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Brassica rapa L., which includes Chinese cabbage, turnip, and pak choi, has more complex flowering time regulation than does Arabidopsis thaliana due to the presence of multiple paralogous flowering time genes. FLOWERING LOCUS C (FLC) is one of the key genes regulating flowering time. Although there is a single gene in A. thaliana, there are four FLC paralogs in B. rapa. BrFLC1, BrFLC2, and BrFLC3 are involved in regulating flowering time, whereas BrFLC5 is deemed a pseudogene because of a mutation (from G to A) in the splice site of the third intron. However, some accessions do not have this mutation, and a flowering-time quantitative trait locus (QTL) covering BrFLC5 associated with late flowering has been identified, suggesting that some accessions in B. rapa have a functional BrFLC5 gene. However, it has not been shown whether BrFLC5 acts as a floral repressor. To examine the allelic variation of BrFLC5, we genotyped 310 B. rapa accessions and found 19 had homozygous and 81 had heterozygous putative functional BrFLC5 alleles. BrFLC5 acts as a floral repressor when overexpressed in A. thaliana. Variation in the BrFLC5 expression level in pre-vernalized plants was identified and this transcriptional variation was not associated with the G/A polymorphism in the third intron. However, higher BrFLC5 expression in pre-vernalized plants is associated with 584 bp insertion in the promoter region. The possibility that a high expression of a functional BrFLC5 could contribute to producing premature bolting-resistant lines in B. rapa vegetables is discussed.

Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a "shock" that stimulates genome re-organization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained obscure. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the investigated RILs. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as unexpectedly common events in plant reproduction.

Tuberous stem of kohlrabi is an important agronomic trait, however, the molecular basis of tuberization is poorly understood. To elucidate the tuberization mechanism, we conducted a comparative transcriptomic analysis between kohlrabi and broccoli at 10 and 20 days after germination (DAG) as tuberous stem initiated between these time points. A total of 5580 and 2866 differentially expressed transcripts (DETs) were identified between genotypes (kohlrabi vs. broccoli) and growth stages (10 DAG vs. 20 DAG), respectively, and most of the DETs were down-regulated in kohlrabi. Gene ontology (GO) and KEGG pathway enrichment analyses showed that the DETs between genotypes are involved in cell wall loosening and expansion, cell cycle and division, carbohydrate metabolism, hormone transport, hormone signal transduction and in several transcription factors. The DETs identified in those categories may directly/indirectly relate to the initiation and development of tuberous stem in kohlrabi. In addition, the expression pattern of the hormone synthesis related DETs coincided with the endogenous IAA, IAAsp, GA, ABA, and tZ profiles in kohlrabi and broccoli seedlings, that were revealed in our phytohormone analysis. This is the first report on comparative transcriptome analysis for tuberous stem formation in kohlrabi at early growth periods. The resulting data could provide significant insights into the molecular mechanism underlying tuberous stem development in kohlrabi as well as in other tuberous organ forming crops.

There is a wide variation of flowering time among lines of Brassica rapa L. Most B. rapa leafy (Chinese cabbage etc.) or root (turnip) vegetables require prolonged cold exposure for flowering, known as vernalization. Premature bolting caused by low temperature leads to a reduction in the yield/quality of these B. rapa vegetables. Therefore, high bolting resistance is an important breeding trait, and understanding the molecular mechanism of vernalization is necessary to achieve this goal. In this study, we demonstrated that BrFRIb functions as an activator of BrFLC in B. rapa. We showed a positive correlation between the steady state expression levels of the sum of the BrFLC paralogs and the days to flowering after four weeks of cold treatment, suggesting that this is an indicator of the vernalization requirement. We indicate that BrFLCs are repressed by the accumulation of H3K27me3 and that the spreading of H3K27me3 promotes stable FLC repression. However, there was no clear relationship between the level of H3K27me3 in the BrFLC and the vernalization requirement. We also showed that if there was a high vernalization requirement, the rate of repression of BrFLC1 expression following prolonged cold treatments was lower.

The fusarium yellows resistance (YR) gene FocBo1 was previously identified and the DNA markers were developed to assist the breeding of YR cultivars in Brassica oleracea. However, the further analysis revealed discrepancies between the phenotypes and the genotypes predicted by those DNA markers in cabbage commercial cultivars. Since this discrepancy seemed to be due to unknown susceptible alleles of focbo1, we sequenced the gene in 19 accessions to determine the sequence variations between alleles and found that there were two resistant FocBo1 alleles and six susceptible alleles in the investigated population. The newly designed PCR markers detected three mutations in the susceptible alleles that generate premature termination codons. These were shown to accurately distinguish resistant and susceptible alleles in more than 200 accessions of B. oleracea inbred lines and cultivars. The study revealed that the locus is represented by 37.2% resistant and 62.8% susceptible alleles within seventy-eight commercial cultivars. Structural analysis of the gene revealed that a part of the allelic variation comes from intragenic recombination between alleles. Our results enable a more precise prediction of the phenotype by marker assisted selection, promoting the production of YR cultivars in B. oleracea.

Flowering time is an important agronomic trait for Brassica rapa crops, and previous breeding work in Brassica has successfully transmitted other important agronomic traits from donor species. However, there has been no previous attempts to produce hybrids replacing the original Brassica FLC alleles with alien FLC alleles. In this paper, we introduce the creation of a chromosome substitution line (CSSL) containing a homozygous introgression of Flowering Locus C from Brassica oleracea (BoFLC2) into a B. rapa genomic background, and characterize the CSSL line with respect to the parental cultivars. The preferential transmission of alien chromosome inheritance and the pattern of transmission observed during the production of the CSSLs are also discussed.

Flowering time is an important agronomic trait for Brassica rapa crops, and previous breeding work in Brassica has successfully transmitted other important agronomic traits from donor species. However, there has been no previous attempts to produce hybrids replacing the original Brassica FLC alleles with alien FLC alleles. In this paper, we introduce the creation of a chromosome substitution line (CSSL) containing a homozygous introgression of Flowering Locus C from Brassica oleracea (BoFLC2) into a B. rapa genomic background, and characterize the CSSL line with respect to the parental cultivars. The preferential transmission of alien chromosome inheritance and the pattern of transmission observed during the production of the CSSLs are also discussed.

Lilies and tulips (Liliaceae family) are economically very important ornamental bulbous plants. Here, we summarize major breeding goals, the role of an integrated method of cut-style pollination and fertilization followed by embryo rescue and mitotic and meiotic polyploidization involved in new assortment development. Both crops have been subjected to extensive interspecific hybridization followed by selection. Additionally, spontaneous polyploidization has played a role in their evolution. In lilies, there is a tendency to replace diploids with polyploid cultivars, whereas in tulip a majority of the cultivars that exist today are still diploid except for triploid Darwin hybrid tulips. The introduction of molecular cytogenetic techniques such as genomic in situ hybridization (GISH) permitted the detailed studies of genome composition in lily and tulip interspecific hybrids and to follow the chromosome inheritance in interspecific crosses. In addition, this review presents the latest information on phylogenetic relationship in lily and tulip and recent developments in molecular mapping using different DNA molecular techniques.

The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F1 hybrid Chinese cabbage cultivar "W77". Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent. We designed cleaved amplified polymorphic sequence (CAPS) markers using specific mutations found at Eco RI restriction sites in the parental lines and confirmed their Mendelian segregation by constructing a linkage map using 96 F2 plants derived from the F1 hybrid cultivar, "W77". Our results and data will be a useful genomic resource for future studies of gene function and metagenomic studies in Chinese cabbage.

Resistant and susceptible lines in Brassica rapa have different immune responses against Fusarium oxysporum inoculation. Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans (Foc) is an important disease of Brassicaceae; however, the mechanism of how host plants respond to Foc is still unknown. By comparing with and without Foc inoculation in both resistant and susceptible lines of Chinese cabbage (Brassica rapa var. pekinensis), we identified differentially expressed genes (DEGs) between the bulked inoculated (6, 12, 24, and 72 h after inoculation (HAI)) and non-inoculated samples. Most of the DEGs were up-regulated by Foc inoculation. Quantitative real-time RT-PCR showed that most up-regulated genes increased their expression levels from 24 HAI. An independent transcriptome analysis at 24 and 72 HAI was performed in resistant and susceptible lines. GO analysis using up-regulated genes at 24 HAI indicated that Foc inoculation activated systemic acquired resistance (SAR) in resistant lines and tryptophan biosynthetic process and responses to chitin and ethylene in susceptible lines. By contrast, GO analysis using up-regulated genes at 72 HAI showed the overrepresentation of some categories for the defense response in susceptible lines but not in the resistant lines. We also compared DEGs between B. rapa and Arabidopsis thaliana after F. oxysporum inoculation at the same time point, and identified genes related to defense response that were up-regulated in the resistant lines of Chinese cabbage and A. thaliana. Particular genes that changed expression levels overlapped between the two species, suggesting that they are candidates for genes involved in the resistance mechanisms against F. oxysporum.

As climatic changes occur over the coming decades, our scientific understanding of plant responses to environmental cues will become an increasingly important consideration in the breeding of agricultural crops. This review provides a summary of the literature regarding vernalization research in Brassicaceae, covering both the historical origins of vernalization research and current understanding of the molecular mechanisms behind the regulatory pathways involved in vernalization and subsequent inflorescence. We discuss the evolutionarily conserved biology between the model organism Arabidopsis thaliana and the Brassica genus of crop cultivars and contrast the differences between the genera to illustrate the importance of Brassica-specific research into vernalization.

Brassica rapa is an important oilseed crop species next to B. napus in Brassicaceae. However, genetic improvement of B. rapa oilseeds has not been intensively conducted compared to B. napus, which resulted in the limited number of low erucic acid (LEA) cultivars, which is an essential trait for edible oil materials. Candle and Tobin are LEA B. rapa cultivars bred in Canada that are closely related to each other; however, the causal mutation has not been identified. This study was initially aimed to investigate whether the alleles of BrFAE1, the gene encoding a key enzyme for erucic acid synthesis, in Candle and Tobin have mutations impairing their functions. An insertion of the long terminal repeat (LTR) retrotransposon, designated as BRACOPIA, was identified in the 5′ end of the coding region of the gene in both Candle and Tobin. BRACOPIA disrupted the transcription in developing seeds, resulting in a loss of function allele designated as brfae1re. Next, we found that Span, the world’s first LEA B. rapa cultivar developed in Canada, has brfae1re, suggesting that the BRACOPIA insertion is the founder mutation of Canadian LEA B. rapa cultivars. Finally, we investigated the distribution of BRACOPIA family retrotransposons in the Brassica genus, and found that they are present in both the A and C genomes, but the activity has been kept rather modest. Since brfae1re is easily distinguishable from the wild-type allele by PCR, the identification of this mutation could enhance LEA breeding in B. rapa.

In previous studies on precise computation methods of iron loss, it has been shown that the 1-D dynamic magnetic field analysis with hysteresis in post-processing is effective. However, there is a problem in that the hysteresis makes the convergence of nonlinear iterations unstable. This paper proposes a stabilization method for the 1-D dynamic magnetic field analysis with hysteresis. The proposed method is characterized as an approach for improving the initial value and the step size in the Newton–Raphson method. The results of this paper showed that the convergence characteristic of the nonlinear 1-D magnetic field analysis for variety flux density waveforms of each part in an electric motor is improved using the proposed method.

Chinese cabbage ( Brassica rapa L. var. pekinensis ) is an important vegetable in Asia. Most Japanese commercial cultivars of Chinese cabbage use an F 1 hybrid seed production system because of the high yielding cultivars produced. An efficient method for predicting hybrid performance in the parental generations is desired, and genetic distance between parental lines might be a good indicator of the level of hybrid vigor in a cross. Information concerning the genetic relationships among parental candidate inbred lines is useful for variety protection. The number of DNA markers available that can be used to assess the purity of inbred lines is limited in B. rapa . The aim of this study is to use DNA markers to assess the genetic distance between inbred lines to examine early developmental and yield heterosis so as to develop methods for selecting the best parental lines for the production of hybrids. We screened highly polymorphic SSR and CAPS markers to assess the genetic uniformity of inbred lines and characterize their genetic relationship. We examined the early size and yield heterosis in 32 F 1 hybrids of Chinese cabbage. There was a moderate correlation in mid-parent heterosis between leaf size at 21 days after sowing and harvested biomass but not in best-parent heterosis. In contrast there was no correlation between genetic distance and mid-parent or best-parent heterosis, indicating that genetic distance does not predict the heterosis phenotype.

Chinese cabbage (Brassica rapa L. var. pekinensis) is an important vegetable in Asia, and most Japanese commercial cultivars of Chinese cabbage use an F1 hybrid seed production system. Self-incompatibility is successfully used for the production of F1 hybrid seeds in B. rapa vegetables to avoid contamination by non-hybrid seeds, and the strength of self-incompatibility is important for harvesting a highly pure F1 seeds. Prediction of agronomically important traits such as disease resistance based on DNA markers is useful. In this dataset, we identified the S haplotypes by DNA markers and evaluated the strength of self-incompatibility in Chinese cabbage inbred lines. The data described the predicted disease resistance to Fusarium yellows or clubroot in 22 Chinese cabbage inbred lines using gene associated or gene linked DNA markers. Keywords: Brassica rapa, F1 hybrid cultivar, Marker assisted selection, Fusarium yellows, Clubroot disease, Self-incompatibility

The fusarium yellows resistance (YR) gene FocBo1 was previously identified and the DNA markers were developed to assist the breeding of YR cultivars in Brassica oleracea. However, the further analysis revealed discrepancies between the phenotypes and the genotypes predicted by those DNA markers in cabbage commercial cultivars. Since this discrepancy seemed to be due to unknown susceptible alleles of focbo1, we sequenced the gene in 19 accessions to determine the sequence variations between alleles and found that there were two resistant FocBo1 alleles and six susceptible alleles in the investigated population. The newly designed PCR markers detected three mutations in the susceptible alleles that generate premature termination codons. These were shown to accurately distinguish resistant and susceptible alleles in more than 200 accessions of B. oleracea inbred lines and cultivars. The study revealed that the locus is represented by 37.2% resistant and 62.8% susceptible alleles within seventy-eight commercial cultivars. Structural analysis of the gene revealed that a part of the allelic variation comes from intragenic recombination between alleles. Our results enable a more precise prediction of the phenotype by marker assisted selection, promoting the production of YR cultivars in B. oleracea.

Low erucic acid (LEA) rapeseed, which has accumulated mutant fatty acid elongase genes at the BnFAE1.1 and BnFAE1.2 loci of the A- and C-genome, respectively, is an important oilseed crop. Short growing turnip rape (B. rapa) is also important as a catch crop in the continuous cropping of rice in Asia but there is no LEA B. rapa cultivar for cultivation in South Asia. In order to develop LEA turnip rape cultivars, high erucic acid turnip rape cultivars were interspecifically crossed as recurrent parents to a canola quality rapeseed. In the meantime, we monitored incorporation of the mutant bnfae1.1 (e1) gene into A-genome of turnip rape, using a dCAPS primer pair, which can amplify PCR fragment only for the mutant e1 gene from A-genome. The early backcross progenies showed poor seed set, but which was improved in advanced progenies. Finally, homozygous e1e1 genotypes were established in the selfed progenies of BC2–BC3, and their LEA content was confirmed by gas-chromatography analysis. Our results and promising lines will contribute to LEA-trait selection in turnip rape and rapeseed breeding.

Cabbage (Brassica oleracea L. var. capitata) is an important vegetable worldwide. Most Japanese commercial cultivars of cabbage use an F1 hybrid seed production system. The purity of F1 hybrid seeds is important and the assessment of purity based on DNA markers can be highly accurate. In addition, selection of agronomically important traits such as disease resistance based on DNA markers is useful for breeding of cabbage. The aim of this study is to demonstrate the effectiveness of DNA marker-assisted selection in cabbage. In this study we distinguished the parental S haplotypes in 35 F1 hybrid cultivars by combining several linked DNA markers. Thirty-one highly polymorphic simple sequence repeats (SSR) markers were screened from 175 reported SSR markers, which are useful for assessment of the purity of F1 hybrid seeds. We examined the relationship between the DNA marker based genotype and the phenotype by an inoculation test of clubroot disease. A co-dominant PCR–RFLP marker was developed for selection of Fusarium yellows resistance and the genotypes using this marker were consistent with inoculation test in all tested samples.

Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans is an important disease of Brassica worldwide. To identify a resistance (R) gene against Fusarium yellows in Chinese cabbage (Brassica rapa var. pekinensis), we analyzed differential expression at the whole genome level between resistant and susceptible inbred lines using RNA sequencing. Four hundred and eighteen genes were significantly differentially expressed, and these were enriched for genes involved in response to stress or stimulus. Seven dominant DNA markers at putative R-genes were identified. Presence and absence of the sequence of the putative R-genes, Bra012688 and Bra012689, correlated with the resistance of six inbred lines and susceptibility of four inbred lines, respectively. In F(2) populations derived from crosses between resistant and susceptible inbred lines, presence of Bra012688 and Bra012689 cosegregated with resistance, suggesting that Bra012688 and Bra012689 are good candidates for fusarium yellows resistance in Chinese cabbage.

Brassica napus is a leading oilseed crop throughout many parts of the world. It is well adapted to long day photoperiods, however, it does not adapt well to short day subtropical regions. Short duration B. napus plants were resynthesized through ovary culture from interspecific crosses in which B. rapa cultivars were reciprocally crossed with B. oleracea. From five different combinations, 17 hybrid plants were obtained in both directions. By self-pollinating the F1 hybrids or introgressing them with cultivated B. napus, resynthesized (RS) F3 and semi-resynthesized (SRS) F2 generations were produced, respectively. In field trial in Bangladesh, the RS B. napus plants demonstrated variation in days to first flowering ranging from 29 to 73 days; some of which were similar to cultivated short duration B. napus, but not cultivated short duration B. rapa. The RS and SRS B. napus lines produced 2-4.6 and 1.6-3.7 times higher yields, respectively, as compared to cultivated short duration B. napus. Our developed RS lines may be useful for rapeseed breeding not only for subtropical regions, but also for areas such as Canada and Europe where spring rapeseed production can suffer from late spring frosts. Yield and earliness in RS lines are discussed.

Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.

Throughout the world, clubroot disease is one of the most damaging diseases affecting Brassica oleracea. To develop marker-assisted selection (MAS) that could assist the incorporation of durable clubroot resistance (CR) into cultivars, previous genetic analyses have identified several CR quantitative trait loci (CR–QTL). However, the independent and cumulative effects of each CR locus against various isolates have rarely been tested. Previously, we identified one major CR–QTL and four minor CR–QTL in the F2 plants from broccoli doubled haploid (DH) line × cabbage DH line of B. oleracea. In the present study, to clarify their effectiveness for controlling disease involving various isolates, inoculation testing was conducted in genotypes with various combinations of the CR genes, which were selected using the DNA markers closely associated with each CR–QTL. In exploring the overall disease incidence, it was apparent that a single involvement of the major CR gene located in the PbBo(Anju)1 locus, or accumulation of CR genes in the minor CR–QTL, is not enough to confer sufficient resistance. One major CR gene in the QTL PbBo(Anju)1 locus plus two to three minor CR genes conferred moderate resistance. The genotype in which all of the CR genes locating in the five QTL including PbBo(Anju)1 were accumulated showed the highest resistance, and it was broadly resistant against six isolates. Accumulation of several CR genes by MAS is necessary to conduct CR breeding in B. oleracea. Our developed DNA markers can be used efficiently to make selections of required loci for the acquisition of resistance, and use of these markers will be a powerful tool for CR breeding in B. oleracea.

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) is possibly the most important disease of Brassica worldwide. To compare chromosomal positions of Xcc resistance loci in Brassica oleracea between the present and published studies and to develop marker assisted selection (MAS) to resistance against Xcc race 1, we constructed a B. oleracea map, including pW, pX and BoCL markers that were closely linked to previously reported Xcc resistance QTLs. We also analyzed Xcc resistance QTLs by improving our previously reported map derived from the cross of a susceptible double-haploid line (GC P09) with a resistant double-haploid line (Reiho P01). In the nine linkage groups obtained (C1-C9), the major QTL, XccBo(Reiho)2, was derived from Reiho with a maximum LOD score (7.7) in C8. The QTL (LOD 4.4) located in C9, XccBo(GC)1 was derived from the susceptible GC. The other QTL (LOD 4.4), XccBo(Reiho)1, was found in C5. Based on common markers, it was possible to compare our finding Xcc resistance QTLs with the B. oleraceaXcc loci reported by previous authors; XccBo(Reiho)1 and XccBo(GC)1 may be identical to the Xcc resistance QTLs reported previously or a different member contained in the same resistance gene cluster. Our map includes public SSR markers linked to Xcc resistance genes that will promote pyramiding Xcc resistance genes in B. oleracea. The present study will also contribute to a better understanding of genetic control of Xcc resistance.

Epigenetic regulation is crucial for the development of plants and for adaptation to a changing environment. Recently, genome-wide profiles of histone modifications have been determined by a combination of chromatin immunoprecipitation (ChIP) and genomic tiling arrays (ChIP on chip) or ChIP and high-throughput sequencing (ChIP-seq) in species including Arabidopsis thaliana, rice and maize. Validation of ChIP analysis by PCR or qPCR using positive and negative regions of histone modification is necessary. In contrast, information about histone modifications is limited in Chinese cabbage, Brassica rapa. The aim of this study was to develop positive and negative control primer sets for H3K4me3 (trimethylation of the 4(th) lysine of H3), H3K9me2, H3K27me3 and H3K36me3 in B. rapa. The expression and histone modification of four FLC paralogs in B. rapa, before and after vernalization, were examined using the method developed here. After vernalization, expression of all four BrFLC genes was reduced, and accumulation of H3K27me3 was observed in three of them. As with A. thaliana, the vernalization response and stability of FLC repression correlated with the accumulation of H3K27me3. These results suggest that the epigenetic state during vernalization is important for high bolting resistance in B. rapa. The positive and negative control primer sets developed here revealed positive and negative histone modifications in B. rapa that can be used as a control for future studies.

Fusarium wilt caused by Fusarium oxysporum f. sp. conglutinans is one of the most important diseases of Brassica crops, resulting in severe reductions in yield and quality. To characterize the inheritance pattern of fusarium resistance, a cross between a susceptible broccoli and a resistant cabbage was subjected to segregation analysis. Results indicated that resistance was controlled by a single dominant allele. This gene was named Foc-Bo1 and mapped to linkage group seven (O7) by both the segregation test and quantitative trait locus (QTL) analysis. The QTL on O7 was detected with a logarithm of odds score (LOD) of 19.5, which was above the threshold value with genome-wide 1% significance level (2.01). A minor QTL was also detected on O4 with a LOD score of 2.06. Inoculation tests indicated that stable expression of fusarium resistance at high temperatures required Foc-Bo1 homozygosity. The association between Foc-Bo1 and the closest simple sequence repeat marker (KBrS003O1N10) was analyzed in three F3 populations. Based on these studies, KBrS003O1N10 represents an effective marker-assisted selection (MAS) tool for breeding fusarium wilt resistance into Brassica oleracea crops. To our knowledge, this is the first paper to map the fusarium-resistance gene in Brassica species and to validate the effectiveness of MAS in improving fusarium resistance in these important plants.

Midgut juice of Plutella xylostella strain PXR which is resistant to Cry1Ac was biochemically characterized relative to the susceptible PXS strain. The midgut juice of PXR (PXR-Juice) was shown to process Cry1Ac protoxin to 60 kDa active toxin with the same processing pattern as that of juice from PXS (PXS-Juice) in SDS–PAGE. PXS larvae which were given the Cry1Ac toxin pre-processed with PXR-Juice were killed with the same rate as that with Cry1Ac pre-activated by trypsin. PXR-Juice was found to contain three times larger amount of 66 kDa protein (P66) than PXS-Juice and the N-terminal amino acid sequence of P66 was matched to that of glucosinolate sulfatase in data base search. The protein band of P66 was coincided with the band of p-nitro phenyl sulfatase activity in zymogram. P66 purified to homogeneity in SDS-PAGE bound to Cry1Ac and soybean agglutinin, and KD for Cry1Ac was estimated to be 718 nM with surface plasmon resonance analysis. Using purified sulfatase, Km and Vmax were estimated and involvement of the enzyme in the PXR resistance was discussed.

The effect of nitrous oxide gas (N 2 O) treatment on the induction of 2n male gametes and 4n embryo in Lilium x formolongi hort. was examined. Lilium × formolongi hort. is an artificial hybrid between Lilium longiflorum Thunb. and Lilium formosanum Wall. In general the members in the genus Lilium are propagated vegetatively. However, Lilium x formolongi hort. is exceptionally propagated by seeds and blooms 6-8 months after sowing. Seeds of Lilium × formolongi hort. cultivars 'Raizan' was sown in a plastic tray with 200 holes on 5 February 2008 and seedlings bearing 2-3 leaves were transplanted in 10.5 cm (in diameter) pots on 5 May, grown under ambient conditions in a green house. When the first flower bud of each plant were reached 15-30 mm in length, these buds were sampled consecutively and observed by the aceto-carmine squash method to determine the meiotic stage of pollen mother cells. The buds ranging from 19-23 mm in length contained pollen grains at prophase I to tetrad. Immediately after the staging of pollen grains, plants with the buds in the same length were treated with N 2 O gas for 48h at 6 atm at room temperature. The diameter of mature pollen grains in metaphase, obtained from the plants with buds of 22 mm in length at the time of exposure to N 2 O gas, ranged from 76 to 169 μm, although those from untreated ones ranged from 62 to 95 μm. For the induction of 4n embryo, plants were treated with N 2 O gas for 72h at 6 atm 13 days after the pollination. Plants with pollinated ovaries grew visually normal after the treatment with N 2 0 gas and these capsules were harvested 75-85 days after pollination. We obtained many plantlets from these capsules. Of 49 randomly selected seedlings, 22 were revealed to be tetraploid by flow cytometry. We could demonstrate that N 2 O gas treatment was useful for the manipulation of both male gamete as well as zygotic embryo for breeding Lilium x formolongi on polyploid level.

To perform comparative studies of CR (clubroot resistance) loci in Brassica oleracea and Brassica rapa and to develop marker-assisted selection in B. oleracea, we constructed a B. oleracea map, including specific markers linked to CR genes of B. rapa. We also analyzed CR-QTLs using the mean phenotypes of F(3) progenies from the cross of a resistant double-haploid line (Anju) with a susceptible double-haploid line (GC). In the nine linkage groups obtained (O1-O9), the major QTL, pb-Bo(Anju)1, was derived from Anju with a maximum LOD score (13.7) in O2. The QTL (LOD 5.1) located in O5, pb-Bo(GC)1, was derived from the susceptible GC. Other QTLs with smaller effects were found in O2, O3, and O7. Based on common markers, it was possible to compare our finding CR-QTLs with the B. oleracea CR loci reported by previous authors; pb-Bo(GC)1 may be identical to the CR-QTL reported previously or a different member contained in the same CR gene cluster. In total, the markers linked to seven B. rapa CR genes were mapped on the B. oleracea map. Based on the mapping position and markers of the CR genes, informative comparative studies of CR loci between B. oleracea and B. rapa were performed. Our map discloses specific primer sequences linked to CR genes and includes public SSR markers that will promote pyramiding CR genes in intra- and inter-specific crosses in Brassica crops. Five genes involved in glucosinolates biosynthesis were also mapped, and GSL-BoELONG and GSL-BoPro were found to be linked to the pb-Bo(Anju)1 and Bo(GC)1 loci, respectively. The linkage drag associated with the CR-QTLs is briefly discussed.

We established an in situ hybridization (ISH) technique by modification of hybridization probes with locked nucleic acids (LNAs) and demonstrated isoform-specific localization of transcripts of Brassica rapanitrilase (BrNIT-T) genes in clubroot tissue infected with Plasmodiophora brassicae. Chimeric oligo DNA probes containing LNAs demonstrated highly improved specificities and could discriminate between BrNIT-T1 and BrNIT-T2. These LNA-containing probes were applied to ISH. BrNIT-T1 was strongly expressed in cells containing expanding secondary plasmodia of P. brassicae, but not in cells containing resting spores. On the other hand, BrNIT-T2 transcripts were localized in noninfected cells rather than infected cells during the clubroot growth phase but coexisted with mature resting spores at a later phase of clubroot development. Immunostaining for indole-3-acetic acid (IAA) revealed IAA accumulation in cells containing growing plasmodia. IAA immunostaining in infected cells was reduced as the pathogen formed resting spores, but the signal was again enhanced in cells containing mature resting spores at a later phase of infection, suggesting that IAA is involved in both the early growth and the latest maturation phase of clubroot development. Expression of BrNIT-T1 and BrNIT-T2 in turnip roots was upregulated by exogenous treatment with cytokinin and jasmonic acid, respectively. Thus, these two phytohormones are possible triggers of abnormal IAA production in clubroot tissue via induction of the respective nitrilase. Given these results, we propose a model for isoform-specific roles of B. rapa nitrilases in auxin biosynthesis involved in phytohormone crosstalk during development of clubroot disease.

Most Liliaceae plants have the tetrasporic Fritillaria-type embryo sac and normally form diploid embryos and pentaploid endosperms derived from a 4:1 maternal-to-paternal genome ratio (4m:1p) after double fertilization. Here we characterize embryo sac and endosperm formation in Tulipa spp. of Liliaceae. Chromosome analysis using seeds derived from 2x x 2x crosses of Tulipa gesneriana (2n = 2x = 24) identified diploid chromosome number in the endosperm. Similarly, flow cytometric analysis confirmed diploid endosperm formation in T. gesneriana, T. fosteriana (2n = 2x = 24) and T. greigii (2n = 2x = 24). To further study the possible mechanism of diploid endosperm formation, we made interploidy crosses of triploid (2n = 3x = 36) x diploid in which aneuploid seeds with various chromosome numbers (2n = 25-36) were produced. Again, flow cytometric analysis confirmed the same ploidy level in both embryos and endosperms at all aneuploidy levels, suggesting that only a single haploid polar nucleus contributes to endosperm formation at fertilization. Histological observation further confirmed the physical separation of two polar nuclei by a large vacuole in the Fritillaria-type embryo sac of T. gesneriana that appeared to prevent the fusion of the two polar nuclei that originated at the micropylar and chalazal ends before fertilization. Taken together, these results indicate that diploid endosperms (1m:1p) are normally formed in Tulipa spp. by fusion of the micropylar polar nucleus (n) and a spermatid (n) but not by normal triple fusion. We also show that tulip endosperm partially overcomes the triploid block mechanism that occurs in interploidy crosses. Based on these observations, the possible role of triple nuclear fusion in double fertilization is discussed.

Genomic in situ hybridization (GISH) was used to understand the process of interspecific tulip hybrid diploid (2n = 2x = 24), triploid (2n = 3x = 36) and tetraploid (2n = 4x = 48) cultivar formation. Simultaneous hybridization of differentially labelled genomic probes enabled chromosomes derived from T. gesneriana and T. fosteriana to be distinguished in all cultivars tested. Diploid cultivar ‘Shirayukihime’ contained one set of chromosomes from T. gesneriana and one set from T. fosteriana. In triploid cultivars ‘Come Back’, ‘Diplomate’, ‘Pink Impression’ and ‘Oxford’, 24 chromosomes were derived from T. gesneriana and 12 chromosomes originated from T. fosteriana. The genome of tetraploid cultivar ‘Ollioules’ comprised 36 chromosomes from T. gesneriana and 12 chromosomes from T. fosteriana. In all tulip hybrids, GISH signals were localized predominately in telomeric/subtelomeric and intercalary regions of T. gesneriana chromosomes, whereas T. fosteriana chromosomes were painted more evenly along the chromosome length. In triploid and tetraploid cultivars, cross-hybridization to putative rRNA gene sites was observed at telomeric and intercalary locations of some chromosomes, although additional experiments are needed to identify what kind of repetitive DNA families are arranged as nested elements interspersed in the tulip genome. INTRODUCTION Tulip is one of the most important ornamental crops. Every year many new cultivars are introduced to the market, some of which have been made by interspecific hybridization between genotypes of cultivated tulips (Tulipa gesneriana) and other Tulipa species (Van Eijk et al., 1991; Van Creij et al., 1997). Crosses between T. gesneriana and T. fosteriana are especially successful (Van Eijk et al., 1991; Van Creij et al., 1997), most of which are triploid (2n=36), whereas a few are diploid (2n=24) and tetraploid (2n=48). Vigorous traits such as large flowers, sturdy stems and large plant size are exhibited primarily by the triploid forms. Because of their distinct traits, these vigorous forms were given a classification of their own in the tulip classification list (Killingback, 1990), and are referred to as Darwin Hybrid Tulips. Because most of the diploid forms obtained from crosses between T. gesneriana and T. fosteriana do not show vigorous growth, they are classified in other horicultural groups; for example, ‘Shirayukihime’, is registered under Single Late Tulips. From these crosses, over 50 cultivars of Darwin Hybrid Tulips have been developed so far; most are triploid, one cultivar ‘Spring Song’ is a diploid, and a few are tetraploids (e.g., cultivar ‘Ollioules’ (Van Scheepen, 1996; Okazaki et al., 2005)). The triploid Darwin Hybrid Tulips have spontaneously resulted from unreduced gametes. By studying karyotype in tulips, Marasek et al. (2006) demonstrated that the Darwin Hybrid Tulips tested have two copies of the T. gesneriana genome and one copy of the T. fosteriana genome, indicating that T. gesneriana has supplied the diploid gamete. However, identification of the genome constitution of Darwin Hybrid Tulips using GISH has thus far been limited to the triploid cultivar ‘Yellow Dover’. For most Darwin Hybrid Tulip cultivars, little is known about their genome consitution, especially for the tetraploid form. In addition, it is unknown whether homologous recombination has occurred in polyploid genotypes between T. gesneriana and T. fosteriana chromosomes. 133 Proc. XX Intl. Eucarpia Symp. (Sect. Ornamentals) on Breeding for Beauty (Vol II) Eds. A. Mercuri and T. Schiva Acta Hort. 743, ISHS 2007 The objective of the present study was to use GISH to determine the genome composition in diploid (2n = 2x = 24), triploid (2n = 3x = 36) and tetraploid (2n = 4x = 48) tulip cultivars, which were obtained from interspecific crosses between T. gesneriana and T. fosteriana. MATERIALS AND METHODS Plant Materials The following tulip genotypes were used in this study: diploid cultivar ‘Shirayukihime’ (2n = 2x = 24), which was obtained from the interspecific hybridization between T. gesneriana and T. fosteriana (Kimura, 2002) and belongs to the classification group Single Late Tulips; triploid cultivars ‘Come Back’, ‘Diplomate’, ‘Pink Impression’ and ‘Oxford’ (2n = 3x = 36) (Darwin Hybrid Tulips); and tetraploid cultivar ‘Ollioules’ (Darwin Hybrid Tulips) (2n = 4x = 48). Cultivars were classified according to Van Scheepen (1996). Bulbs were obtained from the Toyama Bulb Growers Association, Japan. Chromosome Preparation Root tips were pre-treated with 0.05% colchicine at 18°C for 2.5 h and fixed in 3:1 (v/v) absolute ethanol:glacial acetic acid and stored at −20C. Root tips were washed in enzyme buffer (0.01 M sodium citrate, pH 4.8) for 20 min prior to digestion in an enzyme mixture containing 2% (w/v) cellulase Onozuka-RS (Yakult Honsha Co., LTD. Japan) and 1% (w/v) pectolyase Y-23 (Kyowa Chemical Products Co., LTD. Japan) for 2.5 h at 37oC. Meristems were squashed in a drop of 45% acetic acid, cover slips were removed by freezing on dry ice and preparations were dehydrated in absolute ethanol and air-dried. DNA Probes and In Situ Hybridization Total genomic DNA from ‘Red Emperor’ (T. fosteriana; 2n = 2x = 24) and ‘Queen of Night’ (T. gesneriana; 2n = 2x = 24) was extracted from the leaves using the standard cetyltrimethylammonium bromide (CTAB) method (Murray and Thompson, 1980). DNA was sonicated to yield 1–10-kb fragments and labelled by nick translation with either tetramethyl-rhodamine-5-dUTP (T. fosteriana) or digoxigenin-11-dUTP (T. gesneriana) (Roche). Autoclaved T. sacstatila DNA (100–500 bp) was used as blocking DNA in 30–75× excess of the probes. The method for in situ hybridization and probe detection followed Hasterok et al. (2001) with minor modifications. Slides were pre-treated with RNase A (100 μg/ml) for 1 h at 37oC, then washed in 2× SSC, post-fixed in 1% formaldehyde in PBS buffer for 10 min, washed again in 2× SSC and dehydrated in absolute ethanol. The hybridization mixture consisted of 50% deionized formamide, 10% dextran sulphate, 2× SSC, 1% SDS and probe DNA (200 ng of each per slide). The hybridization mixture was denatured at 75oC for 10 min and chilled on ice. Chromosome preparations and pre-denatured probes were denatured at 70oC for 10 min. Hybridization was carried out overnight in a humid chamber at 37oC followed by stringent washes in 2× SSC for 15 min at room temperature and in 0.1× SSC for 30 min at 42oC. The digoxigenated probe was immunodetected using the standard protocol with FITC-conjugated anti-digoxigenin (Roche). The chromosomes were counterstained with 1 μg/ml 4,6-diamidino-2-phenylindole (DAPI, Sigma) in Vectashield (Vector Laboratories). Images of fluorescently stained chromosomes were acquired using a digital camera attached to a microscope (BX51N, Olympus, Japan) with an appropriate filter and then processed using software (DP Manager, Olympus, Japan). RESULTS AND DISCUSSION Distribution of GISH Signals Simultaneous application of differentially labelled ‘Queen of Night’ (T. gesneriana) (green) and ‘Red Emperor’ (T. fosteriana) (red) total genomic DNA probes

Fusarium oxysporum f. sp. conlutinans (Foc) is a serious root-invading and xylem-colonizing fungus that causes yellowing in Brassica oleracea. To comprehensively understand the interaction between F. oxysporum and B. oleracea, composition of the xylem sap proteome of the non-infected and Foc-infected plants was investigated in both resistant and susceptible cultivars using liquid chromatography-tandem mass spectrometry (LC-MS/MS) after in-solution digestion of xylem sap proteins. Whole genome sequencing of Foc was carried out and generated a predicted Foc protein database. The predicted Foc protein database was then combined with the public B. oleracea and B. rapa protein databases downloaded from Uniprot and used for protein identification. About 200 plant proteins were identified in the xylem sap of susceptible and resistant plants. Comparison between the non-infected and Foc-infected samples revealed that Foc infection causes changes to the protein composition in B. oleracea xylem sap where repressed proteins accounted for a greater proportion than those of induced in both the susceptible and resistant reactions. The analysis on the proteins with concentration change >=2 fold indicated a large portion of up- and down-regulated proteins were those acting on carbohydrates. Proteins with leucine-rich repeats and legume lectin domains were mainly induced in both resistant and susceptible system, so was the case of thaumatins. Twenty-five Foc proteins were identified in the infected xylem sap and ten of them were cysteine-containing secreted small proteins that are good candidates for virulence and/or avirulence effectors. The findings of differential response of protein contents in the xylem sap between the non-infected and Foc-infected samples as well as the Foc candidate effectors secreted in xylem provide valuable insights into B. oleracea-Foc interactions.

Tetraploid varieties of lilies have superior agronomic traits such as large flowers and resistance to physiological disorders. In the present study, we attempted to induce 2n pollen of Asiatic hybrid lilies by arresting the meiotic process with nitrous oxide (N2O) gas. To determine which meiotic stage is optimal for induction of 2n pollen, plants with attached buds at different meiotic stages were treated with N2O for 24 h in a pressure-tolerant cylinder. A few 2n pollen grains were induced using plants with anthers in prophase I, whereas mixed pollen grains of differing size were produced using plants undergoing meiotic metaphase predominantly in anthers. Although normal lily pollen grains are elliptical, nitrous oxide exposure induced giant pollen grains that appeared spherical. Flow cytometry analysis showed that the giant pollen grains were diploid. When mixed pollen that included normal and giant pollen was crossed to tetraploid cultivars, the resulting seedlings were tetraploid and aneuploid, indicating that the giant pollen grains were diploids that could generate tetraploid seedlings through fusion to diploid eggs supplied from a tetraploid female parent. Thus, treatment with N2O is useful for the production of 2n lily pollen and may provide a new approach for tetraploid lily breeding.

The FLC gene product is an inhibitor of flowering in Arabidopsis. FLC homologs in Brassica species are thought to control vernalization. We cloned four FLC homologs (BoFLCs) from Brassica oleracea. Three of these, BoFLC1, BoFLC3 and BoFLC5, have been previously characterized. The fourth novel sequence displayed 98% sequence homology to the previously identified gene BoFLC4, but also showed 91% homology to BrFLC2 from Brassica rapa. Phylogenetic analysis showed that this clone belongs to the FLC2 clade. Therefore, we designated this gene BoFLC2. Based on the segregation of RFLP, SRAP, CAPS, SSR and AFLP loci, a detailed linkage map of B. oleracea was constructed in the F(2) progeny obtained from a cross of B. oleracea cv. Green Comet (broccoli; non-vernalization type) and B. oleracea cv. Reiho (cabbage; vernalization type), which covered 540 cM, 9 major linkage groups. Six quantitative trait loci (QTL) controlling flowering time were detected. BoFLC1, BoFLC3 and BoFLC5 were not linked to the QTLs controlling flowering time. However, the largest QTL effect was located in the region where BoFLC2 was mapped. Genotyping of F(2 )plants at the BoFLC2 locus showed that most of the early flowering plants were homozygotes of BoFLC-GC, whereas most of the late- and non-flowering plants were homozygotes of BoFLC-Rei. The BoFLC2 homologs present in plants of the non-vernalization type were non-functional, due to a frameshift in exon 4. Moreover, duplications and deletions of BoFLC2 were detected in broccoli and a rapid cycling line, respectively. These results suggest that BoFLC2 contributes to the control of flowering time in B. oleracea.

In order to develop a method to measure resistance to Alternaria brassicicola (cause of dark leaf spot disease) in Brassica rapa, the effects of inoculum concentration, leaf stage, leaf age and incubation temperature of inoculation on infection were studied under controlled conditions using several B. rapa genotypes. Three inoculation methods (cotyledon, detached leaf and seedling inoculation) were evaluated for this purpose. The detached leaf inoculation test was the most suitable for screening B. rapa genotypes because clear symptoms were observed on the leaves in less than 24 h, and there was a significant positive correlation between the results from the detached leaf inoculation test and the seedling inoculation test, an established method considered to yield reliable results. In addition, it was very easy to screen plants for resistance on a large scale and to maintain standard physical conditions using detached leaves. For successful infection, inoculum concentration should be adjusted to 5 × 104 conidia ml−1, and incubation temperature should be between 20 °C and 25 °C. The 3rd/4th true leaves from 30 day-old plants were optimal for inoculation. In a screening test using 52 cultivars of B. rapa, the detached leaf test effectively discriminated between various levels of partial resistance among cultivars. As a result, we identified two cultivars, viz Saori and Edononatsu, as highly resistant and five cultivars, viz Tokinashi Taisai, Yajima Kabu, Purara, Norin-F1-Bekana and Tateiwa Kabu, as having borderline resistance.