Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis)
© Liu et al.; licensee BioMed Central Ltd. 2013
Received: 10 April 2013
Accepted: 22 August 2013
Published: 30 August 2013
Cytokinins (CKs) have significant roles in various aspects of plant growth and development, and they are also involved in plant stress adaptations. The fine-tuning of the controlled CK levels in individual tissues, cells, and organelles is properly maintained by isopentenyl transferases (IPTs) and cytokinin oxidase/dehydrogenases (CKXs). Chinese cabbage is one of the most economically important vegetable crops worldwide. The whole genome sequencing of Brassica rapa enables us to perform the genome-wide identification and functional analysis of the IPT and CKX gene families.
In this study, a total of 13 BrIPT genes and 12 BrCKX genes were identified. The gene structures, conserved domains and phylogenetic relationships were analyzed. The isoelectric point, subcellular localization and glycosylation sites of the proteins were predicted. Segmental duplicates were found in both BrIPT and BrCKX gene families. We also analyzed evolutionary patterns and divergence of the IPT and CKX genes in the Cruciferae family. The transcription levels of BrIPT and BrCKX genes were analyzed to obtain an initial picture of the functions of these genes. Abiotic stress elements related to adverse environmental stimuli were found in the promoter regions of BrIPT and BrCKX genes and they were confirmed to respond to drought and high salinity conditions. The effects of 6-BA and ABA on the expressions of BrIPT and BrCKX genes were also investigated.
The expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT) and substantial duplicated genes are lost during the long evolutionary history. Genes produced by segmental duplication events have changed their expression patterns or may adopted new functions and thus are obtained. BrIPT and BrCKX genes respond well to drought and high salinity stresses, and their transcripts are affected by exogenous hormones, such as 6-BA and ABA, suggesting their potential roles in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. The appropriate modulation of endogenous CKs levels by IPT and CKX genes is a promising approach for developing economically important high-yielding and high-quality stress-tolerant crops in agriculture.
Cytokinins (CKs) are a class of plant hormones that have significant roles in various aspects of plant growth and development, including apical dominance, shoot or root branching, leaf expansion, lateral bud growth, photosynthesis, seed germination, floral transition, and leaf senescence . Moreover, these hormones participate in biomass distribution  and the response to environmental stimuli [3–5]. CKs signals are sensed and transduced by the two-component signal (TCS) system; the availability of CKs in suitable concentrations in the right place and at the right time is necessary for their interaction with a specific receptor. The fine-tuning of hormone levels in individual tissues, cells, and organelles must be properly maintained by the biosynthetic and metabolic enzymes . CKs synthesis in plants is catalyzed by a family of isopentenyl transferases (IPTs) via the methylerythritol phosphate (MEP) and mevalonate (MVA) pathways [3, 7, 8]. Further studies reveal that ATP/ADP IPTs control the biosynthesis of isopentenyladenine (iP)- and trans-zeatin (tZ)-type CKs, whereas tRNA IPTs are responsible for the synthesis of cis-zeatin (cZ)-type CKs [3, 7]. The irreversible degradation of CKs and their derivatives is catalyzed by CK oxidase/dehydrogenases (CKXs), which are encoded by a small gene family. The substrate specificities of IPTs have been proven to vary, depending on the origin and species . Similarly, CKX enzymes have their own substrate specificity, with various spatial and temporal expression patterns .
The IPT and CKX gene families in various plants have been identified and cloned, including those in Arabidopsis thaliana[10, 11], Oryza sativa[12, 13], Zea mays[14, 15], Glycine max, Solanum lycopersicum, Triticum aestivum, Hordeum vulgare, Sorghum bicolor, and Populus trichocarpa, among others. A putative ATP/GTP binding site (P-loop motif) exists in all of the deduced protein sequences of IPT, whereas CKX protein sequences have FAD- and CK-binding domains. The functions of IPT and CKX genes have likewise been extensively studied. The overexpression of AtIPT4 caused CK-independent shoot formation on calli . The overexpression of ZmIPT2 in Arabidopsis produced transgenic plants with phenotypes indicative of CKs overproduction . Transgenic tobacco with 35S-GmIPT1 similarly had the typical phenotypes of CKs overproduction . The enhanced expression of an IPT gene designated as Sho showed CK-specific effects, including enhanced shooting and reduced apical dominance, as well as delayed senescence and flowering . In Arabidopsis, the ckx3/ckx5 double mutant had higher CKs content, which caused the mutants to have more flower primordia, larger flowers, more siliques, and more seeds; the total seed yield of these mutants increased by 55%, as compared with the wild-type . Ashikari et al.  conclusively showed that the reduced expression of Gn1a, a gene for OsCKX2, caused CKs accumulation in rice inflorescence meristems and increased the number of reproductive organs, thereby enhancing the grain yield by 21%. RNAi was more recently used in barley to silence HvCKX1, which increased both the grain number and grain weight . The potential use of CK-related genes in seed size and seed mass determination will become an active field of study in the future. Meanwhile, increasing evidence suggests that CKs are involved in stress response [27–29]. Nishiyama et al.  proposed a model for the roles of bioactive CKs and antagonistic ABA under different stresses. All CK-deficient plants with reduced levels of different CKs exhibited strong stress-tolerant phenotypes; the majority of AtIPT and AtCKX genes were repressed by stress and ABA treatments. The IPT and CKX genes in maize and soybean similarly responded to drought and salt conditions [16, 31]. Given that water deficit and high-salinity stresses have become limiting factors for crop and vegetable production and quality, these studies may provide new insights into breeding stress-resistant plants.
Brassica rapa is one of the most economically important vegetable crops worldwide. The whole genome sequencing of B. rapa (Chiifu-401-42), by The Brassica rapa Genome Sequencing Project Consortium (2011), enables us to undertake the genome-wide identification and functional analysis of the gene families related to the morphological diversity and agronomic traits of Brassica crops . Furthermore, B. rapa serves as a crucial reference for understanding polyploidy-related crop genome evolution because of its agronomic importance and phylogenetic relationships .
Ando et al.  isolated cDNA fragments of five putative cytokinin synthase genes from B. rapa (BrIPT1, -3, -5, -7, and −8) and examined their expression levels using Northern blot analysis. O’Keefe et al.  identified BrIPT1, -3, and −5 as well as BrCKX1, -2, -3, and −5 in rapid-cycling Brassica; their expression levels during pod and seed development were examined. However, Brassicaceae genomes have undergone three rounds of whole genome duplication (WGD); these genomes are referred to as 1R, 2R, and 3R, which are equivalent to the γ, β, and α duplication events, and Brassica genomes have undergone another whole genome triplication (WGT) after speciation from Arabidopsis thaliana at approximately 17–20 MYA (million years ago) [36–38], leading to significantly increased duplicated gene numbers in B. rapa. A total of 41,174 protein-coding genes were identified in the B. rapa genome, which were roughly 1.5 times as many genes as those found in A. thaliana (27,411 genes in TAIR10) . Accordingly, we hypothesized that the number of BrIPT and BrCKX genes would be greater than that of their Arabidopsis counterparts. The main objectives of our study were to identify all the IPT and CKX genes in B. rapa, to analyze the physiological and biochemical properties of their encoded proteins, to explore their gene expression patterns, to discover the mechanisms of their responses to abiotic stresses and exogenous plant hormones, and to identify several potential genes for breeding to increase plant production, quality, and stress-resistance. Furthermore, we intended to gain genome-level insights into the divergence, variation, and evolution of the BrIPT and BrCKX gene families.
Identification and annotation of the BrIPT and BrCKX genes of B. rapa
IPT gene family in Brassica rapa , along with their molecular details and relevant genomic information
CKX gene family in Brassica rapa , along with their molecular details and relevant genomic information
The BrIPT genes were distributed on 7 out of 10 chromosomes (except for A05, A06, and A08), belonging to the three sub-genomes (LF, MF1, and MF2). The ORF lengths of the BrIPT genes ranged from 906 bp to 1395 bp, which encoded polypeptides of 301 aa to 464 aa with predicted molecular weights ranging from 33.6 kD to 52.4 kD. The theoretical pI ranged from 5.75 to 9.26. The BrIPT genes were all predicted to be localized in the chloroplasts. Similarly, the BrCKX genes were also distributed on 7 out of 10 chromosomes (except for A01, A06, and A08). The ORF lengths of the BrCKX genes were longer than those of the BrIPT genes; these ORFs ranged from 1101 bp to 4431 bp and encoded polypeptides of 366 aa to 1476 aa with predicted molecular weights ranging from 42.8 kD to 162.7 kD. The theoretical pI ranged from 4.92 to 8.71. The predicted subcellular localization of the BrCKX genes varied and included the chloroplast, mitochondria, and secretory pathways. Protein glycosylation contributes to regulation of enzymatic activity, translocation, and protein stability; thereby, adding an additional and important level of complexity to CKX regulation . Similar to the ZmCKX genes, the BrCKX genes possessed 2 to 12 predicted glycosylation sites.
Gene structure and conserved domain analysis of BrIPT and BrCKX genes
Chromosomal mapping and duplications of BrIPT and BrCKX genes
Phylogenetic relationships of the BrIPT and BrCKX gene families
Evolutionary patterns and divergence of IPT and CKX genes in the Cruciferae family
Tissue or organ-specific expression of BrIPT and BrCKX genes
Stress-inducible cis-regulatory elements in the promoter regions of BrIPT and BrCKX genes
The cis-regulatory elements, which are located in the upstream regions of genes, act as the binding sites for TFs; thus, these sequences have essential roles in determining the tissue-specific or stress-responsive expression patterns of genes . Increasing evidence has showed that genes responsive to multiple stimuli are closely correlated with cis-regulatory elements in their promoter regions [56, 57]. To further understand transcriptional regulation and the potential functions of the BrIPT and BrCKX genes, putative promoter regions in the 2000 bp sequences upstream of the transcriptional start site were used to identify putative stress-responsive cis-regulatory elements. Several abiotic stress elements were found (Additional file 9 and Additional file 10). One salt-stress (S000453), one heat-stress (S00030), one cold-stress (S000407), one wound-stress (S000457), and three drought-stress (S000176, S000408, and S000415) cis-elements were common in the promoter regions of the BrIPT and BrCKX genes. Therefore, B. rapa may adapt to stressful environments by changing its CKs content. Particularly, BrIPT3-1, BrIPT3-2, and BrCKX3-2 had up to 32, 26, and 24 cold-stress elements (S000407), respectively. The number of drought-stress elements (S000415) in BrCKX5 reached 28. The other remaining genes likewise possessed abundant stress-inducible cis-regulatory elements. The tRNA IPT genes in Arabidopsis were notably unaffected by the mineral nutrients, auxin, and CK concentrations . By contrast, three tRNA IPT genes in B. rapa, BrIPT2, BrIPT9-1, and BrIPT9-2 were also rich in the five types of cis-regulatory elements based on our results. Therefore, we hypothesized that the tRNA IPT genes might also have important functions in the adaptation to adverse environmental stimuli. Moreover, 0.4 and 1.2 abiotic stress-inducible cis-elements per promoter were found in the GmIPT and GmCKX genes, respectively . Similarly, BrCKX genes had relatively more stress-responsive elements than BrIPT genes.
Expression profiles of BrIPT and BrCKX genes under drought and salt stress
Effects of exogenous 6-BA and ABA on the expressions of BrIPT and BrCKX genes
The expansion and loss of BrIPT and BrCKX genes following hexaploidy formation by WGT
Brassicaceae genomes have undergone three rounds of whole genome duplication (WGD) and Brassica genomes have undergone another whole genome triplication (WGT) after speciation from Arabidopsis thaliana[36–38]. B. rapa is believed to have emerged from the Brassica progenitor approximately 8 MYA . Considering WGT of the Brassica genomes, the IPT and CKX genes should have approximately three times as many members as that of Arabidopsis. However, we could only identify 13 IPT genes and 12 CKX genes in B. rapa, thereby suggesting a substantial loss of genes following hexaploidy formation by WGT. Gene loss was likewise observed for the CRF and PG gene families in B. rapa (unpublished data). Consistent with previous studies, the triplicated B. rapa genome contained only approximately twice the number of genes in Arabidopsis because of genome shrinkage . Previous studies showed that AtIPT6 is non-functional in the Wassilewskija (Ws) ecotype because of a frame-shift mutation , but is a functional gene in the Columbia (Col) ecotype . By contrast, AtIPT4 is a functional gene in all ecotypes . Excluding a possible pseudogene, AtIPT6, the genomes of A. lyrata, and A. thaliana had equal numbers of IPT and CKX genes, thereby reflecting their relatively stable genome evolution because of a short separation time. However, both homologous genes of AtIPT4 and AtIPT6 in B. rapa were not found. Ando et al.  and O’Keefe et al.  identified several BrIPT and BrCKX genes, but still failed to obtain BrIPT4 and BrIPT6. Thus, the homologous genes of AtIPT4 and AtIPT6 were probably lost in B. rapa during the long evolutionary history. Gene loss was a more common phenomenon in distantly related species. Le et al.  reported that AtIPT1, AtIPT4, AtIPT6, AtIPT8, and GmIPT01 appeared to originate from a common ancestor. These genes expanded and were then retained in Arabidopsis but not in soybean after the speciation event. Genes with high homology to AtIPT1, AtIPT4, AtIPT6, and AtIPT8 were also not found in rice , maize , and tomato . We did not find homologs for AtIPT4 and AtIPT6 in this study. Nevertheless, genes homologous with AtIPT1 and AtIPT8 were identified in B. rapa, namely, BrIPT1-1, BrIPT1-2, BrIPT8-1, and BrIPT8-2. These genes all belonged to Group I with close relationships. Another piece of supporting evidence was that another IPT gene was found in B. napus, BnIPT1, which was homologous to AtIPT1. The evolutionary mechanism of IPT genes in various species is still waiting to be clarified.
The IPT and CKX genes in the bryophyte P. patens
The IPT and CKX genes have been discovered in the cyanobacteria Nostoc and the phytopathogen Rhodococcus fascians, respectively, with a large genetic distance from the other IPT and CKX genes. None of the IPT and CKX sequences have been found in green algae . Schmuelling et al.  proposed that the presence of putative CKX sequences in cyanobacteria suggested that plant CKX genes might evolved from ancient chloroplast genes, which probably originated from the endosymbiosis of cyanobacteria. To date, the bryophyte P. patens is the earliest known terrestrial plant with IPT and CKX genes. Moreover, previous studies showed that the complete set of proteins in the CK signaling pathway first appeared in the said bryophyte . Genes involved in the two-component system (TCS) of the P. patens were identified and characterized . Thus, the CK metabolic pathway, and its signal transduction pathway imply that P. patens is the earliest species to have achieved a finely tuned control over CK homeostasis via biosynthesis that diverged to conquer land.
Evolutionary patterns of IPT and CKX genes in the Cruciferae family
Since the tetraploidization of the A. thaliana ancestor 30–35 MYA, a wave of chromosomal rearrangements has modified its genome architecture. The majority of rearrangements had occurred before the Arabidopsis–Brassica split at 20–24 MYA; thus, the segmental architecture of the A. thaliana genome was predominantly conserved in Brassica[49, 51, 63]. We made a genome-level comparison with the three sequenced cruciferous species (B. rapa, A. thaliana, and A. lyrata). By analyzing the corresponding relationships of the IPT and CKX genes on chromosomes, traces of chromosomal rearrangement were easily captured. Brassica genomes have undergone whole genome triplication (WGT) after speciation from Arabidopsis thaliana, leading to significantly increased duplicated genes. Duplicated genes occur as the tandem duplicated genes and segmental duplicated genes. For the IPT and CKX genes in B. rapa, no tandem duplicated genes were found, but five pairs of segmental duplicates were found among 13 BrIPT genes, and three pairs of segmental duplicates were found among 12 BrCKX genes, suggesting that the expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT). The K a (non-synonymous substitution rates) and K s (synonymous substitution rates) is a measure to explore the mechanism of gene divergence after duplication. Large-scale duplication events are defined as simultaneous duplications of genes. Assuming a molecular clock, the synonymous substitution rates (K s ) of these duplicates are expected to be similar over time. There are, however, substantial rate variations among genes . We used the relative K s measure as the proxy for time to evaluate the divergence time between B. rapa and Arabidopsis. The K s values of the duplicated paralogs in B. rapa were notably much smaller than the values of the duplicated orthologous genes between B. rapa and Arabidopsis, further confirming that the duplicated IPT and CKX genes in B. rapa were produced during the whole genome triplication (WGT) after speciation from Arabidopsis.
Changed expression patterns of the duplicated BrIPT and BrCKX genes
Duplication occurs in an individual and may be retained or lost in the population, similar to a point mutation . Unless the presence of an extra amount of gene product is advantageous, two genes with identical functions are unlikely to be stably maintained in the genome. Theoretical population genetics predicates that both duplicates can be stably maintained when they differ in some aspects of their functions . Sub-functionalization and neo-functionalization are two evolutionary fates of duplicated genes. These may account for the varied expression patterns of paralogs. Our study showed BrIPT1-1 and 1–2, as well as BrCKX2-1, -2-2, -3-1, -3-2, -5, -7-1 and −7-2, were mainly expressed in the reproductive organs, whereas BrIPT3-1, -3-2, -5-1 and −5-2, as well as BrCKX4 and −6 had major transcripts in the vegetative organs. Even the segmental duplicated gene pairs had inconsistent expression profiles. For instance, BrCKX1-1 was mainly expressed in roots while BrCKX1-2 maintained at high levels in stamens, flowers and petals. Meanwhile, BrCKX1-3 was ubiquitously expressed, with relatively high levels in the petals and pistils. Likewise, a few duplicated gene pairs (GmIPT08 and GmIPT10; GmCKX05 and GmCKX06; GmCKX12 and GmCKX14) have undergone expression divergence in soybean . The response mechanisms of the two gene families varied for the different types of stresses. In this study, the BrIPT5-1 was continuously induced by salt treatment, with 7-fold elevated expression levels. However, BrCKX1-3 was suppressed, with dropped expression levels. The expressions of the majority of the CKX family in Arabidopsis, namely, CKX2, CKX4, CKX5, and CKX7, decreased with salt treatment; whereas expressions of the remaining three genes (CKX1, CKX3 and CKX6) increased . Meanwhile, increasing evidence indicated that the response to environmental stresses for plant IPT and CKX genes was tissue or organ-dependent. Stress induced ZmCKX1 expressions in leaves, but it had an opposite effect in roots . The induction levels in the V6-stage leaves of soybean were correlated with the age of the trifoliate leaves; the older the leaf, the higher the induction. GmIPT09 and GmIPT13 were significantly induced by drought in the V6-stage leaves; the degree of induction of these genes was higher in the younger trifoliate leaves . All these proofs strongly supported the hypothesis that daughter genes originated from a common parental gene might adopt part of the functions of their parental gene [67–69] or acquire new functions .
The possible roles of tRNA IPT genes in plants
Three tRNA IPT genes (BrIPT2, BrIPT9-1, and BrIPT9-2) were identified to have unique gene structures and expression patterns in B. rapa. AtIPT2, AtIPT9, ZmIPT1, ZmIPT10, OsIPT9, and OsIPT10 likewise belong to this group of tRNA IPT genes. The tRNA IPT genes are responsible for the synthesis of cZ-type CKs. Based on the data from various bioassays [71, 72], the tZ was found to be a bioactive substance whereas cZ was reported to have a weak biological effect. Moreover, the 35S-linked AtIPT2 did not induce CK responses in calli when CKs were absent . Despite the presumed inactivity of cZ as a free hormone, the presence of free cZ-type CKs in plant tissues has been repeatedly reported. Some plant species contain detectable levels of diverse cZ-type CKs, which are occasionally the predominant group of total CKs. Gajdosova et al.  hypothesized that the cZ-type CKs may function as delicate regulators of the CK responses in plants under growth-limiting conditions. Similar to AtIPT2 and AtIPT9, BrIPT2, BrIPT9-1, and BrIPT9-2, were ubiquitously expressed. The tRNA IPT genes in B. rapa notably responded to adverse environmental stresses, thereby indicating that the cZ biosynthesized by tRNA IPT genes may be also involved in stress resistance.
In summary, in this study we identified 13 IPT and 12 CKX genes in Chinese cabbage genome. The gene structures, conserved domains and phylogenetic relationships were analyzed. Duplications, evolutionary patterns and divergence of the IPT and CKX genes were investigated. We also characterized their expression patterns in various tissues and organs, their responses to abiotic stresses and exogenous phytohormones. To date, this is the first genome-wide study of the IPT and CKX gene families in B. rapa. Our results will help to enhance the understanding of the evolution of dynamic functions and fates for these BrIPT and BrCKX genes. Chinese cabbage is one of the most important vegetables and is widely cultivated. Unveiling the roles of BrIPT and BrCKX genes in plant growth, development and stress adaptation processes may help molecular breeders to develop economically important high-yielding and high-quality stress-tolerant crops in agriculture.
Identification of IPT and CKX gene families in B. rapa genome
The Arabidopsis IPT and CKX genes were used as seed sequences to search the Brassica Database (BRAD; version 1.1; http://brassicadb.org/brad/) and the NCBI database (http://www.ncbi.nlm.nih.gov). A total of 13 BrIPT and 12 BrCKX candidate genes were identified based on BLASTN and BLASTP searches with a cut-off expect value of 100. To ensure that no additional related genes were overlooked by the database search, the identified BrIPT and BrCKX genes were used as query sequences in additional multiple database searches to confirm the initial list of genes. Similarly, the IPT and CKX genes from Arabidopsis lyrata, Populus trichocarpa, and Physcomitrella patens were identified from the A. lyrata genome (version 1.0; http://genome.jgi-psf.org/Araly1/Araly1.info.html), the poplar genome assembly (version 1.1; http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html), and the P. patens genome assembly (version 1.1; http://genome.jgi-psf.org/Phypa1_1/Phypa1_1.info.html), respectively. The Pfam database (http://pfam.janelia.org/)  and the Conserved Domain Database (CDD) of the National Center for Biotechnology Information (NCBI)  were used to analyze all of the sequences that met the given requirements. Genes that did not contain the known conserved domains and motifs of the gene families were excluded from further analysis.
Multiple sequence alignment and phylogenetic analysis
The online MEME software (http://meme.sdsc.edu/meme/meme.html) was used to identify the BrIPT and BrCKX motifs, with an expected e-value of less than 2×10-30[75, 76]. Multiple sequence alignments were conducted using ClustalX (version 1.81) . Phylogenetic analysis was performed using the neighbor-joining (NJ) method of the MEGA (version 5.0) program . The confidence limits of each branch in the phylogenetic tree were assessed by 1000 bootstrap replications and expressed as percentage values.
Physiological and biochemical property analysis of BrIPT and BrCKX proteins
The isoelectric point (pI) of the BrIPT and BrCKX proteins were predicted using Compute pI/Mwsoftware (http://www.expasy.ch/tools/pi_tool.html) . Their subcellular localization was predicted by the TargetP software of the CBS database (http://www.cbs.dtu.dk/services/TargetP) . The glycosylation sites were predicted using NetNGly (http://www.cbs.dtu.dk/services/NetNGlyc/) (unpublished database).
Cis-element analysis of the putative promoter regions of BrIPT and BrCKX genes
To identify cis-elements in the promoter regions of BrIPT and BrCKX genes, the 2000 bp sequences upstream of the transcriptional start site of each BrIPT and BrCKX gene were chosen. These sequences were used to query the PLACE database (http://www.dna.affrc.go.jp/PLACE/) , and the putative cis-regulatory elements of the promoter sequences were identified.
Chromosome mapping of the IPT and CKX genes in B. rapa, A. thaliana, and A. lyrata
Maps of the chromosomes were drawn using MS Office software, based on the location of each gene along the specific length of each chromosome. Tandem duplications were defined as genes located within 20 loci from each other . Segmental duplications were identified by synteny analysis using an online tool of the Plant Genome Duplication Database (PGDD; http://chibba.agtec.uga.edu/duplication/) .
Evolutionary analysis of homologous genes between B. rapa and A. thaliana
Synteny analysis of the BrIPT and BrCKX genes were performed online using PGDD (http://chibba.agtec.uga.edu/duplication/). The occurrence of duplication events and homologous genes divergence, as well as the selective pressure on duplicated genes, were estimated by calculating synonymous (Ks) and non-synonymous substitutions (Ka) per site between the homologous genes using the LOCUS SEARCH utility of PGDD. The divergence time was calculated using the neutral substitution rate of 1.5×10-8 substitutions per site per year for the chalcone synthase gene (Chs) .
Plant growth and treatments
The plant materials (B. rapa ssp. pekinensis cv. Zhonghan No. 1) were grown at the experimental farm in Zhejiang University until flowering. Steps taken in growing the sampling plants were as follows: First, the seeds were sown on 10 Oct, 2012, and then were transplanted in the field outside after the seedlings with 5~6 pieces true leaves on 15 Nov, 2012. Subsequently, the seedlings were carried out with normal management for about 4 months. Finally, the plants produced flowers after bolting and materials were sampled on 10 Mar, 2013. The roots, floral stems, leaves, flowers, immature siliques, sepals, petals, stamens, pistils, little buds (<1.6 mm), medium-sized buds (1.6 mm to 2.8 mm), and big buds (>2.8 mm) were sampled to analyze the tissue- or organ-specific expression of the different genes. Total roots and main floral stems were chosen. For the leaves materials, young leaves at the second and third nodes from top of the main floral stems were chosen. For the flowers, new opened ones were selected. Immature siliques were defined as siliques about 3 days after pollination and fertilization. The diameters of the floral buds were measured using a Vernier caliper. All the materials were sampled from at least ten plants.
B. rapa ssp. pekinensis cv. Chiifu-401-42 plants were used in the different treatment conditions. All seedlings were grown under a 16 h/8 h light/dark photoperiod, at 25°C ± 1°C, for approximately 3 weeks. Only the second true leaves were sampled to minimize the differences between samples. The nutrient solution was supplemented with 200 mM NaCl for the salt treatments, and the leaves were collected at 0, 3, 8, and 16 h after stress induction. Water was withheld from three-week-old seedlings to initiate the drought treatment, and the leaves were subsequently classified into four levels, according to the degree of drought. Level 0 had normal leaves in well-watered seedlings. At level I (3 days after drought treatment), the leaves started to wither, whereas the leaves were severely withered at Level II (5 days after drought treatment). Level III (7 days after drought treatment) indicated that the whole seedlings had withered. The 3-week-old seedlings were sprayed with 100 μM 6-BA (6-Benzylaminopurine) for the cytokinin treatment and 100 μM ABA for the ABA treatment. The leaves were sampled at 0, 0.5, and 1 h after spraying, and the control was sprayed with double distilled water alone. All the materials sampled were immediately frozen in liquid nitrogen and stored in a refrigerator at −75°C.
RNA extraction and qRT-PCR analysis
The total RNA was extracted using the TRIZOL reagent (Invitrogen, Germany), according to the manufacturer’s instructions. The first cDNA strand was generated using the Takara Reverse Transcription System (Japan) by following the manufacturer’s protocol. A maximum of 1 ug RNA was used for each reverse-transcription reaction. gDNA eraser in the kits was used to eliminate DNA to prevent DNA contamination. qRT-PCR was performed using the primers listed in Additional file 11. The primers were designed using the Primer (version 5.0) software. The specificity of each primer to their target genes was checked using the BLASTN program of BRAD. cDNA templates were firstly homogenized with the EASY Solution in the kits. Up to 2 μL of diluted cDNA were subjected to each qRT-PCR reaction for a final volume of 15 μL, which contained 7.5 μL SYBR Green Master Mix Reagent (Takara, Japan) and 0.3 μL specific primers (3 pmol). The qRT-PCR reactions were performed using a StepOne real-time PCR machine (Bio-RAD, USA), programmed to heat for 30 s at 95°C, followed by 40 cycles of 5 s at 95°C and 45 s at 53–58°C, and at the end, 1 cycle of 1 min at 95°C, 30 s at 50°C and 30 s at 95°C. The specificity of the reactions was verified by melting curve analysis and products were further confirmed by agarose gel electrophoresis. Two biological replicates were performed with three technical replicates for each sample plus the negative control. RNA for each biological replicate pooled from a number of individuals per treatment/tissue. The BrActin1 gene was used as the reference gene. The comparative ΔΔCT method was used to calculate the relative expression levels of the different genes. The data of qRT-PCR were clustered using the average linkage method with Pearson correlation distance metric by Multiple Array Viewer .
This research was partially supported by the Hi-Tech Research and Development Program of China (2012AA100104-4), the Breeding Project of the Sci-tech Foundation of Zhejiang Province (2012C12903), Zhejiang Provincial Natural Science Foundation of China (Y13C150001) and the Key Science & Technology Program of Zhejiang Province (2010C12004). The authors gratefully acknowledge Dr. Jian Wu for his helpful advice. We thank Dr. Youjian Yu, in particular, for the stimulating discussions and for critically reading the manuscript.
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