Comparative Transcriptome Analysis between Two Potato Cultivars in Tuber Induction to Reveal Associated Genes with Anthocyanin Accumulation

Anthocyanins are generally accumulated within a few layers, including the epidermal cells of leaves and stems in plants. Solanum tuberosum cv. ‘Jayoung’ (hereafter, JY) is known to accumulate anthocyanin both in inner tissues and skins. We discovered that anthocyanin accumulation in the inner tissues of JY was almost diminished (more than 95% was decreased) in tuber induction condition. To investigate the transcriptomic mechanism of anthocyanin accumulation in JY flesh, which can be modulated by growth condition, we performed mRNA sequencing with white-colored flesh tissue of Solanum tuberosum cv. ‘Atlantic’ (hereafter, ‘Daeseo’, DS) grown under canonical growth conditions, a JY flesh sample grown under canonical growth conditions, and a JY flesh sample grown under tuber induction conditions. We could identify 36 common DEGs (differentially expressed genes) in JY flesh from canonical growth conditions that showed JY-specifically increased or decreased expression level. These genes were enriched with flavonoid biosynthetic process terms in GO analysis, as well as gene set enrichment analysis (GSEA) analysis. Further in silico analysis on expression levels of anthocyanin biosynthetic genes including rate-limiting genes such as StCHS and StCHI followed by RT-PCR and qRT-PCR analysis showed a strong positive correlation with the observed phenotypes. Finally, we identified StWRKY44 from 36 common DEGs as a possible regulator of anthocyanin accumulation, which was further supported by network analysis. In conclusion, we identified StWRKY44 as a putative regulator of tuber-induction-dependent anthocyanin accumulation.

Intron-retained radish (Raphanus sativus L.) RsMYB1 transcripts found in colored-taproot lines enhance anthocyanin accumulation in transgenic Arabidopsis plants

KEY MESSAGE

Overexpression of the naturally occurring intron-retained (IR) forms of radish RsMYB1 and RsTT8 transcripts in Arabidopsis causes a substantial increase in anthocyanin accumulation. The production of anthocyanins in plants is tightly controlled by the MYB-bHLH-WD40 (MBW) complex. In this study, analysis of four radish (Raphanus sativus L.) inbred lines with different colored taproots revealed that regulatory genes of anthocyanin biosynthesis, RsMYB1 and RsTT8, produce three transcripts, one completely spliced and two intron retention (IR1 and IR2) forms. Transcripts RsMYB1-IR1 and RsMYB1-IR2 retained the 1st (380 nt) and 2nd (149 nt) introns, respectively; RsTT8-IR1 retained the 4th intron (113 nt); RsTT8-IR2 retained both the 3rd (128 nt) and 4th introns. Levels of most IR forms were substantially low in radish samples, but the RsTT8-IR2 level was higher than RsTT8 in red skin/red flesh (RsRf) root. Since all IR forms contained a stop codon within the intron, they were predicted to encode truncated proteins with defective interaction domains, resulting in the inability to form the MBW complex in vivo. However, tobacco leaves transiently co-expressing RsMYB1-IRs and RsTT8-IRs showed substantially higher anthocyanin accumulation than those co-expressing their spliced forms. Consistently, co-expression of constructs encoding truncated proteins with spliced or IR forms of their interaction partner in tobacco leaves did not result in anthocyanin accumulation. Compared with RsMYB1, the overexpression of RsMYB1-IRs in Arabidopsis pap1 mutant increased anthocyanin accumulation by > sevenfold and upregulated the expression of Arabidopsis flavonoid biosynthesis genes including AtTT8. Our results suggest that the stable co-expression of RsMYB1-IRs in fruit trees and vegetable crops could be used to increase their anthocyanin contents.

Alleles disrupting LBD37-like gene by an 136 bp insertion show different distributions between green and purple cabbages (Brassica oleracea var. capitata)

BACKGROUND

In Arabidopsis thaliana (Arabidopsis), clade IIb lateral organ boundary domain (LBD) 37, 38, and 39 proteins negatively regulate anthocyanin biosynthesis and affect nitrogen responses.

OBJECTIVE

To investigate the possible role of LBD genes in anthocyanin accumulations among green and purple cabbages (Brassica oleracea var. capitata), we determined sequence variations and expression levels of cabbage homologs of Arabidopsis LBD37, 38, and 39.

METHODS

DNA and mRNA sequences of BoLBD37, BoLBD37L (BoLBD37-like), BoLBD38, BoLBD38L (BoLBD38-like), and BoLBD39 gene in cabbage were determined. Allelic variations of BoLBD37L alleles in cabbages, resulting from insertions, were validated by genomic DNA PCR. Gene expressions were examined by semi-quantitative reverse transcription (RT-PCR) or quantitative RT-PCR.

RESULTS

Based on the expression analyses, BoLBD37L with two alleles, BoLBD37L-G and BoLBD37L-P, was selected as a candidate gene important for differential anthocyanin accumulation. BoLBD37L-P contains an 136 base pair insertion in the 2nd exon, producing two splicing variants encoding truncated proteins. Most purple cabbage lines were found to have BoLBD37L-P allele as homozygotes or heterozygotes, and only two out of sixty-four purple cabbages were identified as BoLBD37L-G homozygotes. Expression analyses of anthocyanin biosynthesis genes and their upstream regulators, including BoLBD37L, suggest that truncated proteins encoded by splicing variants of BoLBD37L-P may disrupt the BoLBD37L function as repressor.

CONCLUSION

Difference in the C-terminal region of BoLBD37L-G and BolBD37L-P may affect the expression of downstream genes, BoMYB114L and BoTT8, resulting in differential anthocyanin accumulation.

Natural variation in glycine-rich region of Brassica oleracea cold shock domain protein 5 (BoCSDP5) is associated with low temperature tolerance

BACKGROUND

Low temperature (LT) or cold stress is a major environmental stress that seriously affects plant growth and development, limiting crop productivity. Cold shock domain proteins (CSDPs), which are present in most living organism, are involved in RNA metabolisms influencing abiotic stress tolerance.

OBJECTIVE

The aims of this study are to identify target gene for LT-tolerance, like CSDPs, characterize genetics, and develop molecular marker distinguishing LT-tolerance in cabbage (Brassica oleracea var. capitata).

METHODS

Semi-quantitative RT-PCR or qRT-PCR was used in gene expression study. LT-tolerance was determined by electrolyte leakage and PCR with allelic specific primers.

RESULTS

Allelic variation was found in BoCSDP5 coding sequence (CDs) between LT-tolerant (BN106 and BN553) and -susceptible inbred lines (BN107 and BN554). LT-tolerant inbred lines contained variant type of BoCSDP5 (named as BoCSDP5v) which encodes extra CCHC zinc finger domain at C-terminus. Association of LT-tolerance with BoCSDP5v was confirmed by electrolyte leakage and segregation using genetic population derived from BN553 and BN554 cross. Allelic variation in BoCSDP5 gene does not influence the rate of gene expression, but produces different proteins with different number of CCHC zinc finger domains. LT-tolerance marker designed on the basis of polymorphism between BoCSDP5 and BoCSDP5v was confirmed with samples used in previous B. oleracea CIRCADIAN CLOCK ASSOCIATED 1 (BoCCA1) marker validation.

CONCLUSIONS

LT-tolerant allele (BoCSDP5v) is dominant and independent of CBF pathway, and sufficient to generate molecular markers to identify LT-tolerant cabbage when it is used in combination with another marker, like BoCCA1-derived one. Production and analysis of overexpressing plants of BoCSDP1, BoCSDP3, BoCSDP5 and BoCSDP5v will be required for elucidating the function of CCHC zinc finger domains in LT-tolerance.

Molecular characterization of Arabidopsis thaliana LSH1 and LSH2 genes

BACKGROUND

Arabidopsis thaliana genome encodes ten DUF640 (short for domain of unknown function 640)/ALOG (short for Arabidopsis LSH1 and Oryza G1) proteins, also known as light-dependent short hypocotyl (LSH) proteins. While some of the LSH genes regulate organ boundary determination and shade avoidance response, the function of most of these genes remains largely unknown.

OBJECTIVE

In this study, we aimed to characterize the function of AtLSH1 and AtLSH2 in Arabidopsis.

METHODS

We overexpressed AtLSH1 and AtLSH2 (with or without the FLAG tag) in Arabidopsis Col-0 plants under the control of the 35S promoter. We also generated knockout or knockdown lines of these genes by miRNA-induced gene silencing (MIGS). We conducted intensive phenotypic analysis of these transgenic lines, and finally performed RNA-seq analysis of two AtLSH2 overexpression (OX) lines.

RESULTS

Although AtLSH1 and AtLSH2 amino acid sequences showed high similarly, AtLSH2-OX lines showed much higher levels of their transcripts than those of AtLSH1-OX lines. Additionally, overexpression of AtLSH1 and AtLSH2 greatly inhibited hypocotyl elongation in a light-independent manner, and reduced both vegetative and reproductive growth. However, knockout or knockdown of both these AtLSH genes did not affect plant phenotype. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) identified by RNA-seq revealed enrichment of the GO term 'response to stimulus', included phytohormone-responsive genes; however, genes responsible for the abnormal phenotypes of AtLSH2-OX lines could not be identified.

CONCLUSION

Although our data revealed no close association between light and phytohormone signaling components, overexpression of AtLSH1 and AtLSH2 greatly reduced vegetative and reproductive growth of Arabidopsis plants. This property could be used to generate new plants by regulating expression of AtLSH1 and AtLSH2.

Overexpression of Acyl-ACP Thioesterases, CpFatB4 and CpFatB5, Induce Distinct Gene Expression Reprogramming in Developing Seeds of Brassica napus

We examined the substrate preference of Cuphea paucipetala acyl-ACP thioesterases, CpFatB4 and CpFatB5, and gene expression changes associated with the modification of lipid composition in the seed, using Brassica napus transgenic plants overexpressing CpFatB4 or CpFatB5 under the control of a seed-specific promoter. CpFatB4 seeds contained a higher level of total saturated fatty acid (FA) content, with 4.3 times increase in 16:0 palmitic acid, whereas CpFatB5 seeds showed approximately 3% accumulation of 10:0 and 12:0 medium-chain FAs, and a small increase in other saturated FAs, resulting in higher levels of total saturated FAs. RNA-Seq analysis using entire developing pods at 8, 25, and 45 days after flowering (DAF) showed up-regulation of genes for β-ketoacyl-acyl carrier protein synthase I/II, stearoyl-ACP desaturase, oleate desaturase, and linoleate desaturase, which could increase unsaturated FAs and possibly compensate for the increase in 16:0 palmitic acid at 45 DAF in CpFatB4 transgenic plants. In CpFatB5 transgenic plants, many putative chloroplast- or mitochondria-encoded genes were identified as differentially expressed. Our results report comprehensive gene expression changes induced by alterations of seed FA composition and reveal potential targets for further genetic modifications.

Molecular analysis of anthocyanin biosynthesis-related genes reveal BoTT8 associated with purple hypocotyl of broccoli (Brassica oleracea var. italica L.)

Broccoli (Brassica oleracea var. italica L.) is a highly nutritious vegetable that typically forms pure green or purple florets. However, green broccoli florets sometimes accumulate slight purplish pigmentation in response environmental factors, decreasing their market value. In the present study, we aimed to develop molecular markers to distinguish broccoli genotypes as pure green or purplish floret color at the early seedling stage. Anthocyanins are known to be involved in the purple pigmentation in plants. The purplish broccoli lines were shown to accumulate purple pigmentation in the hypocotyls of very young seedlings; therefore, the expression profiles of the structural and regulatory genes of anthocyanin biosynthesis were analyzed in the hypocotyls using qRT-PCR. BoPAL, BoDFR, BoMYB114, BoTT8, BoMYC1.1, BoMYC1.2, and BoTTG1 were identified as putative candidate genes responsible for the purple hypocotyl color. BoTT8 was much more highly expressed in the purple than green hypocotyls; therefore, it was cloned and sequenced from various broccoli lines, revealing SNP and InDel variations between these genotypes. We tested four SNPs (G > A; A > T; G > C; T > G) in the first three exons and a 14-bp InDel (ATATTTATATATAT) in the BoTT8 promoter in 51 broccoli genotypes, and we found these genetic variations could distinguish the green lines, purple lines, and F₁ hybrids. These novel molecular markers could be useful in broccoli breeding programs to develop a true green or purple broccoli cultivar.

Purple Brassica oleracea var. capitata F. rubra is due to the loss of BoMYBL2-1 expression

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.

RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes

Accumulated microarray data are used for assessing gene function by providing statistical values for co-expressed genes; however, only a limited number of Web tools are available for analyzing the co-expression of genes of Brassica rapa. We have developed a Web tool called RapaNet (http://bioinfo.mju.ac.kr/arraynet/brassica300k/query/), which is based on a data set of 143 B rapa microarrays compiled from various organs and at different developmental stages during exposure to biotic or abiotic stress. RapaNet visualizes correlated gene expression information via correlational networks and phylogenetic trees using Pearson correlation coefficient (r). In addition, RapaNet provides hierarchical clustering diagrams, scatterplots of log ratio intensities, related pathway maps, and cis-element lists of promoter regions. To ascertain the functionality of RapaNet, the correlated genes encoding ribosomal protein (L7Ae), photosystem II protein D1 (psbA), and cytochrome P450 monooxygenase in glucosinolate biosynthesis (CYP79F1) were retrieved from RapaNet and compared with their Arabidopsis homologues. An analysis of the co-expressed genes revealed their shared and unique features.

Molecular characterisation and expression profiling of calcineurin B-like (CBL) genes in Chinese cabbage under abiotic stresses

Calcium signals act as a second messenger in plant responses to various abiotic stresses, which regulate a range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, belong to a unique group of calcium sensors that play a role in calcium signalling. However, their identities and functions are unknown in Chinese cabbage. In this study, 17 CBL genes were identified from the Brassica rapa L. (Chinese cabbage) database and Br135K microarray datasets. They were used to construct a phylogenetic tree with known CBL proteins of other species. Analysis of genomic distribution and evolution revealed different gene duplication in Chinese cabbage compared to Arabidopsis. The microarray expression analysis showed differential expression of BrCBL genes at various temperatures. Organ-specific expression was observed by RT-PCR, and qRT-PCR analyses revealed responsiveness of BrCBL genes to cold, drought and salt stresses. Our findings confirm that CBL genes are involved in calcium signalling and regulate responses to environmental stimuli, suggesting this family gene have crucial role to play in plant responses to abiotic stresses. The results facilitate selection of candidate genes for further functional characterisation. In addition, abiotic stress-responsive genes reported in this study might be exploited for marker-aided backcrossing of Chinese cabbage.

Expression of Genes Related to Phenylpropanoid Biosynthesis in Different Organs of Ixeris dentata var. albiflora

Members of the genus Ixeris have long been used in traditional medicines as stomachics, sedatives, and diuretics. Phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate: coenzyme-A (CoA) ligase (4CL), chalcone synthase (CHS), and dihydroflavonol 4-reductase (DFR) are important enzymes in the phenylpropanoid pathway. In this study, we analyzed seven genes from Ixeris dentata var. albiflora that are involved in phenylpropanoid biosynthesis, using an Illumina/Solexa HiSeq 2000 platform. The amino acid sequence alignments for IdPALs, IdC4H, Id4CLs, IdCHS, and IdDFR showed high identity to sequences from other plants. We also investigated transcript levels using quantitative real-time PCR, and analyzed the accumulation of phenylpropanoids in different organs of I. dentata var. albiflora using high-performance liquid chromatography. The transcript levels of IdC4H, Id4CL1, IdCHS, and IdDFR were highest in the leaf. The catechin, chlorogenic acid, ferulic acid, and quercetin contents were also highest in the leaf. We suggest that expression of IdC4H, Id4CL1, IdCHS, and IdDFR is associated with the accumulation of phenylpropanoids. Our results may provide baseline information for elucidating the mechanism of phenylpropanoid biosynthesis in different organs of I. dentata var. albiflora.

Natural variation in CIRCADIAN CLOCK ASSOCIATED 1 is associated with flowering time in Brassica rapa

Flowering time is a very important agronomic trait and the development of molecular markers associated with this trait can facilitate crop breeding. CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a core oscillator component of circadian rhythms that affect metabolic pathways in plants, has been implicated in flowering time control in species of Brassica. CCA1 gene sequences from three Brassica rapa inbred lines, showing either early flowering or late flowering phenotypes, were analyzed and a high level of sequence variation was identified, especially within the fourth intron. Using this information, three PCR primer sets were designed and tested using various inbred lines of B. rapa. The usage of InDel markers was further validated by evaluation of flowering time and high resolution melting (HRM) analysis. Both methods, PCR and HRM, validated the use of newly developed markers. Additional sequence analyses of Brassica plants with diploid (AA, BB, or CC) and allotetraploid genomes further confirmed a large number of sequence polymorphisms in the CCA1 gene, including insertions/deletions in the fourth intron. Our results demonstrated that sequence variations in CCA1 can be used to develop valuable trait-related molecular markers for Brassica crop breeding.

Intracellular Ca(2+) and K(+) concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related 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 Ca(2+) 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 Ca(2+) deficiency, there is limited information on the underlying mechanisms of tip-burn or the relationship between Ca(2+) 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 Ca(2+) 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 Ca(2+) 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. Ca(2+) 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 Ca(2+) 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 Ca(2+) 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 Ca(2+) 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 Ca(2+) 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.

Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa

Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5– 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included ‘response to heat’, ‘response to reactive oxygen species (ROS)’, ‘response to temperature stimulus’, ‘response to abiotic stimulus’, and ‘MAPKKK cascade’. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as HsfB2A (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853), protein kinases, and phosphatases. Among heat stress (HS) marker genes in Arabidopsis, only exportin 1A (XPO1A) (Bra008580, Bra006382) can be applied to B. rapa for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. CYP707A3 (Bra025083, Bra021965), which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including DREB2A (Bra005852), were involved in HS tolerance in both lines, Bra024224 (MYB41) and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data could also provide a springboard for developing molecular markers of HS and for engineering HS tolerant B. rapa.

Suppression of ASKβ (AtSK32), a Clade III Arabidopsis GSK3, Leads to the Pollen Defect during Late Pollen Development

Arabidopsis Shaggy-like protein kinases (ASKs) are Arabidopsis thaliana homologs of glycogen synthase kinase 3/SHAGGY-like kinases (GSK3/SGG), which are comprised of 10 genes with diverse functions. To dissect the function of ASKβ (AtSK32), ASKβ antisense transgenic plants were generated, revealing the effects of ASKβ down-regulation in Arabidopsis. Suppression of ASKβ expression specifically interfered with pollen development and fertility without altering the plants' vegetative phenotypes, which differed from the phenotypes reported for Arabidopsis plants defective in other ASK members. The strength of these phenotypes showed an inverse correlation with the expression levels of ASKβ and its co-expressed genes. In the aborted pollen of ASKβ antisense plants, loss of nuclei and shrunken cytoplasm began to appear at the bicellular stage of microgametogenesis. The in silico analysis of promoter and the expression characteristics implicate ASKβ is associated with the expression of genes known to be involved in sperm cell differentiation. We speculate that ASKβ indirectly affects the transcription of its co-expressed genes through the phosphorylation of its target proteins during late pollen development.

Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa

BACKGROUND

MADS-box transcription factors (TFs) are important in floral organ specification as well as several other aspects of plant growth and development. Studies on stress resistance-related functions of MADS-box genes are very limited and no such functional studies in Brassica rapa have been reported. To gain insight into this gene family and to elucidate their roles in organ development and stress resistance, we performed genome-wide identification, characterization and expression analysis of MADS-box genes in B. rapa.

RESULTS

Whole-genome survey of B. rapa revealed 167 MADS-box genes, which were categorized into type I (Mα, Mβ and Mγ) and type II (MIKC(c) and MIKC*) based on phylogeny, protein motif structure and exon-intron organization. Expression analysis of 89 MIKC(c) and 11 MIKC* genes was then carried out. In addition to those with floral and vegetative tissue expression, we identified MADS-box genes with constitutive expression patterns at different stages of flower development. More importantly, from a low temperature-treated whole-genome microarray data set, 19 BrMADS genes were found to show variable transcript abundance in two contrasting inbred lines of B. rapa. Among these, 13 BrMADS genes were further validated and their differential expression was monitored in response to cold stress in the same two lines via qPCR expression analysis. Additionally, the set of 19 BrMADS genes was analyzed under drought and salt stress, and 8 and 6 genes were found to be induced by drought and salt, respectively.

CONCLUSION

The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MADS-box genes in stress resistance in addition to their growth and developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate genes for genetic engineering of B. rapa.

Response of NBS encoding resistance genes linked to both heat and fungal stress in Brassica oleracea

Environmental stresses, including both abiotic and biotic stresses, cause considerable yield loss in crops and can significantly affect their development. Under field conditions, crops are exposed to a variety of concurrent stresses. Among abiotic and biotic stresses, heat and Fusarium oxysporum, are the most important factors affecting development and yield productivity of Brassica oleracea. Genes encoding the nucleotide-binding site (NBS) motif are known to be related to responses to abiotic and biotic stresses in many plants. Hence, this study was conducted to characterize the NBS encoding genes obtained from transcriptome profiles of two cabbage genotypes with contrasting responses to heat stress, and to test expression levels of selected NBS- leucine reich repeat (LRR) genes in F. oxysporum infected plants. We selected 80 up-regulated genes from a total of 264 loci, among which 17 were confirmed to be complete and incomplete members of the TIR-NBS-LRR (TNL) class families, and another identified as an NFYA-HAP2 family member. Expression analysis using qRT-PCR revealed that eight genes showed significant responses to heat shock treatment and F. oxysporum infection. Additionally, in the commercial B. oleracea cultivars with resistance to F. oxysporum, the Bol007132, Bol016084, and Bol030522 genes showed dramatically higher expression in the F. oxysporum resistant line than in the intermediate and susceptible lines. The results of this study will facilitate the identification and the development of molecular markers based on multiple stress resistance genes related to heat and fungal stress under field conditions in B. oleracea.

Anthocyanin biosynthesis for cold and freezing stress tolerance and desirable color in Brassica rapa

Flavonoids are divided into several structural classes, including anthocyanins, which provide flower and leaf colors and other derivatives that play diverse roles in plant development and interactions with the environment. This study characterized four anthocyanidin synthase (ANS) genes of Brassica rapa, a structural gene of the anthocyanin biosynthetic pathway, and investigated their association with pigment formation, cold and freezing tolerance in B. rapa. Sequences of these genes were analyzed and compared with similar gene sequences from other species, and a high degree of homology with their respective functions was found. Organ-specific expression analysis revealed that these genes were only expressed in the colored portion of leaves of different lines of B. rapa. Conversely, B. rapa anthocyanidin synthase (BrANS) genes also showed responses to cold and freezing stress treatment in B. rapa. BrANSs were also shown to be regulated by two transcription factors, BrMYB2-2 and BrTT8, contrasting with anthocyanin accumulation and cold stress. Thus, the above results suggest the association of these genes with anthocyanin biosynthesis and cold and freezing stress tolerance and might be useful resources for development of cold-resistant Brassica crops with desirable colors as well.

Identification and expression analysis of cold and freezing stress responsive genes of Brassica oleracea

Cold and freezing stress is a major environmental constraint to the production of Brassica crops. Enhancement of tolerance by exploiting cold and freezing tolerance related genes offers the most efficient approach to address this problem. Cold-induced transcriptional profiling is a promising approach to the identification of potential genes related to cold and freezing stress tolerance. In this study, 99 highly expressed genes were identified from a whole genome microarray dataset of Brassica rapa. Blast search analysis of the Brassica oleracea database revealed the corresponding homologous genes. To validate their expression, pre-selected cold tolerant and susceptible cabbage lines were analyzed. Out of 99 BoCRGs, 43 were differentially expressed in response to varying degrees of cold and freezing stress in the contrasting cabbage lines. Among the differentially expressed genes, 18 were highly up-regulated in the tolerant lines, which is consistent with their microarray expression. Additionally, 12 BoCRGs were expressed differentially after cold stress treatment in two contrasting cabbage lines, and BoCRG54, 56, 59, 62, 70, 72 and 99 were predicted to be involved in cold regulatory pathways. Taken together, the cold-responsive genes identified in this study provide additional direction for elucidating the regulatory network of low temperature stress tolerance and developing cold and freezing stress resistant Brassica crops.

Genome-wide transcriptome analysis of two contrasting Brassica rapa doubled haploid lines under cold-stresses using Br135K oligomeric chip

Genome wide transcription analysis in response to stresses is important to provide a basis of effective engineering strategies to improve stress tolerance in crop plants. We assembled a Brassica rapa oligomeric microarray (Br135K microarray) using sequence information from 41,173 unigenes and analyzed the transcription profiles of two contrasting doubled haploid (DH) lines, Chiifu and Kenshin, under cold-treatments. The two DH lines showed great differences in electrolyte leakage below −4°C, but similar patterns from 4°C to −2°C. Cold-treatments induced 885 and 858 genes in Chiifu and Kenshin, respectively. Overall, 134, and 56 genes showed an intrinsic difference in expression in Chiifu and Kenshin, respectively. Among 5,349 genes that showed no hit found (NHF) in public databases, 61 and 24 were specifically expressed in Chiifu and Kenshin, respectively. Many transcription factor genes (TFs) also showed various characteristics of expression. BrMYB12, BrMYBL2, BrbHLHs, BrbHLH038, a C2H2, a WRKY, BrDREB19 and a integrase-type TF were induced in a Chiifu-specific fashion, while a bHLH (Bra001826/AT3G21330), bHLH, cycling Dof factor and two Dof type TFs were Kenshin specific. Similar to previous studies, a large number of genes were differently induced or regulated among the two genotypes, but many genes, including NHFs, were specifically or intrinsically expressed with genotype specificity. Expression patterns of known-cold responsive genes in plants resulted in discrepancy to membrane leakage in the two DH lines, indicating that timing of gene expression is more important to conferring freezing tolerance rather than expression levels. Otherwise, the tolerance will be related to the levels of transcripts before cold-treatment or regulated by other mechanisms. Overall, these results indicate common signaling pathways and various transcriptional regulatory mechanisms are working together during cold-treatment of B. rapa. Our newly developed Br135K oligomeric microarray will be useful for transcriptome profiling, and will deliver valuable insight into cold stresses in B. rapa.

Comprehensive analysis of genic male sterility-related genes in Brassica rapa using a newly developed Br300K oligomeric chip

To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassicarapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility.

Characterization and expression analysis of dirigent family genes related to stresses in Brassica

The dirigent (DIR) genes are playing a vital role in enhancing stress resistance in different crop plants. In this study, we collected 29 DIR like genes, two from a Brassica rapa cv. Osome full length cDNA library and 27 from the B. rapa database designated as B. rapa Dirigent (BrDIR) like genes. Sequence analysis and a comparison study of these genes confirmed that seven were dirigent and the remaining 22 were dirigent like genes. Expression analysis revealed an organ specific expression of these genes. BrDIR2 showed differential responses after Fusarium oxysporum f.sp. conglutinans infection in cabbage. Four Brassica oleracea dirigent like genes highly homologous to BrDIR2 also showed similar responses in cabbage plants infected with this fungus. Moreover, several BrDIR like genes showed significant responses after water, ABA and cold stress treatments in Chinese cabbage. Under water stress, most responsive genes showed the highest expression at 24 h, at which time the acid soluble lignin content of samples under the same stress condition were also highest, indicating a possible relationship between BrDIR like genes and lignin content. Taken together, our results indicate a protective role of BrDIR genes against biotic and abiotic stresses in Brassica.

Ogura-CMS in Chinese cabbage (Brassica rapa ssp. pekinensis) causes delayed expression of many nuclear genes

We investigated the mechanism regulating cytoplasmic male sterility (CMS) in Brassica rapa ssp. pekinensis using floral bud transcriptome analyses of Ogura-CMS Chinese cabbage and its maintainer line in B. rapa 300-K oligomeric probe (Br300K) microarrays. Ogura-CMS Chinese cabbage produced few and infertile pollen grains on indehiscent anthers. Compared to the maintainer line, CMS plants had shorter filaments and plant growth, and delayed flowering and pollen development. In microarray analysis, 4646 genes showed different expression, depending on floral bud size, between Ogura-CMS and its maintainer line. We found 108 and 62 genes specifically expressed in Ogura-CMS and its maintainer line, respectively. Ogura-CMS line-specific genes included stress-related, redox-related, and B. rapa novel genes. In the maintainer line, genes related to pollen coat and germination were specifically expressed in floral buds longer than 3mm, suggesting insufficient expression of these genes in Ogura-CMS is directly related to dysfunctional pollen. In addition, many nuclear genes associated with auxin response, ATP synthesis, pollen development and stress response had delayed expression in Ogura-CMS plants compared to the maintainer line, which is consistent with the delay in growth and development of Ogura-CMS plants. Delayed expression may reduce pollen grain production and/or cause sterility, implying that mitochondrial, retrograde signaling delays nuclear gene expression.

Quantitative trait loci mapping in Brassica rapa revealed the structural and functional conservation of genetic loci governing morphological and yield component traits in the A, B, and C subgenomes of Brassica species

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species.

Development of self-compatible B. rapa by RNAi-mediated S locus gene silencing

The self-incompatibility (SI) system is genetically controlled by a single polymorphic locus known as the S-locus in the Brassicaceae. Pollen rejection occurs when the stigma and pollen share the same S-haplotype. Recognition of S-haplotype specificity has recently been shown to involve at least two S-locus genes, S-receptor kinase (SRK) and S-locus protein 11 or S locus Cysteine-rich (SP11/SCR) protein. Here, we examined the function of S(60), one SP11/SCR allele of B. rapa cv. Osome, using a RNAi-mediated gene silencing approach. The transgenic RNAi lines were highly self-compatible, and this trait was stable in subsequent generations, even after crossing with other commercial lines. These findings also suggested that the resultant self-compatibility could be transferred to commercial cultivars with the desired performances in B. rapa.

Molecular characterization of the Brassica rapa auxin-repressed, superfamily genes, BrARP1 and BrDRM1

Two auxin-repressed superfamily genes, auxin-repressed protein 1 (ARP1) and dormancy-associated protein 1 (DRM1), are highly expressed in both the dormant buds and non-growing tissues of several plant species. To further identify the function of these proteins in Chinese cabbage (Brassica rapa L. ssp. pekinensis), we examined comprehensive expression patterns of BrARP1 and BrDRM1 under various developmental and stress conditions. We also examined these same genes in transgenic Arabidopsis plants. Both genes were expressed in all tissues tested, but their levels were highest in mature tissues accompanied by low levels of the growth-associated marker, B. rapa ribosomal protein 27. Expression of both genes was induced by abiotic stresses, such as chilling, heat shock, and salt treatment. Overexpression of either BrARP1 or BrDRM1 in Arabidopsis causes a reduction in vegetative growth and seed productivity, without affecting morphology. The lengths of petioles and siliques were greatly reduced. Simultaneous expression of both genes showed an additive effect on the growth suppression, resulting in significant reduction in plant size. Knock-out of Arabidopsis ARP1, DRM1, or both, neither affected growth rate nor final size. Results suggest BrARP1 and BrDRM1 are either involved in growth arrest, or stop growth, possibly from inhibition of either cell elongation or cell expansion, thereby creating a "growth brake".

Molecular characterization of stress resistance-related chitinase genes of Brassica rapa

Brassica is an important vegetable group worldwide that is impacted by biotic and abiotic stresses. Molecular biology techniques offer the most efficient approach to address these concerns. Inducible plant defense responses include the production of pathogenesis-related (PR) proteins, and chitinases are very important PR proteins. We collected 30 chitinase like genes, three from our full-length cDNA library of Brassica rapa cv. Osome and 27 from Brassica databases. Sequence analysis and comparison study confirmed that they were all class I-V and VII chitinase genes. These genes also showed a high degree of homology with other biotic stress resistance-related plant chitinases. An organ-specific expression of these genes was observed and among these, seven genes showed significant responses after infection with Fusarium oxysporum f.sp. conglutinans in cabbage and sixteen genes showed responsive expression after abiotic stress treatments in Chinese cabbage. BrCLP1, 8, 10, 17 and 18 responded commonly after biotic and abiotic stress treatments indicating their higher potentials. Taken together, the results presented herein suggest that these chitinase genes may be useful resources in the development of stress resistant Brassica.

Overexpression of AtCHX24, a member of the cation/H⁺ exchangers, accelerates leaf senescence in Arabidopsis thaliana

Leaf senescence, the final stage of leaf development, occurs in an age-dependent manner but can be finely regulated by other developmental and environmental factors. Despite the discovery of many genes involved in leaf senescence, the molecular genetic mechanisms of leaf senescence are still unclear. In this study, an activation-tagging based suppressor screen was performed to identify Arabidopsis genes that could suppress the delayed leaf senescence phenotypes of oresara9-1 (ore9-1) when overexpressed. The suppressor1 of ore9 dominant (sor1-D) was caused by the overexpression of AtCHX24, a putative cation/H(+) exchanger. The sor1-D mutation suppressed the phenotypes of ore9 in age-dependent and dark-induced senescence. Furthermore, the sor1-D mutation restored the delayed senescence phenotypes of ore1 and ore3. The sor1-D mutant also exhibited increased sensitivity to pH changes during dark-induced leaf senescence. Collectively, overexpression of AtCHX24 results in accelerated leaf senescence and these results suggest that AtCHX24 plays an important role in regulating leaf senescence.

Identification of potential microRNAs and their targets in Brassica rapa L

MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20(th) position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

Knock-out mutations of Arabidopsis SmD3-b induce pleotropic phenotypes through altered transcript splicing

SmD3 is a core protein of small nuclear ribonucleoprotein (snRNP) essential for splicing of primary transcripts. To elucidate function of SmD3 protein in plants, phenotypes and gene expression of SmD3 knock-out and overexpressing mutants in Arabidopsis have been analyzed. smd3-a knock-out mutant or SmD3-a and SmD3-b overexpressors did not show phenotypic alteration. Knock-out of SmD3-b resulted in the pleotropic phenotypes of delayed flowering time and completion of life cycle, reduced root growth, partially defective leaf venation, abnormal numbers of trichome branches, and changed numbers of floral organs. Microarray data revealed that the smd3-b mutant had altered expression of genes related to the above phenotypes, indirectly suggesting that changed splicing of these genes may cause the observed phenotypes. Splicing of selected genes was either totally blocked or reduced in the smd3-b mutant, indicating the important role of SmD3-b in the process. A double knock-out mutant of smd3-a and smd3-b could not be generated, indicating possible redundant function of these two genes. All data indicate that SmD3-b may be major component of the spliceosomal snRNP in Arabidopsis, but the function of SmD3-a may be redundant.

Rapid divergence of repetitive DNAs in Brassica relatives

Centromeric, subtelomeric, and telomeric repetitive DNAs were characterized in Brassica species and the related Raphanus sativus and Arabidopsis thaliana. In general, rapid divergence of the repeats was found. The centromeric tandem satellite repeats were differentially distributed in the species studied, suggesting that centromeric repeats have diverged during the evolution of the A/C and B genome lineages. Sequence analysis of centromeric repeats suggested rapid evolution. Pericentromere-associated retrotransposons were identified and showed divergence during the evolution of the lineages as centromeric repeats. A novel subtelomeric tandem repeat from B. nigra was found to be conserved across the diploid Brassica genomes; however, this sequence was not identified in the related species. In contrast to previous studies, interstitial telomere-like repeats were identified in the pericentromeres of Brassica chromosomes, and these repeats may be associated with genomic stability. These results provide insight into genome evolution during polyploidization in Brassica and divergence within the Brassicaceae.

Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences

Chromosomes often serve as one of the most important molecular aspects of studying the evolution of species. Indeed, most of the crucial mutations that led to differentiation of species during the evolution have occurred at the chromosomal level. Furthermore, the analysis of pachytene chromosomes appears to be an invaluable tool for the study of evolution due to its effectiveness in chromosome identification and precise physical gene mapping. By applying fluorescence in situ hybridization of 45S rDNA and CsCent1 probes to cucumber pachytene chromosomes, here, we demonstrate that cucumber chromosomes 1 and 2 may have evolved from fusions of ancestral karyotype with chromosome number n = 12. This conclusion is further supported by the centromeric sequence similarity between cucumber and melon, which suggests that these sequences evolved from a common ancestor. It may be after or during speciation that these sequences were specifically amplified, after which they diverged and specific sequence variants were homogenized. Additionally, a structural change on the centromeric region of cucumber chromosome 4 was revealed by fiber-FISH using the mitochondrial-related repetitive sequences, BAC-E38 and CsCent1. These showed the former sequences being integrated into the latter in multiple regions. The data presented here are useful resources for comparative genomics and cytogenetics of Cucumis and, in particular, the ongoing genome sequencing project of cucumber.

Overexpression of BrMORN, a novel 'membrane occupation and recognition nexus' motif protein gene from Chinese cabbage, promotes vegetative growth and seed production in Arabidopsis

Proteins that contain membrane occupation and recognition nexus (MORN) motifs regulate various aspects of cellular metabolism by localizing proteins in different cellular organelles. The full-length Brassica rapa MORN motif protein (BrMORN) cDNA consists of 1,510 bp encoding 502 deduced amino acids with a predicted molecular mass of 55.8 kDa and an isoelectric point of 9.72. BrMORN is a novel protein composed of two N-terminal transmembrane helices and seven C-terminal MORN motifs and it appears to be localized on the plastid envelope. BrMORN expression was relatively high in actively-growing tissues, but low in mature tissues and under some abiotic stresses. Arabidopsis thaliana plants overexpressing BrMORN showed an enhanced rate of growth, hypocotyl elongation, and increases in the size of vegetative organs and seed productivity under normal growth conditions. In addition, cell size in Arabidopsis plants overexpressing BrMORN was 24% larger than that of wild-type plants, implying that the increase in the size of vegetative organs is due to cell enlargement. The increased size of the vegetative organs also led to increased seed production. Our data suggest that the MORN motif of BrMORN may act at the plastid envelope and facilitate plant growth via cell enlargement.

Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray

Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4 degrees C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa.

Extensive chromosomal polymorphism revealed by ribosomal DNA and satellite DNA loci in 13 Citrus species

Little is known about the chromosomal variability and polymorphism existing in mitotic chromosomes of Citrus, mainly due to lack of reliable chromosomal markers and small chromosome size. To test the hypothesis of chromosomal polymorphism and provide the foundation of the genome organization in the Citrus cultivars, we have developed molecular cytogenetic markers for 13 Citrus species collected from Jeju island, Korea. In this study, we demonstrated that the chromosomal locations of cytogenetic markers are quite variable and extremely polymorphic, in contrast to the previous studies. The data obtained in this study will be of utmost importance in cytological systematics and karyotyping of the Citrus species.

A high-resolution karyotype of cucumber (Cucumis sativus L. 'Winter Long') revealed by C-banding, pachytene analysis, and RAPD-aided fluorescence in situ hybridization

Using molecular cytogenetic DNA markers, C-banding, pachytene analysis, and fluorescence in situ hybridization (FISH), a high-resolution karyotype was established in the cucumber. C-banding showed distinct hetero chro matic bands on the pericentromeric, telomeric, and intercalary regions of the chromosomes. The C-banding patterns were also consistent with the morphology of 4'-6-diamino-2-phenylindole dihydrochloride (DAPI)-stained pachytene chro mosomes. Two repetitive DNA fragments, CsRP1 and CsRP2, were obtained by PCR and localized on the mitotic metaphase and meiotic pachytene chromosomes. CsRP1 was detected on the pericentromeric heterochromatic regions of all chromosomes, except chromosome 1. CsRP2 was detected on 5 (chromosomes 1, 2, 3, 4, and 7) of 7 chromosomes. All homologous chromosome pairs could be distinguished by FISH using 2 RAPD markers. This is the first report on molecular karyotyping of mitotic and meiotic spreads of cucumber.Key words: Cucumis sativus, C-banding, FISH, karyotype, pachytene, RAPD marker, rDNA.

A high-resolution karyotype of Brassica rapa ssp. pekinensis revealed by pachytene analysis and multicolor fluorescence in situ hybridization

A molecular cytogenetic map of Chinese cabbage (Brassica rapa ssp. pekinensis, 2 n=20) was constructed based on the 4'-6-diamino-2-phenylindole dihydrochloride-stained mitotic metaphase and pachytene chromosomes and multicolor fluorescence in situ hybridization (McFISH), using three repetitive DNA sequences, 5S rDNA, 45S rDNA, and C11-350H. The lengths of mitotic metaphase chromosomes ranged from 1.46 microm to 3.30 microm. Five 45S and three 5S rDNA loci identified were assigned to different chromosomes. The C11-350H loci were located on all the mitotic metaphase chromosomes, except chromosomes 2 and 4. The pachytene karyotype consisted of two metacentric (chromosomes 1 and 6), five submetacentric (chromosomes 3, 4, 5, 9 and 10), two subtelocentric (chromosomes 7 and 8), and one acrocentric (chromosome 2) chromosome(s). The mean lengths of ten pachytene chromosomes ranged from 23.7 microm to 51.3 microm, with a total of 385.3 microm, which is 17.5-fold longer than that of the mitotic metaphase chromosomes. In the proposed pachytene karyotype, all the chromosomes of B. rapa ssp. pekinensis can be identified on the basis of chromosome length, centromere position, heterochromatin pattern, and the location of the three repetitive sequences. Moreover, the precise locations of the earlier reported loci of 5S rDNA, 45S rDNA, and Chinese cabbage tandem DNA repeat C11-350H were established using McFISH analysis. We also identified a 5S rDNA locus on the long arm of pachytene bivalent 7, which could not be detected in the mitotic metaphase chromosomes in the present and earlier studies. The deduced karyotype will be useful for structural and functional genomic studies in B. rapa.

Isolation of a gene, PnFL-1, expressed in Pharbitis cotyledons during floral induction

A novel gene, designated PnFL-1, was isolated from flower-induced cotyledons in a short-day plant, Pharbitis nil, using messenger RNA differential display. PnFL-1 has no similarity to genes with known functions in databases, but the deduced amino acid sequence of the gene has 58% homology with a hypothetical protein of Arabidopsis including a phosphatidic acid phosphatase 2 domain. PnFL-1 is a single-copy gene that is expressed during the inductive dark period. Expression of PnFL-1 increased gradually from the 6th to 16th h of a 16-h dark period, and expression was extinguished by a brief exposure to light at the 8th hour of the dark period (night break treatment). PnFL-1 mRNA was found in cotyledons and leaves but not in stems and roots. These results indicate that the transcription of PnFL-1 in Pharbitis may be photoperiodically regulated and associated with photoperiodic events.