- Research article
- Open Access
Accession-specific modifiers act with ZWILLE/ARGONAUTE10 to maintain shoot meristem stem cells during embryogenesis in Arabidopsis
© Tucker et al.; licensee BioMed Central Ltd. 2013
- Received: 4 June 2013
- Accepted: 14 November 2013
- Published: 20 November 2013
Stem cells located in the centre of the shoot apical meristem are required for the repetitive formation of new organs such as leaves, branches and flowers. In Arabidopsis thaliana, the ZWILLE/PINHEAD/AGO10 (ZLL) gene encodes a member of the ARGONAUTE (AGO) protein family and is required to maintain shoot meristem stem cells during embryogenesis. In the Landsberg erecta (Ler) acession, ZLL is essential for stem cell maintenance, whereas in the Columbia (Col) accession its requirement appears masked by genetic modifiers. The genetic basis for this variation has remained elusive.
To understand the impact of natural variation on shoot stem cell maintenance, we analysed 28 wild-type Arabidopsis accessions from around the world and show that ZLL function is essential for stem cell maintenance in accessions mainly originating from Germany, but is dispensable for accessions from other regions. Quantitative Trait Loci (QTL) mapping using Ler/Col recombinant inbred lines indicated that at least five genomic regions, referred to as FLETSCHE (FHE) 1–5, modify ZLL function in stem cell maintenance. Characterisation of Col zll near isogenic lines confirmed that the major QTL, FHE2, is preferentially maintained as a Ler allele in seedlings lacking stem cells, suggesting that this region harbours an important modifier of ZLL function. Comparison of torpedo-stage embryo expression profiles to QTL map data revealed candidate FHE genes, including the Arabidopsis Cyclophilin-40 homologue SQUINT (SQN), and functional studies revealed a previously uncharacterised role for SQN in stem cell regulation.
Multiple genetic modifiers from different Arabidopsis accessions influence the role of ZLL in embryonic stem cell maintenance. Of the five FHE loci modifying stem cell maintenance in Ler-0 and Col-0, FHE2 was the most prominent and was tightly linked to the SQN gene, which encodes a cofactor that supports AGO1 activity. SQN shows variable embryonic expression levels between accessions and altered ZLL-dependency in transgenic assays, confirming a key role in stem cell maintenance. Reduced SQN expression levels in Col-0 correlate with transposon insertions adjoining the transcriptional start site, which may contribute to stem cell maintenance in other ZLL-independent accessions.
- Shoot meristem
- Stem cells
The shoot apical meristem (SAM) is a dynamic system that sustains production of plant organs while constantly integrating developmental and environmental cues[1, 2]. The ability of the SAM to process and buffer these cues is already evident during early stages of embryogenesis, when signals from different embryonic domains, including the vasculature and the epidermis, are integrated to qualitatively influence meristem growth[3, 4]. Many of these signals feed into a core negative feedback loop involving the transcription factor WUSCHEL (WUS) and the CLAVATA1/2/3 (CLV) signaling complex, which act within the meristem to balance stem cell maintenance and cell differentiation[5–7].
In Arabidopsis, mutations in AGO1 and ZLL influence stem cell maintenance in the embryonic meristem and also during subsequent growth[8–11]. The relationship between these two genes is complex, with studies indicating both synergistic and antagonistic functions[11–14]. In general, AGO proteins act as key mediators of small RNA (sRNA) silencing pathways by binding 21–24 nt sRNAs and inducing silencing of complementary RNA or DNA targets. Recent biochemical and genetic evidence suggests that in the embryo, ZLL acts as a miRNA “locker” to sequester microRNA165/6, thereby limiting its incorporation into the active AGO1 RNA-Induced Silencing Complex (RISC)[12, 16]. In the absence of ZLL function, AGO1 is proposed to bind miR165/6 and down-regulate Class III HD-ZIP transcription factors within the embryonic SAM, thereby inducing stem cell differentiation. This pathway likely influences function of WUS in promoting stem cell identity, since WUS-induced CLV3 expression in stem cells is disrupted in zll mutants. ZLL function also appears to be linked to vascular tissues because provascular ZLL expression in the embryo is sufficient to maintain stem cell development, indicating that movement of small RNAs or other signaling molecules may be involved.
In this study we examined the effect of different genomic regions from Ler and Col on ZLL function in shoot stem cell maintenance. QTL analysis indicates that at least five loci, referred to as FLETSCHE (FHE) 1–5, influence stem cell maintenance. Comparison of embryo transcriptomic profiles identified multiple genes showing variable expression in different accessions, including candidates for the FHE loci. One of the candidates for FHE2 represents an allele of SQN, which encodes the Arabidopsis Cyclophilin-40 orthologue and acts as a modifier of ZLL function.
ZLL is required for meristem maintenance in an accession specific manner
The frequency of homozygous seedlings showing shoot stem cell termination in Ler zll alleles varies from 10 to 90%, depending on the mutation[8, 13, 20]. By contrast, the putative null T-DNA insertion mutants zll ago10-1 and zll ago10-3 in the Col accession have no or minimal effects on stem cell maintenance and meristem development (~0.2% in zll ago10-1 [11, 18]). To test if this difference is related to the nature of the respective mutant alleles, zll ago10-1 was backcrossed three times to Ler-0 wild-type. In homozygous Ler zll ago10-1 lines, 29% (n = 194) of the seedlings showed stem cell termination. In a converse experiment, the strong zll-1 EMS mutant allele was introduced into the Col background by crossing Ler zll-1 to Col-0 wild-type. Only a small fraction (0.5%, n = 5736) of the expected 25% zll-1 homozygous F2 seedlings showed defects in stem cell maintenance (Figure 1B, C). This equates to an approximate phenotype of 2% in the homozygous state, compared to 61% (n = 315) in a cross between Ler zll-1 and Ler-0. This indicates that the different expressivity of the zll-1 mutation between Ler-0 and Col alleles is not due to the nature of the mutant alleles, but must be caused by genetic modifiers. To determine if the different requirement for ZLL between Ler and Col might be due to the erecta mutation in Ler, the Col zll ago10-1 allele was crossed to the strong er-102 and intermediate er-103 Col alleles (Figure 1B). Double mutants showed the characteristic erecta phenotype, but did not show an increased frequency of stem cell defects compared to the zll ago10-1 single mutant.
Differences in embryonic meristem size between Ler and Col were also investigated as a possible explanation for the different expressivity of zll mutations. Because the number of L1 cells in the mature embryonic meristem is indicative of the size of the meristem, wild-type embryos from the Ler-0 and Col-0 accessions were stained with propidium iodide and examined by confocal laser microscopy (Figure 1D). Grown under the same conditions, Ler-0 embryos (n = 17) contained ~11.4 (SD +/-1.4) cells in the L1 layer of the meristem at maturity, while Col-0 embryos (n = 25) contained ~10.1 (SD +/-1.5) cells. This indicates that the L1 layer of the Ler-0 embryonic meristem, and hence the meristem itself, contains more cells than the Col-0 meristem (Students t-test P < 0.01). This opposes the hypothesis that a smaller meristem in Ler-0 might be the cause of increased sensitivity to zll mutations, but suggests that fundamental differences in embryonic meristem regulation may contribute to variable zll expressivity in these accessions.
ZLL is required for meristem maintenance in multiple Arabidopsis accessions
The frequency of seedling meristem termination, indicative of stem cell defects during embryogenesis, was assessed in the F2 generation of each accession cross to determine the approximate phenotypic frequency in the homozygous zll-1 state (Figure 2). Of the 28 accessions, five showed stem cell termination in more than 20% of the homozygous seedlings, eight showed a phenotype in 10 to 20%, and fifteen showed a phenotype in less than 10% of seedlings. Curiously, the five accessions that showed the highest zll-1 expressivity, Ler-0, Freiburg-1 (Fe-1), Neuweilnau-0 (Nw-0), Bayreuth-0 (Bay-0) and Enkheim-1 (En-1), were all derived from locations in the southern half of Germany. Despite this geographical association, there is no obvious clustering of these accessions in a phylogenetic tree based on 59 SNPs to suggest they were more related to each other than accessions showing weak stem cell termination phenotypes (Figure 3).
Multiple quantitative trait loci (QTL) influence ZLL-dependent stem cell maintenance
Detection of FLETSCHE ( FHE ) QTL in the Ler/Col RIL population
Near Isogenic zll-1 Lines (NILs) showing shoot stem cell defects preferentially retain genomic regions linked to the Ler FHE loci
Two lines (NIL22 and NIL28) that maintained relatively high frequencies of stem cell termination over several backcrosses were selected for mapping and phenotypic analysis after BC5. Genomic DNA from phenotypic NIL22 BC5F2 plants (n = 48) and NIL28 BC5F2 plants (n = 48) was used for bulk mapping with 19 PCR-based markers (Additional file2) that detect Ler/Col polymorphisms in the vicinity of the predicted FHE QTL and at unlinked sites throughout the genome. In both NILs, PCR results identified a strong bias towards Ler DNA at markers MT435 (~32 cM) and nga168 (~73 cM) on chromosome 2 and ciw9 (~90 cM; zll-1) on chromosome 5, while the rest of the genome was biased towards Col.
Effect of FHE2 and FHE3 genomic regions on stem cell termination in BC 5 zll-1 Col-0 introgression lines
Introgression line (F2plant number)
Frequency of stem cell termination in F3progeny ± SD
NIL28.5 (#8, #16)
10 ± 4% (n = 554)
NIL28.5 (#9) NIL22.5 (#3)
9 ± 1% (n = 783)
5 ± 2% (n = 288)
NIL28.5 (#14, #15)
1 ± 2% (n = 536)
NIL28.5 (#13, #27)
1 ± 0% (n = 902)
Changes in gene expression between ZLL-independent and dependent accessions identify candidates for the FHE loci and downstream pathways
Despite further backcrosses, most zll-1 Col NILs preferentially retained a large fragment of Ler genomic DNA around FHE2Ler which complicated fine mapping. To further delineate putative FHE factors and pathways that influence stem cell maintenance in a ZLL-dependent manner, microarray profiles were generated from specific ZLL-dependent and independent Arabidopsis accessions using Affymetrix ATH1 chips.
Torpedo-stage embryos were harvested separately from four ZLL-dependent accessions (Ler-0, Fe-1, Nw-0, and Bay-0), and three ZLL-independent accessions (Col-0, Van-0 and Ts-1). Consistent with previous SNP genotyping results, none of the accessions showed an identical pattern when genotyped with 14 INDEL markers, confirming that they are genetically unique. Multiple comparisons were made between expression profiles derived from the two groups of accessions by maintaining a minimum of three arrays per group. A total of 439 genes were identified as being differentially expressed in at least one of the comparisons, based on a p-value of <0.05 and a 3-fold expression change (Additional file3). In the most stringent comparison, all of the ZLL-dependent accessions were grouped as replicates and compared to the ZLL-independent accessions. Two genes were identified as being up-regulated and ten were identified as being down-regulated (Additional file4). None of the genes appeared to be tightly linked to the predicted FHE loci from the RIL analysis, suggesting that they may either represent factors that act downstream of the FHE modifiers, they are unrelated to ZLL function, and/or they represent modifiers that escaped detection in the Ler/Col FHE QTL mapping.
FHE2 maps close to the Arabidopsis Cyclophilin-40 homologue SQUINT, which is differentially expressed between Col-0, Fe-1 and Ler-0 accessions
Arabidopsis genes differentially expressed in torpedo stage embryos from Col-0 and Fe-1/Ler-0 and located in the vicinity of predicted FHE QTL
Col vs Fe/Ler (FC)
Serine carboxypeptidase-like 44
CYP705A27 (cytochrome P450)
transposable element gene
Lipid transfer protein (LTP)
similar to MEE4
pollen Ole-e1 allergen
similar to NLI interacting factor
GNS1/SUR4 membrane protein
F-box family protein
germin-like protein, putative
transposable element gene
GERMIN-LIKE PROTEIN 6
glyoxalase I family protein
DC1 domain-containing protein
Changes in SQN expression influence stem cell maintenance in the Ler-0 and Col-0 accessions
Analysis of amiRSQN in Ler zll-1 sqn-4 double mutants
Stem cell termination phenotypes in %
zll-1 SQN +/+
zll-1 sqn-4 amiRSQN#1
zll-1 sqn-4 amiRSQN#2
zll-1 sqn-4 amiRSQN#3
zll-1 sqn-4 amiRSQN#4
zll-1 sqn-4 amiRSQN#5
zll-1 sqn-4 amiRSQN#6
zll-1 sqn-4 amiRSQN#7
Analysis of ectopic SQN expression in Col zll ago10-1 mutants
Seedlings showing meristem termination [%]
zll ago10-1 pAtRPS5a:SQN#1
zll ago10-1 pAtRPS5a:SQN#3
Different genetic backgrounds influence the role of ZLL in stem cell maintenance
Previous studies in Arabidopsis have utilised variation between natural accessions to identify the genetic basis for developmental differences[27, 28], including small RNA-mediated regulation of flowering time, self-incompatibility and root growth. In the current study, natural genetic modifiers that influence stem cell maintenance in the absence of ZLL function were investigated. The aim was to identify novel components that support ZLL in promoting stem cell maintenance through the regulation of WUS activity and/or modification of miRNA function. QTL mapping in a population of Ler/Col RILs and zll-1 Col-0 NILs suggested that five FHE loci can explain 49% of the variance in stem cell maintenance in Ler-0 and Col-0. In all cases, the presence of the Ler FHE alleles with zll-1 resulted in an increased frequency of stem cell termination, consistent with Col zll mutants showing limited degrees of stem cell termination. The Ler/Col RILs were previously analysed for variation in shoot regeneration from tissue culture, which depends on three QTL on chromosomes 1, 4 and 5[32, 33]. The position of these loci is distinct from the FHE QTL, suggesting that the FHE loci are unlikely to be involved in shoot formation per se, and are more likely to be involved in embryonic meristem function.
Our findings also indicate that differences in ZLL-dependency are not limited to the Col-0 and Ler-0 accessions and considerable variation exists between different accessions from North America, Europe and Asia. The two accessions showing the highest frequency of stem cell defects in the presence of zll-1, in 55% and 61% of zll-1 seedlings respectively, were Fe-1 and Ler-0. Limited information is available for the Fe-1 accession, but previous studies of natural genetic variation show that it diverges from Ler and Col in its response to pathogen susceptibility[34, 35]. No obvious phenotypic differences in growth habit, flower development or embryo morphology were detected between Fe-1 and Col-0 to suggest such a prominent difference in response to loss of ZLL function.
Although our analyses are far from saturating, most ZLL-dependent accessions analysed here were collected from regions within middle and southern Germany. Recent advances in SNP detection and the availability of large genomic sequence datasets from diverse accessions allows trait variation to be dissected by genome wide association studies (GWAS), which offers a much higher mapping resolution compared to the RILs[28, 36–38]. The number of accessions analysed in this experiment was insufficient for robust GWAS, but such an approach might be useful in future studies to fine map the FHE loci and to identify additional loci that contribute to ZLL function in stem cell maintenance. Identification of the genes underlying the FHE QTL will show whether the ZLL-dependent accessions share a common recent ancestor containing a set of genetic modifications influencing stem cell maintenance, or if geographical conditions have independently influenced selection of polymorphisms in the modifier loci.
Conserved differences in embryonic gene expression are detected between different Arabidopsis accessions
The first defects in stem cell maintenance in zll-1 mutants are observed at the torpedo stage of embryogenesis, suggesting that FHE modifiers of ZLL function should be active at this stage. Microarray analysis identified multiple genes showing natural variation in embryonic gene expression at the torpedo-stage. These expression profiles suggest it is unlikely that any causative polymorphisms influencing ZLL-dependency in the seven analysed accessions lead to common changes in mRNA expression of the genes underlying the Ler/Col FHE loci. This is not surprising, since the FHE QTL may differ between diverged accessions and the specific polymorphism(s) leading to ZLL-dependency may not lead to a change in mRNA expression, but rather have effects on protein function or accumulation.
Of the 12 genes differentially expressed in the combined ZLL-dependent versus ZLL-independent accessions, none were tightly linked to the Ler/Col FHE loci or had documented functions in meristem development or RNAi. In addition, only two of the genes showed any expression correlation across a developmental series (0.84; At1g78820 vs At5g28770; Genevestigator), suggesting that the group are unlikely to be associated closely in the same pathway. Despite this, it is possible that variable expression of these genes in the different accessions is at least partly dependent on activity of the FHE loci. This is also possible for the remaining 427 genes that showed accession-specific expression during embryogenesis.
A hypomorphic SQUINT allele may support stem cell maintenance in Columbia zll mutants
Restricting the embryonic expression profile comparisons to the three most relevant accessions (Col-0, Ler-0 and Fe-1), in combination with double mutant analysis, identified SQN as a candidate modifier underlying the FHE2 QTL. In Col-0, embryonic SQN expression is 5-fold lower than Ler-0 and Fe-1. Consistent with a role in modifying stem cell development, decreased SQN activity in Ler via sqn-4 and amiRSQN partially rescued stem cell maintenance in the zll-1 background, while increased SQN expression in Col zll ago10-1 induced stem cell termination. Although the effects were greater than the predicted quantitative contribution of the FHE2 QTL, this may be due to the nature of the polymorphisms between SQN Ler and SQN Col . Only synonymous SNPs are present in the SQN coding sequence between Ler-0 and Col-0, indicating that differences in enzyme amino acid sequence cannot explain differences in function. In contrast, significant variations including insertions and deletions are present in the 5’ sequence upstream of the SQN gene (; Additional file5). Notably, a 6.6 kb MULE-related transposon sequence, annotated as At2g15800/At2g15810, is inserted close to the transcriptional start site of SQN. This insertion is located 500 bp upstream of the predicted SQN start codon in Col-0 but is absent from Ler-0 (Additional file5). The presence of this insertion varies between Arabidopsis accessions, and may contribute to natural variation in SQN expression as detected for other genes tightly linked to transposon sequences.
Although variable SQN expression levels correlate with differences in stem cell maintenance in Ler-0, Fe-1 and Col-0, and to a lesser extent in the Bay-0 and Nw-0 accessions, this is not the case in all accessions examined. SQN mRNA levels in the ZLL-independent Ts-1 and Van-0 lines were unchanged relative to Fe-1/Ler-0. Therefore, alternative FHE loci may play a more important role in these accessions. It is possible that some of this variation may be due to subtle transcriptional or post-transcriptional changes in the function of other meristem or RNAi-related genes physically linked to the FHE loci reported here (Additional file6). Further analysis of F2 progeny from Ler zll-1 and Ts-1 or Van-0 crosses will allow the major FHE loci that influence stem cell maintenance in these accessions to be positioned.
Our current model for FHE2 function is based upon a conserved increase in SQN mRNA levels in Ler-0 and Fe-1 compared to Col-0. SQN is predicted to enhance AGO1 activity through function as a co-factor. In combination with a zll mutation, which allows AGO1 greater access to miR165/166, increased levels of SQN in Ler-0 enhance repression of AGO1 targets, such as the Class III HD-ZIPs, and lead to a high frequency of terminal stem cell differentiation. Conversely in Col-0, where embryonic SQN expression is 5-fold lower than Fe-1/Ler-0, AGO1 is less efficient at reducing Class III HD-ZIP expression and inducing stem cell termination in the absence of ZLL function. In line with this, Col zll ago10-1 mutants showed no detectable change in Class III HD-ZIP mRNA levels or other miRNA targets compared to Col-0 wild-type (Additional file7), despite containing a functional AGO1 gene. Only when embryonic SQN expression was increased via the AtRPS5a:SQN construct did a high frequency of Col zll ago10-1 seedlings show meristem termination. Although changes in SQN expression alone cannot account for the drastic differences between zll phenotypes in Col-0 and Ler-0, it is likely that SQN forms part of an important pathway that contributes to ZLL function and FHE activity during stem cell development. Further characterisation of the FHE loci using emerging genomic and genetic resources, in combination with second-site mutagenesis studies in zll ago10-1 , will aid the identification of the responsible loci as well as determine their conservation in diverged Arabidopsis accessions.
Seeds were germinated on soil and grown as described previously. The Col zll ago10-1  and Ler zll-1 mutants have also been described previously. Seeds from the Ler/Col Recombinant Inbred Lines (N4859) and various Arabidopsis accessions were obtained from the Nottingham Arabidopsis stock centre (NASC). Single Nucleotide Polymorphism (SNP) haplotype alignments were created using publically available data (http://www.naturalvariation.org) in Geneious (http://www.geneious.com/). Maximum-likelihood trees were generated in Mega5.2. Defects in stem cell maintenance were scored in seedlings between 11–15 days post germination. Seedlings that contained an empty apex, a single filament, a single leaf or two leaves in place of a viable shoot meristem, were scored as showing stem cell defects, as per previous studies[8, 10]. Although phenotypic zll mutants terminate primary meristem development, secondary adventitious meristems produce viable flowers that can be used for crossing.
The number of cells in the embryonic meristem was determined by staining with propidium iodide and confocal laser microscopy as described previously. Confocal laser microscopy was performed at the Life Imaging Center (LIC, Freiburg).
All new markers used in this study were PCR based, and designed from the Cereon collection to detect insertions/deletions (INDELs) or single nucleotide polymorphisms (SNPs) by derived cleaved amplified polymorphism (dCAPS) primers. Primer sequences are shown in Additional file8.
Molecular map information for the Ler/Col RILs was downloaded from the NASC website (http://Arabidopsis.info/RI_data/full_markers.text). QTL analysis was performed with the software package PlabMQTL using composite interval mapping[48, 49] and a multiple regression procedure. Cofactors were selected based on the modified Bayesian Information Criterion and critical Logarithm of the odds (LOD) thresholds were determined empirically with 1,000 random permutations. The proportion of variance explained by the detected QTL (p) was obtained from the adjusted R2 value of the QTL model and the proportion of variance explained by individual QTL by normalizing to sum up to the total p.
Torpedo-stage embryos were dissected from maturing seeds in 1×PBS and stored on ice for no longer than 1 hour before snap freezing in liquid nitrogen. Approximately 100 embryos were harvested from each accession. RNA was extracted using the RNeasy Plant Minikit (with on-column DNAse treatment; Qiagen) according to manufacturer’s instructions. 10 μg total RNA was hybridised to Affymetrix ATH1 chips at ATLAS Biolabs (Berlin, Germany). Expression analysis and normalisation was performed in R using the RMA package, following a previously established pipeline
Three artificial miRNAs targeting SQN were designed using the Web MicroRNA designer program; http://wmd3.weigelworld.org/cgi-bin/webapp.cgi and cloned into the pJet2.1 expression vector. After sequencing, the amiRNA constructs were sub-cloned via BamHI digest into pEG278. Finally, p35S:amiRSQN-term was cloned into the PacI site of the pGreen II destination vector. Plant transformation was carried out by Agrobacterium-mediated floral dipping. After selection of T1 and T2 transformants, T3 homomozygous lines were used for final analysis.
To generate pAtRPS5a:SQN, genomic DNA of SQN was amplified by oFR126-Fr/oFR127-Rev primers harboring LIC cloning fragments and subcloned into the pJet2.1 expression vector. After sequencing, the SQN genomic fragment was cloned using the LIC cloning protocol, into a modified pGreenII vector containing the AtRPS5a promoter, LIC cloning site and Nos terminator. Full primer details are available on request.
Availability of supporting data
The microarray data sets supporting the results of this article are available in the Gene Expression Omnibus (GEO) repository, accessible via the GSE47884 identifier.
We thank Sabine Kenz, Lindsey Thompson, Sonia Bosca, Elise Tucker, Isabel Bäurle, Michael Lenhard, and other members of the Laux laboratory for technical assistance and discussions. This work was supported by an EMBO long-term postdoctoral fellowship, the DFG through SFB592 and the ARC Centre of Excellence in Plant Cell Walls (MT), the DFG through the German Excellence Initiative, BIOSS2 and by the EU-cofunded INTERREG IV Project A17 “ITP-TIP” (ERDF) (TL).
- Aichinger E, Kornet N, Friedrich T, Laux T: Plant stem cell niches. Annu Rev Plant Biol. 2012, 63: 615-636. 10.1146/annurev-arplant-042811-105555.View ArticlePubMedGoogle Scholar
- Murray JA, Jones A, Godin C, Traas J: Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling. Plant Cell. 2012, 24 (10): 3907-3919. 10.1105/tpc.112.102194.PubMed CentralView ArticlePubMedGoogle Scholar
- Tucker MR, Laux T: Connecting the paths in plant stem cell regulation. Trends Cell Biol. 2007, 17 (8): 403-410. 10.1016/j.tcb.2007.06.002.View ArticlePubMedGoogle Scholar
- Knauer S, Holt AL, Rubio-Somoza I, Tucker EJ, Hinze A, Pisch M, Javelle M, Timmermans MC, Tucker MR, Laux T: A protodermal miR394 signal defines a region of stem cell competence in the arabidopsis shoot meristem. Dev Cell. 2013, 24 (2): 125-132. 10.1016/j.devcel.2012.12.009.View ArticlePubMedGoogle Scholar
- Mayer KFX, Schoof H, Haecker A, Lenhard M, Jürgens G, Laux T: Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell. 1998, 95: 805-815. 10.1016/S0092-8674(00)81703-1.View ArticlePubMedGoogle Scholar
- Schoof H, Lenhard M, Haecker A, Mayer KFX, Jürgens G, Laux T: The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell. 2000, 100: 635-644. 10.1016/S0092-8674(00)80700-X.View ArticlePubMedGoogle Scholar
- Brand U, Fletcher JC, Hobe M, Meyerowitz EM, Simon R: Dependence of stem cell fate in Arabidopsis on a feedback loop regulated by CLV3 activity. Science. 2000, 289: 617-9. 10.1126/science.289.5479.617.View ArticlePubMedGoogle Scholar
- Moussian B, Schoof H, Haecker A, Jürgens G, Laux T: Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J. 1998, 17 (6): 1799-1809. 10.1093/emboj/17.6.1799.PubMed CentralView ArticlePubMedGoogle Scholar
- Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C: AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 1998, 17 (1): 170-180. 10.1093/emboj/17.1.170.PubMed CentralView ArticlePubMedGoogle Scholar
- Tucker MR, Hinze A, Tucker EJ, Takada S, Jurgens G, Laux T: Vascular signalling mediated by ZWILLE potentiates WUSCHEL function during shoot meristem stem cell development in the Arabidopsis embryo. Development. 2008, 135 (17): 2839-2843. 10.1242/dev.023648.View ArticlePubMedGoogle Scholar
- Mallory AC, Hinze A, Tucker MR, Bouche N, Gasciolli V, Elmayan T, Lauressergues D, Jauvion V, Vaucheret H, Laux T: Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLoS Genet. 2009, 5 (9): e1000646-10.1371/journal.pgen.1000646.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhu H, Hu F, Wang R, Zhou X, Sze SH, Liou LW, Barefoot A, Dickman M, Zhang X: Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell. 2011, 145 (2): 242-256. 10.1016/j.cell.2011.03.024.PubMed CentralView ArticlePubMedGoogle Scholar
- Lynn K, Fernandez A, Aida M, Sedbrook J, Tasaka M, Masson P, Barton MK: The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development. 1999, 126 (3): 469-481.PubMedGoogle Scholar
- Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O: Widespread translational inhibition by plant miRNAs and siRNAs. Science. 2008, 320 (5880): 1185-1190. 10.1126/science.1159151.View ArticlePubMedGoogle Scholar
- Vaucheret H: Plant ARGONAUTES. Trends Plant Sci. 2008, 13 (7): 350-358. 10.1016/j.tplants.2008.04.007.View ArticlePubMedGoogle Scholar
- Manavella PA, Weigel D, Wu L: Argonaute10 as a miRNA locker. Cell. 2011, 145 (2): 173-174. 10.1016/j.cell.2011.03.045.View ArticlePubMedGoogle Scholar
- Liu Q, Yao X, Pi L, Wang H, Cui X, Huang H: The ARGONAUTE10 gene modulates shoot apical meristem maintenance and leaf polarity establishment by repressing miR165/166 in Arabidopsis. Plant J. 2008, 58 (1): 27-40.View ArticlePubMedGoogle Scholar
- Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y: The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol. 2008, 49 (4): 493-500. 10.1093/pcp/pcn043.View ArticlePubMedGoogle Scholar
- Vollbrecht E, Reiser L, Hake S: Shoot meristem size is dependent on inbred background and presence of the maize homeobox gene, knotted1. Development. 2000, 127: 3161-3172.PubMedGoogle Scholar
- Moussian B, Haecker A, Laux T: ZWILLE buffers meristem stability in Arabidopsis thaliana. Dev Genes Evol. 2003, 213 (11): 534-540. 10.1007/s00427-003-0359-z.View ArticlePubMedGoogle Scholar
- Torii KU, Mitsukawa N, Oosumi T, Matsuura Y, Yokoyama R, Whittier RF, Komeda Y: The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats. Plant Cell. 1996, 8: 735-746.PubMed CentralView ArticlePubMedGoogle Scholar
- Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, Agren J, Bossdorf O, Byers D, Donohue K: The scale of population structure in Arabidopsis thaliana. PLoS Genet. 2010, 6 (2): e1000843-10.1371/journal.pgen.1000843.PubMed CentralView ArticlePubMedGoogle Scholar
- Lister C, Dean C: Recombinant inbred lines for mapping rflp and phenotypic markers in arabidopsis-thaliana. Plant J. 1993, 4 (4): 745-750. 10.1046/j.1365-313X.1993.04040745.x.View ArticleGoogle Scholar
- Berardini TZ, Bollman K, Sun H, Poethig RS: Regulation of vegetative phase change in Arabidopsis thaliana by cyclophilin 40. Science. 2001, 291 (5512): 2405-2407. 10.1126/science.1057144.View ArticlePubMedGoogle Scholar
- Prunet N, Morel P, Thierry AM, Eshed Y, Bowman JL, Negrutiu I, Trehin C: REBELOTE, SQUINT, and ULTRAPETALA1 function redundantly in the temporal regulation of floral meristem termination in Arabidopsis thaliana. Plant Cell. 2008, 20 (4): 901-919. 10.1105/tpc.107.053306.PubMed CentralView ArticlePubMedGoogle Scholar
- Smith MR, Willmann MR, Wu G, Berardini TZ, Moller B, Weijers D, Poethig RS: Cyclophilin 40 is required for microRNA activity in Arabidopsis. Proc Natl Acad Sci USA. 2009, 106 (13): 5424-5429. 10.1073/pnas.0812729106.PubMed CentralView ArticlePubMedGoogle Scholar
- Weigel D: Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 2012, 158 (1): 2-22. 10.1104/pp.111.189845.PubMed CentralView ArticlePubMedGoogle Scholar
- Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT: Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010, 465 (7298): 627-631. 10.1038/nature08800.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhai J, Liu J, Liu B, Li P, Meyers BC, Chen X, Cao X: Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet. 2008, 4 (4): e1000056-10.1371/journal.pgen.1000056.PubMed CentralView ArticlePubMedGoogle Scholar
- Nasrallah ME, Liu P, Sherman-Broyles S, Boggs NA, Nasrallah JB: Natural variation in expression of self-incompatibility in Arabidopsis thaliana: implications for the evolution of selfing. Proc Natl Acad Sci USA. 2004, 101 (45): 16070-16074. 10.1073/pnas.0406970101.PubMed CentralView ArticlePubMedGoogle Scholar
- Mouchel CF, Briggs GC, Hardtke CS: Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. Genes Dev. 2004, 18 (6): 700-714. 10.1101/gad.1187704.PubMed CentralView ArticlePubMedGoogle Scholar
- Lall S, Nettleton D, DeCook R, Che P, Howell SH: Quantitative trait loci associated with adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis. Genet. 2004, 167 (4): 1883-1892. 10.1534/genetics.103.025213.View ArticleGoogle Scholar
- DeCook R, Lall S, Nettleton D, Howell SH: Genetic regulation of gene expression during shoot development in Arabidopsis. Genet. 2006, 172 (2): 1155-1164.View ArticleGoogle Scholar
- Wang Y, Meng Y, Zhang M, Tong X, Wang Q, Sun Y, Quan J, Govers F, Shan W: Infection of Arabidopsis thaliana by Phytophthora parasitica and identification of variation in host specificity. Mol Plant Pathol. 2011, 12 (2): 187-201. 10.1111/j.1364-3703.2010.00659.x.View ArticlePubMedGoogle Scholar
- Grant MR, McDowell JM, Sharpe AG, de Torres ZM, Lydiate DJ, Dangl JL: Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis. Proc Natl Acad Sci USA. 1998, 95 (26): 15843-15848. 10.1073/pnas.95.26.15843.PubMed CentralView ArticlePubMedGoogle Scholar
- Seren U, Vilhjalmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M: GWAPP: a Web application for genome-wide association mapping in arabidopsis. Plant Cell. 2012, 24 (12): 4793-4805. 10.1105/tpc.112.108068.PubMed CentralView ArticlePubMedGoogle Scholar
- Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey MJ, Werner P, Harrap D: Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci USA. 2010, 107 (50): 21611-21616. 10.1073/pnas.1010179107.PubMed CentralView ArticlePubMedGoogle Scholar
- Alheit KV, Maurer HP, Reif JC, Tucker MR, Hahn V, Weissmann EA, Wurschum T: Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack). BMC Genomics. 2012, 13: 235-10.1186/1471-2164-13-235.PubMed CentralView ArticlePubMedGoogle Scholar
- Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P: Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinf. 2008, 2008: 420747-Google Scholar
- Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011, 477 (7365): 419-423. 10.1038/nature10414.View ArticlePubMedGoogle Scholar
- Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011, 43 (10): 956-963. 10.1038/ng.911.View ArticlePubMedGoogle Scholar
- Wang X, Weigel D, Smith LM: Transposon variants and their effects on gene expression in Arabidopsis. PLoS Genet. 2013, 9 (2): e1003255-10.1371/journal.pgen.1003255.PubMed CentralView ArticlePubMedGoogle Scholar
- Laux T, Mayer KFX, Berger J, Jürgens G: The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development. 1996, 122: 87-96.PubMedGoogle Scholar
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28 (10): 2731-2739. 10.1093/molbev/msr121.PubMed CentralView ArticlePubMedGoogle Scholar
- Wurschum T, Gross-Hardt R, Laux T: APETALA2 regulates the stem cell niche in the Arabidopsis shoot meristem. Plant Cell. 2006, 18 (2): 295-307. 10.1105/tpc.105.038398.PubMed CentralView ArticlePubMedGoogle Scholar
- Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL: Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 2002, 129 (2): 440-450. 10.1104/pp.003533.PubMed CentralView ArticlePubMedGoogle Scholar
- Utz HF: PlabMQTL Manual - Software for meta-QTL analysis with composite interval mapping. Version 0.5s. 2012, University of Hohenheim: Institute of Plant Breeding, Seed Science and Population GeneticsGoogle Scholar
- Jansen RC, Stam P: High resolution of quantitative traits into multiple loci via interval mapping. Genet. 1994, 136 (4): 1447-1455.Google Scholar
- Zeng ZB: Precision mapping of quantitative trait loci. Genet. 1994, 136 (4): 1457-1468.Google Scholar
- Haley CS, Knott SA: A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb). 1992, 69 (4): 315-324. 10.1038/hdy.1992.131.View ArticleGoogle Scholar
- Baierl A, Bogdan M, Frommlet F, Futschik A: On locating multiple interacting quantitative trait loci in intercross designs. Genet. 2006, 173 (3): 1693-1703. 10.1534/genetics.105.048108.View ArticleGoogle Scholar
- Churchill GA, Doerge RW: Empirical threshold values for quantitative trait mapping. Genet. 1994, 138 (3): 963-971.Google Scholar
- D’Onofrio C, Cox A, Davies C, Boss PK: Induction of secondary metabolism in grape cell cultures by jasmonates. Funct Plant Biol. 2009, 36 (4): 323-338. 10.1071/FP08280.View ArticleGoogle Scholar
- Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D: Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell. 2006, 18 (5): 1121-1133. 10.1105/tpc.105.039834.PubMed CentralView ArticlePubMedGoogle Scholar
- Hellens R, Mullineaux P, Klee H: Technical focus:a guide to agrobacterium binary Ti vectors. Trends Plant Sci. 2000, 5 (10): 446-451. 10.1016/S1360-1385(00)01740-4.View ArticlePubMedGoogle Scholar
- Eschenfeldt WH, Lucy S, Millard CS, Joachimiak A, Mark ID: A family of LIC vectors for high-throughput cloning and purification of proteins. Methods Mol Biol. 2009, 498: 105-115. 10.1007/978-1-59745-196-3_7.PubMed CentralView ArticlePubMedGoogle Scholar
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