Additional file 9. Table S8. The positively regulated genes by both NaCl treatment and SRMT. The order of these genes was based on their expressions in SRMT overexpressing lines compared with WT.
The integration of science and education is an effective way for universities to cultivate students in cutting-edge innovative interests. Epigenetics is the expansion of classical genetics, the corresponding experimental courses of which have not been integrated into the current teaching system. In this paper, by taking advantage of our laboratory's research on the DNA methylation maintenance gene, OsMET1-2 in rice, we have integrated our innovative findings in the education curriculum, and built a comprehensive teaching system on experimentation research, which greatly stimulates the curiosity of the students. Taking the OsMET1-2 mutants and its isogenic wild-type rice plants as experimental materials, this course has successfully demonstrated a causal link between genetic mutation and epigenetic variation, a topic widely interested by the students in learning genetics and epigenetics. Through the practice of this course, students have a deeper understanding of the important role of epigenetic modifications, their scientific research capabilities have been greatly improved, thereby strongly supporting the cultivation of top innovative talents among the students.
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nursery bed fertilization was applied in thetest.Six treatments that were repeated 3 times were
arranged. Resultsshow that proper dosage of fertilizers is essentlal for the seedlings touptake
the nutrient elements. When the content of N,P. K in the leafin July and August is
3.5%-4.0%,0.2%-0.3%, and 1.0%or above,rspectively, the seedlings tend to grow well.Under
such test condition,the optimal dosage of N and P2O5 is per ha 180kg and 120kgrespectively.
miR-145 is highly expressed in vascular cells, where it regulates phenotypic switching and vascular homeostasis, but its role in carotid artery stenosis (CAS) is controversial. In the present study, the expression of miR-145 was assessed by real time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in human samples (both plasma and/or endarterectomy samples) from patients with symptomatic CAS and in controls without CAS. The mouse carotid artery ligation (CAL) model was used to determine the role of miR-145 on vascular smooth muscle cells in vivo (VSMCs) by using a mimic of or an inhibitor of miR-145. We found that miR-145 expression was significantly reduced in the plasma and plaque from patients with CAS (p less than 0.01). The expression of miR-145 in the mouse CAL model, as assessed by qRT-PCR, was significantly reduced compared to the carotid arteries of the control group (p less than 0.01). In vitro, enhancement or inhibition of miR-145 in VSMCs demonstrated that miR-145 significantly inhibited proliferation of VSMCs (p less than 0.05); in vivo, enhancement of miR-145 significantly inhibited neointimal formation in the CAL model (p less than 0.01). These results demonstrate that the expression of miR-145 is reduced in human CAS, miR-145 plays a critical role in CAS by modulation of VSMC proliferation, suggesting that MiR-145 may present a potential therapeutic option for treating CAS.
Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22,000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.
Hybridization is a prominent evolutionary force promoting plant diversification, either with or without subsequent genome doubling (Abbott et al., 2013; Soltis et al., 2014; Yakimowski & Rieseberg, 2014). The Aegilops–Triticum complex is an ideal system to investigate how natural hybridization and allopolyploidization have caused species diversification (Matsuoka, 2011). Recently, Marcussen et al. (2014) proposed the tantalizing scenario that the ancestral D lineage originated via homoploid hybridization between ancient A and B lineages some five million years ago (Mya) (the definition of A, B and D lineages shown in Fig. 1). Evidence for this mode of origin was derived from phylogenomic and population genetic analyses of nuclear genes, but without taking into account the evolutionary history and chloroplast topology of this species complex. Meanwhile, in a recent issue of New Phytologist, Gornicki et al. (2014) reported the chloroplast phylogeny of the Triticum–Aegilops complex based on 25 chloroplast genomes of eight modern A, S and D genome diploid species and four polyploid wheat species, but they did not address the origin of the D genome. Here, by re-analyzing critical data used by both studies and additional data, we present evidence for a more complex hybrid origin of the D genome of A. tauschii. To date, 13 diploid species of the Triticum–Aegilops complex, which belong to eight distinct but related genome groups (A, D, S, M, C, U, N and T), have been identified (Table 1) and which are variously and sometimes sympatrically distributed in the Middle East (Lilienfeld, 1951; Gill & Friebe, 2002; Huang et al., 2002). The A, B and D genomes, harbored by diploid species T. urartu, A. speltoides (or a closely related species) and A. tauschii, respectively, are established as the diploid genome donors of the A-, B- and D-subgenomes of hexaploid bread wheat, T. aestivum (Cox, 1998; Huang et al., 2002; Petersen et al., 2006). The remaining genomes harbored by the diploid species (except the T genome) are found in polyploid Aegilops species (Gill & Friebe, 2002). Eighteen naturally occurring allopolyploid species have been described (Table 1), which also are widely distributed across the Near East. On the basis of plant habit, spike morphology and cytological data, Zohary & Feldman (1962) classified these allopolyploid species into three major genome groups (called cytological clusters), which are A, U and D (Table 1). Variation patterns of the three cytological clusters led to the hypothesis that the current allopolyploid species within each cluster probably evolved from only a few initial amphidiploids (Zohary & Feldman, 1962; Feldman, 1965; Pazy & Zohary, 1965). This hypothesis is further supported by cytological and phylogenetic analyses showing that the A-, U- and D-genomes have indeed donated the maternal genome to most of the current polyploid species (Kimber & Tsunewaki, 1988; Meimberg et al., 2009; Tsunewaki, 2009). Together, these attributes suggest that hybridization, either at the homoploid level or followed by polyploidization, has occurred frequently within the Triticum–Aegilops complex. Marcussen et al. (2014) proposed that all extant diploid species of the Aegilops–Triticum complex are derived from A, B and D lineages (Fig. S6 in Marcussen et al., 2014). Phylogenomic analyses based on nuclear genome sequences revealed that the phylogenetic positions of A (T. monococcum/T. urartu), B (A. speltoides) and D (A. tauschii) genome species varied among nuclear genes, with topologies A (B, D) and B (A, D) each being about twice as common as D (A, B) (Table 1 in Marcussen et al., 2014). However, evidence for the homoploid hybrid origin of A. tauschii derives from phylogenomic analyses of modern S, A and D genomes, without taking into account the other genomes (e.g. M, N, T, U and C) within this species complex. Given that the breadth of taxonomic sampling could affect the identification of hybridization events, we re-analyzed the topologies of the four focal genomes (A, S, D and Ssh) for the 275 nuclear genes used in Marcussen et al. (2014), who proposed a homoploid hybrid origin of the D lineage (Table S4 in Marcussen et al., 2014). If the D lineage species were formed from a single homoploid hybridization event, as proposed by Marcussen et al. (2014), then all species derived from this event would be expected to cluster together at most nuclear genes. However, our results showed that the two D lineage species, A. tauschii and A. sharonensis, are separated in 40% of the 209 gene trees (Supporting Information Fig. S1). Marcussen et al. (2014) also reported a distinct hybrid pattern for A. sharonensis, with only c. 25% of the 275 gene trees reflecting B-lineage ancestry. Indeed, Waines & Johnson (1972) have documented that A. sharonensis is a hybrid between A. longissima and A. bicornis. In addition, cytogenetic analyses revealed that modern S* genome species (D lineage) are closer to A. speltoides (B lineage) than to A. tauschii (D lineage) (Kihara, 1954). Based on these observations, we hypothesize that the origin of A. tauschii may be more complicated than envisioned by Marcussen et al. (2014). Additional information bearing on the history of the Triticum–Aegilops complex may derive from analysis of chloroplast genomes, which are maternally inherited in this species complex (Fukasawa, 1959; Kihara, 1959). The cpDNA topology of this group has been investigated in previous studies using selected genes (Hirai & Tsunewaki, 1981; Terachi et al., 1987; Wang et al., 1997; Yamane & Kawahara, 2005; Meimberg et al., 2009), and more recently whole genome sequences (Gornicki et al., 2014; Middleton et al., 2014). These studies focused on the origin of domesticated wheat and phylogenetic relationships within the Triticum–Aegilops complex. For example, Gornicki et al. (2014) revealed a basal clade of A. speltoides and A. tauschii grouped together with four S* genome species (A. longissima, A. searsii, A. sharonensis and A. bicornis). However, the other diploid genome (e.g. M genome) and polyploid species within Triticum–Aegilops complex were not included in their study. Middleton et al. (2014) also reported a similar chloroplast topology with five A, S, D diploid species and three polyploid species (including M genome), but the S* genome species were not included in their study. To encompass all diploid and polyploid genomes in a single framework, we retrieved 20 whole chloroplast genome sequences from GenBank deposited by Gornicki et al. (2014) and Middleton et al. (2014) and conducted neighbor-joining phylogenetic analysis using MEGA 6 (Tamura et al., 2013) (Fig. 1). The resulting topology showed that the chloroplast genome of A. tauschii (D genome) is more closely related to that of other D and all S* genome species (including A. sharonensis) than it is to either the A. speltoides (S genome) or T. monococcum/T. urartu (A genome) chloroplast genomes. This result would not be expected under the scenario of a single homoploid hybrid origin of A. tauschii, in which case the cpDNA of A. tauschii would be expected to be more similar to that of either the A or B genome lineages. Marcussen et al. (2014) proposed that A. tauschii originated from homoploid hybridization between A. speltoides and the ancestor of modern T. urartu/T. monococcum. If this were the case, A. tauschii would be expected to share a chloroplast genome with one of these two putative progenitor lineages. However, the chloroplast topology reveals that A. tauschii is cladistically nested between the A and remaining S* and M genomes (Fig. 1). One possible explanation for the apparent discrepancy between the cpDNA-derived phylogeny and the interpretation of Marcussen et al. (2014) is that A. speltoides itself underwent later hybridization(s), in which it captured the chloroplast genome from some other species in the B genome lineage. As shown in the chloroplast topology, however, A. speltoides is basal in the clade, differing phylogenetically and quantitatively from the remaining species in the Triticum–Aegilops complex. The latter is evidenced in an analysis of single nucleotide polymorphisms (SNPs), in which A. speltoides shares fewer SNPs with the remaining genomes than they do with each other (Table 2). These attributes indicate that A. speltoides possesses a rather distinct chloroplast genome. In addition, the number of shared SNPs between D and A genomes is only slightly higher than between D and M or between D and S* genomes (Table 2), suggesting that the D genome is equidistant from the A, S* and M genomes. An alternative scenario is that the origin of the D genome lineage that gave rise to A. tauschii is more complex than that proposed by Marcussen et al. (2014). For example, A. speltoides and T. urartu/T. monococcum could have evolved from the ancient B and A genomes, respectively, with the remaining species (including the modern D, S* and M genomes in Fig. 1) of Triticum–Aegilops complex derived from the ancient D lineage (Fig. 2a). If the ancient D lineage were to have evolved through a single homoploid hybridization between A and B lineages, it would be expected to phylogenetically cluster with either of its two donors and have a cpDNA genome that is much more like one parent than the other. The chloroplast topology reveals that the ancient D lineage clusters together with A lineage (Fig. 1). Indeed, the number of shared SNPs between the A and D lineages is higher than that between the B and D lineages (Table 2). Under this hypothesis, recent hybridization might be responsible for the distinct hybrid pattern of modern A. tauschii and A. sharonensis in the phylogenomic analyses. Another possibility for the origin of modern A. tauschii is a chloroplast capture model (Fig. 2b). Under this scenario A and B lineages were involved in homoploid hybridization, leading to the formation of an A. tauschii-like nuclear genome (ancestry of modern A. tauschii), which was followed by hybridization(s) with a third species in the S*/M genomes. In this case, modern A. tauschii captured the chloroplast genome from S*/M genome species without much nuclear introgression. Alternatively, modern A. tauschii might have originated from homoploid hybridization between the A and B lineages, but the hybridization event was preceded by an earlier hybridization with a third species that donated the S*/M lineage chloroplast genome to the maternal parent of the later homoploid hybridization event (Fig. 2c). If this were the case, modern A. tauschii would have evolved with A and B lineage nuclear genomes, but with a S*/M type chloroplast genome. Taken together, our integrated re-evaluation, while confirming the hybrid nature of A. tauschii, points clearly to a more complex history of the species than that proposed by Marcussen et al. (2014), one that may have involved multiple rounds of both recent and ancient hybridizations. All chloroplast genome sequences deposited by Gornicki et al. (2014) and Middleton et al. (2014) were retrieved from GenBank. Aegilops speltoides, JQ740834, NC_022135; A. sharonensis, KJ614419; A. bicornis, KJ614417; A. longissima, KJ614416; A. searsii, KJ614415; A. tauschii, JQ754651, NC_022133; Triticum monococcum, KC912690, NC_021760; T. urartu, KC912693, NC_021762; T. aestivum, KC912694; A. cylindrica, KF534489, NC_023096; A. geniculata, KF534490, NC_023097; Hordeum vulgare, KC912687; Secale cereale, KC912691, NC_021761. The authors thank Xutong Wang, Fengxue Shi and Cui Zhang for assistance with data analyses. This study was supported by the National Natural Science Foundation of China (31290210, 31470010) and the Program for Introducing Talents to Universities (B07017). Please note: Wiley Blackwell are not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Background Grafting has been extensively used to enhance the performance of horticultural crops. Since Charles Darwin coined the term "graft hybrid" meaning that asexual combination of different plant species may generate products that are genetically distinct, highly discrepant opinions exist supporting or against the concept. Recent studies have documented that grafting enables exchanges of both RNA and DNA molecules between the grafting partners, thus providing a molecular basis for grafting-induced genetic variation. DNA methylation is known as prone to alterations as a result of perturbation of internal and external conditions. Given characteristics of grafting, it is interesting to test whether the process may cause an alteration of this epigenetic marker in the grafted organismal products. Methodology/Principal Findings We analyzed relative global DNA methylation levels and locus-specific methylation patterns by the MSAP marker and locus-specific bisulfite-sequencing in the seed plants (wild-type controls), self- and hetero-grafted scions/rootstocks, selfed progenies of scions and their seed-plant controls, involving three Solanaceae species. We quantified expression of putative genes involved in establishing and/or maintaining DNA methylation by q-(RT)-PCR. We found that (1) hetero-grafting caused extensive alteration of DNA methylation patterns in a locus-specific manner, especially in scions, although relative methylation levels remain largely unaltered; (2) the altered methylation patterns in the hetero-grafting-derived scions could be inherited to sexual progenies with some sites showing further alterations or revisions; (3) hetero-grafting caused dynamic changes in steady-state transcript abundance of genes encoding for a set of enzymes functionally relevant to DNA methylation. Conclusions/Significance Our results demonstrate that inter-species grafting in plants could produce extensive and heritable alterations in DNA methylation. We suggest that these readily altered, yet heritable, epigenetic modifications due to interspecies hetero-grafting may shed one facet of insight into the molecular underpinnings for the still contentious concept of graft hybrid.