and belongs to family Asteraceae (1). In June 2012, a leaf spot disease was observed on the leaf surface of F. japonicum at a forest research plot Jinju, Gyeongnam province, Korea. More than 95% of F. japonicum plants were infected and leaf spot symptom appeared in the regions under our investigation. Light brownish symptoms initially developed and the spot size gradually increased and turned dark brown with an irregular shape as the disease progressed (spot size 1 to 10 mm in diameter). At the late stage of disease, spots became hollow and completely dehydrated. The infected leaves were easily crumbled, possibly due to dryness. To isolate the causal agent, the infected leaves were surface disinfected and pieces of leaves were placed on water agar (WA). Nine isolates were isolated from 10 pieces of the infected leaves. Fungi mycelia from the WA were transferred on potato dextrose agar (PDA) and incubated at 28°C for 7 days. The colonies were purple navy to black and conidia spores developed on the media. The morphological characteristics of spores were multi-septate, dark brown, pyriform, and 6.7 to 12.8 × 22.2 to 38.4 μm. The spores had 1 to 4 transverse and 0 to 3 longitudinal septa. The morphological characteristics of the isolates showed considerably similar to well-known Alternaria tenuissima (2). The leaf spot disease caused by A. cinerariae of F. japonicum was reported from Japan (3). Spores of A. cinerariae are golden brown to brown with 3 to 9 transverse and 0 to 6 longitudinal septa and are 87.5 × 28.7 μm (avg.) (3). To verify pathogenicity of the isolate, the pure cultured fungi on the PDA medium was taken (4 mm in diameter) and placed on healthy leaves of Leopard plant. The artificially inoculated leaves were placed on wet filter paper in Petri dishes and incubated at 25°C and 80% humidity. At 7 days after inoculation, similar disease symptoms developed on 8 out of 10 infected Leopard plant leaves. The pathogen was reisolated from artificially infected leaves. To identify in molecular biology level, genomic DNA was extracted and the ITS-rDNA region was amplified using universal primers ITS1 and ITS4. The amplified PCR product was purified and sequenced (528 bp) with ITS1 and ITS4 primers for both directions and then deposited in GenBank (Accession No. KC415611.1). The BLAST search showed that it matched previously reported A. tenuissima with 100% identity. To the best of our knowledge, this is the first report of Leopard plant leaf spot disease in Korea. References: (1) E. Y. Kim et al. J. Ethnopharmacol. 146:40, 2013. (2) E. G. Simmons. Page 1 in: Alternaria Biology, Plant Diseases and Metabolites. J. Chelchowski and A. Visconti, eds. Elsevier, Amsterdam, 1992. (3) T. Sakoda et al. Res. Bull. Pl. Prot. Japan 46:73, 2010.

Sophorae Radix (Sophora flavescens Aiton) has long been used in traditional medicine in East Asia due to the various biological activities of its secondary metabolites. Endogenous contents of phenolic compounds (phenolic acid, flavonol, and isoflavone) and the main bioactive compounds of Sophorae Radix were analyzed based on the qualitative HPLC analysis and evaluated in different organs and at different developmental stages. In total, 11 compounds were detected, and the composition of the roots and aerial parts (leaves, stems, and flowers) was significantly different. trans-Cinnamic acid and p-coumaric acid were observed only in the aerial parts. Large amounts of rutin and maackiain were detected in the roots. Four phenolic acid compounds (benzoic acid, caffeic acid, ferulic acid, and chlorogenic acid) and four flavonol compounds (kaempferol, catechin hydrate, epicatechin, and rutin) were higher in aerial parts than in roots. To identify putative genes involved in phenolic compounds biosynthesis, a total of 41 transcripts were investigated. Expression patterns of these selected genes, as well as the multiple isoforms for the genes, varied by organ and developmental stage, implying that they are involved in the biosynthesis of various phenolic compounds both spatially and temporally.

Figure S2. Schematic illustration of the strategy used to clone BoMYBL2–1 from various B. oleracea species. A: Genomic region around the BoMYBL2–1 based on information obtained from two different databases (upper: http://brassicadb.org/brad ; Liu et al. 2014; lower: http://plants.ensembl.org/Brassica_oleracea/Info/Index ; Parkin et al. 2014). B: Illustration showing the positions of the fragments, amplified using different combinations of primer sets, used to assemble the entire promoter and coding sequence of BoMYBL2–1. The yellow block represents a 159 bp repeat sequence. All primer sets are listed in Table 2. BoLPR2 is B. oleracea multicopper oxidase LPR2; BoPUB10 is B. oleracea U-box domain-containing protein 10. (DOCX 72 kb)

Figure S3. Results of genomic DNA-PCR preformed to detect the presence or absence of genes regulating anthocyanin biosynthesis other than BoMYBL2–1. A: B. oleracea var. capitata F. alba or rubra varieties with contrasting characteristics in anthocyanin accumulation were selected for analysis; varieties with green and purple colors are indicated in green or purple. B: PCR analysis of other varieties of B. oleracea. The color of each variety is indicated above each lane. (DOCX 293 kb)

Figure S5. Comparison of different BoMYBL2–1 nucleotide sequences obtained from cabbages. Shaded regions indicate exon sequences. Sequences corresponding to Bol016162 from B. oleracea var. capitata were omitted. (DOCX 31 kb)

Table S2. List of primer sequences used in RT-PCR and genomic PCR analyses of BoMYBL2. (DOCX 32Â kb)

Figure S1. Total anthocyanin content (A) of samples of the cabbages (B) shown in Fig. 1. (DOCX 109 kb)

Table S1. Primers used to clone BoMYBL2. (DOCX 19Â kb)

Figure S4. Expression of genes associated with anthocyanin biosynthesis in various purple cabbages. Daebakna is a green cabbage used as a reference. (DOCX 387Â kb)

The aerial surfaces of plants are covered with a wax layer that serves the essential functions of limiting non-stomatal water loss and acting as protective barrier against environmental stresses. We selected two broccoli lines, bloomed (MC91) and bloomless (MC117), and analyzed their phenotypes related to cuticular wax accumulation. The total wax amount was 1.93-fold higher in MC91 leaves compared to MC117 leaves. All of the studied cuticular wax compounds were 1.07–3.79-fold higher in MC91 plants compared to MC117 plants except for the C 31 alkane. The wax compositions did not essentially different between the two broccoli lines, but some compounds were found at significantly higher levels in MC91 plants compared to MC117 plants, mainly reflecting differences in C 29 alkanes, C 29 secondary alcohols and C 29 ketones. To investigate gene regulation by bloom phenotype, we analyzed the mRNA expression patterns of various cuticular wax biosynthetic genes. Our results revealed that LACS1 , KCS1 , KCR1 , ECR , CER3 and MAH1 were expressed more in MC91 plants compared to MC117 plants at both 3 and 10 weeks. The expression levels of the studied cuticular wax biosynthetic genes were significantly induced by drought stress, which is known to induce cuticular wax deposition. Together, these results show that the cuticular wax accumulation of broccoli is regulated by cuticular wax biosynthetic gene expression and can be affected by environmental signals.

To characterize of the pathogenicity gene from the soft rot pathogen Pantoea sp. PPE7 in Pleurotus eryngii , we constructed over 10,000 kanamycin-resistant transposon mutants of Pantoea sp. strain PPE7 by transposon mutagenesis. One mutant, Pantoea sp. NPPE9535, did not cause a soft rot disease on Pleurotus eryngii was confirmed by the pathogenicity test. The transposon was inserted into the wzc gene and the disruption of the wzc gene resulted in the reduction of polysaccharide production and abolished the virulence of Pantoea sp. strain PPE7 in P. eryngii . Analysis of the hydropathic profile of this protein indicated that it is composed of two main domains: an N-terminal domain including two transmembrane α-helices and a C-terminal cytoplasmic domain consisting of a tyrosine-rich region. Comparative analysis indicated that the amino acid sequence of Wzc is similar to that of a number of proteins involved in the synthesis or export of polysaccharides in other bacterial species. Purified GST-Wzc was found to affect the phosphorylation of tyrosine residue in vivo . These results showed that the wzc gene might play an important role in the virulence of Pantoea sp. strain PPE7 in P. eryngii .

Plants must constantly adjust their growth and defense responses to deal with the wide variety of stresses they encounter in their environment. Among phytohormones, brassinosteroids (BRs) are an important group of plant steroid hormones involved in numerous aspects of the plant lifecycle including growth, development and responses to various stresses including insect attacks. Here, we show that BRs regulate glucosinolate (GS) biosynthesis and function in insect herbivory. Preference tests and larval feeding experiments using the generalist herbivore, diamondback moth (Plutella xylostella), revealed that the larvae prefer to feed on Arabidopsis thaliana brassinosteroid insensitive 1 (bri1-5) plants over wild-type Ws-2 or BRI1-Flag (bri1-5 background) transgenic plants, which results in an increase in larval weight. Analysis of GS contents showed that 3-(methylsulfinyl) propyl GS (C3) levels were higher in bri1-5 than in Ws2 and BRI1-Flag transgenic plants, whereas sinigrin (2-propenylglucosinolate), glucoerucin (4-methylthiobutylglucosinolate) and glucobrassicin (indol-3-ylmethylglucosinolate) levels were lower in this mutant. We investigated the effect of brassinolide (BL) on GS biosynthesis in Arabidopsis and radish (Raphanus sativus L.) by monitoring the expression levels of GS biosynthetic genes, including MAM1, MAM3, BCAT4 and AOP2, which increased in a BL-dependent manner. These results suggest that BRs regulate GS profiles in higher plants, which function in defense responses against insects.

Kohlrabi (Brassica oleracea var. gongylodes L.) is an important vegetable of the Brassicaceae family. The main edible part of kohlrabi is the swollen stem. The purple cultivars make anthocyanin mainly in the peel of the swollen stem, while in the leaf, it is limited to the midrib, but green cultivars do not. Anthocyanins are advantageous for both plants as well as humans. Two anthocyanin compounds were detected by high pressure liquid chromatography (HPLC) only in the peel of the purple kohlrabi cultivar. Three MYBs, three bHLHs, and one WD40 TF were identified as the candidate regulatory genes in kohlrabi. There was an abundance of transcript levels for the late biosynthetic genes more specifically for BoF3′H, BoDFR, BoLDOX, and BoGST in the purple peel while scarcely detectable in other tissues for both cultivars. The expression of BoPAP2 and BoTT8 was higher in the peel of the purple cultivar than the green cultivar. The expression of BoMYBL2.2 orthologue of Arabidopsis MYBL2, a negative regulator of anthocyanins, was dramatically decreased in the purple peel. The expression of BoACO1, a key gene for ethylene biosynthesis, and BoNCED3, an important gene of the ABA pathway, was down- and upregulated, respectively, in the peel of purple kohlrabi.

Cultivated strawberry (Fragaria × ananassa Duch.) is a high value horticultural crop. In this study, the genetic diversity of 160 strawberry accessions was determined using five highly polymorphic simple sequence repeat (SSR) markers. Sixty different alleles were identified, with allele frequencies in the range of 0.006 to1. Similarity scores were in the range of 0.034 to 0.963 (average: 0.507). The accessions were categorized into five groups. Group 1 contained two diploid Fragaria vesca species and one unknown accession. Group 2 contained one accession (F x ananassa). Group 3 contained 20 F × ananassa accessions and six unknown accessions. Group 4 contained 48 F. × ananassa accessions, one octaploid Fragaria chiloensis species, and six unknown accessions while Group 5 contained 69 F. × ananassa accessions and six unknown accessions. Accessions within a pedigree were frequently grouped together. A total of 30 novel accessions were categorized alongside existing accessions. These results will allow breeders to develop strategies which incorporate more genetic diversity into new cultivars.

The bacterial pathogen Pantoea sp. strain PPE7 causes severe soft rot disease in the king oyster mushroom, Pleurotus eryngii. Typical symptoms of the disease include a dark-brown water drop at early stages of infection, ultimately leading to soft rot accompanied with an offensive odour. In this study, we showed that inoculation of Flammulina velutipes and Agaricus bisporus mushrooms with Pantoea sp. strain PPE7 also resulted in severe disease, including water-soaked lesions and soft rot symptoms. Treatment with chlorine solution (175 to 700 ppm active chlorine) significantly reduced the incidence of soft rot symptoms in Pleurotus eryngii. However, exposure to concentrations greater than 350 ppm caused harmful effects such as bleaching on the cap of the fruit body. Calcium hypochlorite solutions with 175 ppm active chlorine were effective for reducing soft rot disease of Pleurotus eryngii without affecting the mushroom yield.

In this study, we investigated anthocyanin accumulation and gene expression in response to light and dark conditions during the development of white and red cabbage seedlings. Two-day-old white cabbage seedlings expressed the highest transcript level for most of the genes under light conditions. Red cabbage also showed higher expression under light than under dark conditions, although gene expression (evaluated based on transcript levels normalized to that of a housekeeping gene) in 2-day-old red cabbage sprouts was much lower than that in the corresponding white cabbage sprouts. Trends in anthocyanin accumulation were similar for red and white cabbage but much greater accumulation was observed in red cabbage. Anthocyanin levels were higher in seedlings grown under light conditions compared to those grown under dark conditions for both cabbage cultivars. Especially, red cabbage accumulated 1.94–4.05 times greater total anthocyanin in 4-, 6-, 8-, and 10-day-old seedlings, when compared to white cabbage cultivar under light/dark and dark conditions. Our findings can improve understanding of the effects of light on accumulation of secondary metabolites in the seedling stages of various crops.

The functions of DUF640/ALOG (Arabidopsis LSH1 and Oryza G1) domain proteins, which are found in most land plants, have not been well characterized, but some of these proteins regulate inflorescence architecture in rice and specify organ boundaries in Arabidopsis. Arabidopsis DUF640-domain genes are initially identified as LIGHT-SENSITIVE HYPOCOTYLS (LSH) genes. Chinese cabbage leaves have large, white midribs and photosynthetic leaf blades (or lamina). A DUF640 domain gene of Brassica rapa, BrLSH2, is specifically expressed in the midrib of Chinese cabbage. Arabidopsis and rice possess ten LSH family genes, but B. rapa has 24 LSH genes, which can be categorized into two or four groups based on sequence identity. Here, we examined the expression patterns of the LSHs in various Brassica species and analyzed the promoter sequence of the BrLHS2 gene. The transcript levels of most LSH genes were very high in the midrib but low in the leaf blade. These genes were evenly expressed throughout the petiole region of Korean cabbage and highly expressed in the leaf base region near the stem and in the border area in B. oleracea. In addition, BrLSHs were expressed in both bundle and mesophyll cells of the midrib. These expression patterns suggest the possible use of these genes to generate leafy vegetables with altered leaf morphology. The BrLSH2 promoter, which contains auxin- and cytokinin-responsive elements as well as leaf development-related elements, may confer midrib-specific expression, suggesting that this promoter may be useful for the production of midrib-targeted transgenic Chinese cabbage.

AtRGP (AT4G17080, Arabidopsis thaliana reduction in growth and productivity) contains two N-terminal transmembrane helices and seven membrane occupation and recognition nexus motifs at its C-terminus, and associates with phosphatidylinositol phosphate kinase. To elucidate the function of AtRGP, we employed mutant plants to analyze gene expression, plant phenotypes, protein localization, structure and function of the chloroplast, and freezing tolerance. Overexpression of AtRGP increased growth rate, hypocotyl elongation, leaf size, seed production, photosynthetic rate, and freezing tolerance, and promoted chloroplast organization and stacking of grana. By contrast, Atrgp null mutants exhibited a smaller plant size, reduced seed production, photosynthetic rate, and freezing tolerance, and displayed abnormal chloroplast organization with insufficient stacking of grana. Considering these data, we postulate that AtRGP may bind transiently to the chloroplast envelope and interact with other proteins under certain conditions, thereby regulating cellular processes involved in growth and abiotic stress responses.

The diamondback moth, Plutella xylostella (L.), is a major pest responsible for destroying cabbage and other Brassica vegetable crops. A diamondback moth-resistant cabbage line was studied by comparing its metabolite profiles with those of a susceptible cabbage. Fourier transform infrared spectroscopy analysis revealed that carbohydrates, aromatic compounds, and amides were the major factors that distinguished the resistant and susceptible genotypes. Gas chromatography-time-of-flight mass spectrometry profiled 46 metabolites, including 19 amino acids, 15 organic acids, 8 sugars, 3 sugar alcohols, and 1 amine in two genotypes and F1 hybrid cabbages. The levels of glycolic acid, quinic acid, inositol, fumaric acid, glyceric acid, trehalose, shikimic acid, and aspartic acid were found to be very significantly different between the resistant and susceptible genotypes with a P value of

The oriental melon (Cucumis melo var. makuwa), called 'chamoe' in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2-3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes.

Lee, Y. H., Kim, M. K., Lee, J., Heo, J. Y., Kang, T. H., Kim, H. and Yun, H. D. 2013. Organic fertilizer application increases biomass and proportion of fungi in the soil microbial community in a minimum tillage Chinese cabbage field. Can. J. Soil Sci. 93: 271–278. This study evaluated the variations in soil microbial communities in a minimum tillage upland field used for Chinese cabbage (Brassica rapa L.) cultivation by their fatty acid methyl ester (FAME) and chemical properties. Replicated plots received organic fertilizer (OF), chemical fertilizer (CF), and no fertilizer (NF), and microbial communities were analyzed in the early season, mid-season and harvesting stages. The electrical conductivity of the CF soil at mid-season was significantly higher than that of the OF and NF soils (P < 0.05), whereas the NO3-N content at the harvesting stage was significantly lower in the CF soil than in the OF soil (P < 0.05). The average microbial biomasses in the OF soils during the Chinese cabbage growing period were approximately 1.03∼1.27 times higher for fungi, Gram-negative bacteria, total bacteria, total FAMEs, Gram-positive bacteria, and arbuscular mycorrhizal fungi (AMF). Organic fertilizer had a significantly lower ratio of cy19:0 to 18:1ω7c then CF (P < 0.001), which indicates that a decrease in microbial stress was caused by organic matter soil inputs and the lack of chemical amendments. Communities of fungi in OF soils were significantly larger than those in CF soils (P < 0.001) indicating fungi are potentially responsible for the microbial community differentiation between the OF and CF treatments in an upland field. However, the average microbial communities in the OF soils were approximately 0.86 times lower for actinomycetes and 0.95 times lower for AMF. In communities of total bacteria (P < 0.001), Gram-negative (P < 0.001) and Gram-positive bacteria (P < 0.01), the interaction between the growth stage and the fertilizer showed significant differentiation. Further work is needed to relate the seasonal variation and impact of fertilization on microbial communities to productivity of Chinese cabbage in Korea.

Abiotic stresses such as extreme temperatures frequently limit plant growth and productivity of major crop species. To identify temperature-stress responsive genes in Brassica rapa ssp. pekinensis, we conducted a comparative transcriptome analysis of two contrasting genotypes, the inbred lines Chiifu and Kenshin, under and heat-shock conditions. Of 23,929 unigenes deposited on a Br24K microarray, 17,603 genes were significantly expressed. Chiifu expression profiles were more prevalent under , and those of Kenshin were more prevalent under heat-shock. Previously characterized genes, with little exception, show similar changes to temperature stress. We found that a relatively large number of genes were expressed in response to temperature stress and genotype, amounting to 24 and 126 genes from and heat-shock conditions, respectively. These genes could be used in molecular marker development for either high or low temperature-resistant Brassica spp. Only ten genes, including TCH4 and CBL1, were up-regulated in both genotypes under all stress treatments, implying possible candidates for broad spectrum, stress-resistant crop production.

Calcium is an essential plant macronutrient that has unique structural and signaling roles related to tip-burn disorder in Brassica spp. crops. For two types of cabbage inbred lines, tip-burn susceptible and resistant, we measured and compared major macronutrient cations, including Ca(2+), in leaves. In both lines, Ca(2+), Mg(2+), Na(+), and K(+), accumulated more in leaf base than in leaf apex. Ca(2+) and K(+) were >2 times more abundant in the tip-burn resistant line, while Na(+) was higher in the susceptible line. Ca(2+) differences between the two lines resulted from differential accumulation of calcium into cell vacuoles. We profiled major vacuolar Ca(2+) transporters, in both cabbage lines, by growth time and intercellular Ca(2+) concentration. Expression pattern of several Ca(2+) transporter genes differed between tip-burn susceptible and resistant lines by growth time points. We also identified promoter regions of the major Ca(2+) vacuole transporter genes, CAX1, ACA4, and ACA11, which displayed hormonal, light and defense-related cis-acting regulatory elements. Finally, transporter genes in the two cabbage lines responded differently to abiotic stresses, demonstrating diversity in gene regulation among orthologous genes.

Background One of the most important members of the genus Brassica, cabbage, requires a relatively high level of calcium for normal growth (Plant Cell Environ 7: 397–405, 1984; Plant Physiol 60: 854–856, 1977). Localized Ca2+ deficiency in cabbage leaves causes tip-burn, bringing about serious economic losses (Euphytica 9:203–208, 1960; Ann Bot 43:363–372, 1979; Sci Hortic 14:131–138, 1981). Although it has been known that the occurrence of tip-burn is related to Ca2+ deficiency, there is limited information on the underlying mechanisms of tip-burn or the relationship between Ca2+ and tip-burn incidence. To obtain more information on the genetic control of tip-burn symptoms, we focused on the identification of genes differentially expressed in response to increasing intracellular Ca2+ and K+ concentrations in B. oleracea lines derived from tip-burn susceptible, tip-burn resistant cabbages (B. oleracea var. capitata), and kale (B. oleracea var. acephala). Results We compared the levels of major macronutrient cations, including Ca2+ and K+, in three leaf segments, the leaf apex (LA), middle of leaf (LM), and leaf base (LB), of tip-burn susceptible, tip-burn resistant cabbages, and kale. Ca2+ and K+ concentrations were highest in kale, followed by tip-burn resistant and then tip-burn susceptible cabbages. These cations generally accumulated to a greater extent in the LB than in the LA. Transcriptome analysis identified 58,096 loci as putative non-redundant genes in the three leaf segments of the three B. oleracea lines and showed significant changes in expression of 27,876 loci based on Ca2+ and K+ levels. Among these, 1844 loci were identified as tip-burn related phenotype-specific genes. Tip-burn resistant cabbage and kale-specific genes were largely related to stress and transport activity based on GO annotation. Tip-burn resistant cabbage and kale plants showed phenotypes clearly indicative of heat-shock, freezing, and drought stress tolerance compared to tip-burn susceptible cabbages, demonstrating a correlation between intracellular Ca2+ and K+ concentrations and tolerance of abiotic stress with differential gene expression. We selected 165 genes that were up- or down-regulated in response to increasing Ca2+ and K+ concentrations in the three leaf segments of the three plant lines. Gene ontology enrichment analysis indicated that these genes participated in regulatory metabolic processes or stress responses. Conclusions Our results indicate that the genes involved in regulatory metabolic processes or stress responses were differentially expressed in response to increasing Ca2+ and K+ concentrations in the B. oleracea leaf. Our transcriptome data and the genes identified may serve as a starting point for understanding the mechanisms underlying essential macronutrient deficiencies in plants, as well as the features of tip-burn in cabbage and other Brassica species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2512-x) contains supplementary material, which is available to authorized users.

Experimental Brassica oleracea (tip-burn susceptible, tip-burn resistant, and kale) leaf and the accumulation of Ca2+ in epidermal cells (updated to Lee et al., 2013). (DOCX 744 kb)

Selected up- or down-regulated genes based on increasing Ca2+ and K+ concentration in the three lines with three different leaf positions. (DOCX 169 kb)

Phenotypic appearance (A) and gene qRT-PCR results (B) of two cabbages (tip-burn susceptible and resistant lines) and kale under heat-shock stress, freezing-stress and drought stress conditions. (DOCX 2128 kb)

Functional categorization of tip-burn related phenotype-specific expressed genes. (DOCX 103 kb)

Summary of read number. (DOCX 29 kb)

Transporter genes with significantly altered transcript levels. (DOCX 51 kb)