Identification of Quantitative Trait Loci Controlling High Calcium Response in Arabidopsis thaliana

Natural variation for primary root growth response to high Ca stress in Arabidopsis thaliana was studied by screening a series of accessions (ecotypes) under high Calcium (40 mM CaCl₂ ) conditions. The genetic basis of this variation was further investigated by QTL analysis using recombinant inbred lines from Landsberg erecta (Ler)×Cape Verde Islands (Cvi) cross. Four QTLs were identified in chromosome 1, 2 and 5,and named response to high Calcium (RHCA) 1–4. The three QTLs (RHCA1, RHCA2 and RHCA4) were further confirmed by analysis of near isogenic lines harboring Cvi introgression fragments in Ler background. Real-time PCR analysis showed that several genes associated with high Ca response including SMT1 and XHT25 have changed expression pattern between Ler and near isogenic lines. These results were useful for detecting molecular mechanisms of plants for high Ca adaption.     

Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements

Background

Histone H3 lysine 27 tri-methylation and lysine 9 di-methylation are independent repressive chromatin modifications in Arabidopsis thaliana. H3K27me3 is established and maintained by Polycomb repressive complexes whereas H3K9me2 is catalyzed by SUVH histone methyltransferases. Both modifications can spread to flanking regions after initialization and were shown to be mutually exclusive in Arabidopsis.

Results

We analyzed the extent of natural variation of H3K27me3 in the two accessions Landsberg erecta (Ler) and Columbia (Col) and their F1 hybrids. The majority of H3K27me3 target genes in Col were unchanged in Ler and F1 hybrids. A small number of Ler-specific targets were detected and confirmed. Consistent with a cis-regulatory mechanism for establishing H3K27me3, differential targets showed allele-specific H3K27me3 in hybrids. Five Ler-specific targets showed the active mark H3K4me3 in Col and for this group, differential H3K27me3 enrichment accorded to expression variation. On the other hand, the majority of Ler-specific targets were not expressed in Col, Ler or 17 other accessions. Instead of H3K27me3, the antagonistic mark H3K9me2 and other heterochromatic features were observed at these loci in Col. These loci were frequently flanked by transposable elements, which were often missing in the Ler genome assembly.

Conclusion

There is little variation in H3K27me3 occupancy within the species, although H3K27me3 targets were previously shown as overrepresented among differentially expressed genes. The existing variation in H3K27me3 seems mostly explained by flanking polymorphic transposable elements. These could nucleate heterochromatin, which then spreads into neighboring H3K27me3 genes, thus converting them to H3K9me2 targets.     

Interaction of jasmonic acid and blue light in the regulation of arabidopsis morphogenesis

The effects of blue light (BL) and jasmonic acid (JA) on morphogenesis of Arabidopsis thaliana (L.) Heynh seedlings of genotypes Col and Ler and their mutants, namely, axr1-3 and jar1-1 mutants resistant to IAA and JA, respectively, and a CRY1 photoreceptor-deficient mutant hy4 were studied. Both 1 μM JA and BL exposure retarded hypocotyl growth of Ler, Col, and jar1-1 seedlings, whereas JA had no effect on hypocotyl growth of axr1-3, but the suppression of hypocotyl growth of this mutant by BL was even more noticeable than that of Ler, Col, and jar1-1. JA and BL applied simultaneously inhibited hypocotyl growth of axr1-3 and especially of Ler, Col, and jar1-1 more than either of factors applied separately. The hy4 mutant did not respond to BL, whereas JA stimulated its hypocotyl growth. JA did not change the cotyledon size of Col, axr1-3, and jar1-1 and reduced the cotyledon size of Ler and hy4. BL enhanced the cotyledon growth of all wild-type and mutant plants used in the study. The cotyledon sizes of all plants except Ler were also increased when JA and BL were applied together. Some of the growth responses correlated with the endogenous IAA and ABA contents. Thus, for example, the hypocotyl and cotyledon growth retardation of Ler seedlings in the presence of JA correlated with a reduced level of free IAA and a considerable increase in the free ABA level in plants grown both in darkness and in BL. Under other growth conditions, no correlation between the endogenous IAA and ABA levels and A. thaliana seedling growth was noted. The interaction between the signal transduction pathways triggered by BL and JA at the early stages of arabidopsis morphogenesis is discussed on the basis of Col, Ler, axr1-3, and jar1-1 hypocotyl growth responses.     

Perturbation of Parentally Biased Gene Expression during Interspecific Hybridization

Interspecific hybridization often induces epigenetic remodeling that leads to transposon activation, gene expression changes, and loss of imprinting. These genomic changes can be deleterious and contribute to postzygotic hybrid incompatibility. In Arabidopsis, loss of genomic imprinting of PHERES1 and presumed failure of Polycomb Repressive Complex contributes to seed inviability observed in A. thaliana X A. arenosa interspecific hybrids. We used this species pair to further analyze the relationship between parentally biased gene expression and postzygotic hybrid incompatibility using two A. thaliana accessions, Col-0 and C24, with differential seed survival. We found that parentally biased expression was perturbed to a similar degree in both A. thaliana hybrids for PHERES1, HDG3, and six other normally paternally expressed genes. We propose that early genome remodeling and loss of imprinting of seed development genes induces lethality in both compatible and incompatible hybrids.     

Light-related loci controlling seed germination in Ler x Cvi and Bay-0 x Sha recombinant inbred-line populations of Arabidopsis thaliana

Background and Aims

Dormancy is a complex trait finely regulated by hormones and environmental factors. The phytochromes that sense red:far-red (R:FR) are the sole photoreceptors involved in the termination of dormancy and the induction of germination by light. The aims of this study were to identify and characterize loci controlling this process in seeds of Arabidopsis thaliana.

Methods

Recombinant inbred lines (RILs) derived from Landsberg erecta and Cape Verde Islands (Ler × Cvi), and Bayreuth and Shahdara (Bay-0 × Sha) were used to map loci related to light effects in seeds previously exposed to chilling and after-ripening periods.

Key Results

Substantial genetic variation was found between accessions of A. thaliana in the induction of germination by light. Twelve loci were identified under R, FR or darkness, some of which were novel loci: DOG8, DOG9, DOG13, DOG14 and DOG15 detected in the Ler × Cvi RIL population; and DOG10, DOG11 and DOG12 mapped in the Bay-0 × Sha RIL population. Furthermore, independent loci were mapped for the induction of germination by low fluence (DOG-LF1 and DOG-LF2) and very low fluence of light (DOG-VLF1) in the Ler × Cvi RIL population. Several loci were confirmed and characterized after different after-ripening and chilling treatments through near-isogenic lines (NILs) and heterogeneous inbred families (HIFs).

Conclusions

The results show that one group of loci act in a wide range of environmental scenarios, whereas a smaller group of loci are relevant only under a narrower set of conditions when the influence of the most-prevalent loci is reduced as a consequence of changes in the physiological status of the seeds. In addition, the identification of specific loci controlling the action modes of the phytochromes improves our understanding of the two independent signalling pathways that promote germination in response to light.Key words: Arabidopsis thaliana, dormancy, germination, phytochromes, very-low-fluence response (VLFR), low-fluence response (LFR), natural genetic variation, quantitative trait loci (QTL), recombinant inbred line (RIL), near-isogenic line (NIL) heterogeneous inbred family (HIF)     

The Role of Cryptochrome 1 and Phytochromes in the Control of Plant Photomorphogenetic Responses to Green Light

We studied the role of cryptochrome 1 (CRY1) and phytochromes in the photomorphogenetic responses of plants to the middle-wavelength region of photosynthetically active radiation. A comparison was performed of green light (GL) action on growth, GA activity and IAA and ABA contents during seedling deetiolation of two Arabidopsis thaliana (L.) Heynh lines of Landsnerg erecta ecotype (wild type Ler and mutant hy4) and of Phaseolus vulgaris L. It was shown that a growth responses of Ler hypocotyls to GL of 515 nm and Ler cotyledons to GL of 542 nm were weaker than those of the hy4 mutant defected in the CRY1 synthesis. Far-red light (730 nm) neutralized the effect of GL (533 nm) on the phytohormone balance in the primary kidney bean leaves. The data obtained permit a supposition that plants possess several photoregulatory systems functioning under GL of higher (515 nm) and lower emission energy (542–553 nm). A possible operation of GL receptors, other than cryptochrome 1 and phytochromes, is discussed.     

eQTL Mapping of Transposon Silencing Reveals a Position-Dependent Stable Escape from Epigenetic Silencing and Transposition of AtMu1 in the Arabidopsis Lineage

Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a smaller scale and how transposons are targeted for silencing. Here, we exploited differential silencing of the AtMu1c transposon in the Arabidopsis thaliana accessions Columbia (Col) and Landsberg erecta (Ler). The difference persisted in hybrids and recombinant inbred lines and was mapped to a single expression quantitative trait locus within a 20-kb interval. In Ler only, this interval contained a previously unidentified copy of AtMu1c, which was inserted at the 3′ end of a protein-coding gene and showed features of expressed genes. By contrast, AtMu1c(Col) was intergenic and associated with heterochromatic features. Furthermore, we identified widespread natural AtMu1c transposition from the analysis of over 200 accessions, which was not evident from alignments to the reference genome. AtMu1c expression was highest for insertions within 3′ untranslated regions, suggesting that this location provides protection from silencing. Taken together, our results provide a species-wide view of the activity of one transposable element at unprecedented resolution, showing that AtMu1c transposed in the Arabidopsis lineage and that transposons can escape epigenetic silencing by inserting into specific genomic locations, such as the 3′ end of genes.     

Effect of jasmonic acid on morphogenesis and photosynthetic pigment level in Arabidopsis seedlings grown under green light

The role of jasmonic acid (JA) in plant photomorhogenesis under green light (GL) was studied. The effect of GL of different intensity (8.1 and 18.1 W/m²) with or without 1 μM JA treatment on growth of plants and photosynthetic pigment level was compared for two types of Arabidopsis thaliana (L.) Heynh. Landsberg erecta ecotype plants: Ler, the wild type, and hy4, a mutant. A much more pronounced growth of hypocotyls and cotyledons of Ler plants in GL was observed compared to that of hy4 with suppressed cryptochrome 1 (cry1), a GL photoreceptor. Treatment with JA in GL caused retardation of hypocotyl and cotyledon growth of Ler plants; however, it stimulated their growth in hy4 plants. JA reduced the chlorophyll a and total carotenoids levels in cotyledons of Arabidopsis plants in GL. Blocked GL signal transduction due to the absence of cry1 in hy4, as well as the higher intensity of GL reduced the negative effect of exogenous JA on growth of cotyledons and photosynthetic pigments. The data obtained provide a basis for discussion of interaction between the JA and GL signals in the growth regulation controlled by cry1. Original Russian Text ? I.F. Golovatskaya, R.A. Karnachuk, 2008, published in Fiziologiya Rastenii, 2008, Vol. 55, No. 2, pp. 240–244.     

Accession-dependent action potentials in Arabidopsis

Plant excitability, as measured by the appearance and circulation of action potentials (APs) after biotic and abiotic stress treatments, is a far lesser and more versatile phenomenon than in animals. To examine the genetic basis of plant excitability we used different Arabidopsis thaliana accessions. APs were induced by wounding (W) with a subsequent deposition (D) of 5 μL of 1 M KCl onto adult leaves. This treatment elicited transient voltage responses (APs) that were detected by 2 extracellular electrodes placed at a distance from the wounding location over an experimental time of 150 min. The first electrode (e1) was placed at the end of the petiole and the beginning of the leaf, and the second (e2) electrode was placed on the petiole near the center of the rosette. All accessions (Columbia (Col), Wassilewskija (Ws) and Landsberg erecta (Ler)) responded to the W & D treatment. After W & D treatment was performed on 100 plants for each accession, the number of APs ranged from 0 to 37 (median 8, total 940), 0 to 16 (median 5, total 528) and 0 to 18 (median 2, total 296) in Col, Ws and Ler, respectively. Responding plants (>0 APs) showed significantly different behaviors depending on their accessions of origin (i.e., Col 91, Ws 83 and Ler 76%). Some AP characteristics, such as amplitude and speed of propagation from e1 to e2 (1.28 mm s⁻¹), were the same for all accessions, whereas the average duration of APs was similar in Col and Ws, but different in Ler. Self-sustained oscillations were observed more frequently in Col than Ws and least often in Ler, and the mean oscillation frequency was more rapid in Col, followed by Ws, and was slowest in Ler. In general, Col was the most excitable accession, followed by Ws, and Ler was the least excitable; this corresponded well with voltage elicited action potentials. In conclusion, part of Arabidopsis excitability in AP responses is genetically pre-determined.     

Recognition and Activation Domains Contribute to Allele-Specific Responses of an Arabidopsis NLR Receptor to an Oomycete Effector Protein

In plants, specific recognition of pathogen effector proteins by nucleotide-binding leucine-rich repeat (NLR) receptors leads to activation of immune responses. RPP1, an NLR from Arabidopsis thaliana, recognizes the effector ATR1, from the oomycete pathogen Hyaloperonospora arabidopsidis, by direct association via C-terminal leucine-rich repeats (LRRs). Two RPP1 alleles, RPP1-NdA and RPP1-WsB, have narrow and broad recognition spectra, respectively, with RPP1-NdA recognizing a subset of the ATR1 variants recognized by RPP1-WsB. In this work, we further characterized direct effector recognition through random mutagenesis of an unrecognized ATR1 allele, ATR1-Cala2, screening for gain-of-recognition phenotypes in a tobacco hypersensitive response assay. We identified ATR1 mutants that a) confirm surface-exposed residues contribute to recognition by RPP1, and b) are recognized by and activate the narrow-spectrum allele RPP1-NdA, but not RPP1-WsB, in co-immunoprecipitation and bacterial growth inhibition assays. Thus, RPP1 alleles have distinct recognition specificities, rather than simply different sensitivity to activation. Using chimeric RPP1 constructs, we showed that RPP1-NdA LRRs were sufficient for allele-specific recognition (association with ATR1), but insufficient for receptor activation in the form of HR. Additional inclusion of the RPP1-NdA ARC2 subdomain, from the central NB-ARC domain, was required for a full range of activation specificity. Thus, cooperation between recognition and activation domains seems to be essential for NLR function.     

Evolutionary Process of the Genomic Sequence Around the 100 Map Unit of Chromosome 1 in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Comparative analysis of nucleotide sequences of the genomic region located around 100 map unit of chromosome 1 using two accessions, Columbia (Col) and Landsberg erecta (Ler), of Arabidopsis thaliana was performed. High divergence was detected between them, and the length of the Ler sequence was half of corresponding sequence of Col. This divergence occurred by tandem duplication, deletion of large regions, and insertion of unrelated sequences. These events led to the high polymorphism of plant disease resistant genes, which are located in the analyzed region. It is highly probable that two-round duplication occurred, and the insertion sequences are transposable elements. The data suggest that the analyzed region had been evolving until quite recently.     

Quantitative trait loci involved in regulating seed oil composition in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> and their evolutionary implications

Fatty acid composition is an important determinant of seed oil quality. Overall, 72 QTL for 12 fatty acid traits that control seed oil composition were identified in four recombinant inbred line (RIL) populations (Ler-0 × Sha, Ler-0 × Col-4, Ler-2 × Cvi, Ler-0 × No-0) of Arabidopsis thaliana. The identified QTL explained 3.2–79.8% of the phenotypic variance; 33 of the 59 QTL identified in the Ler-0 × Sha and the Ler-0 × Col RIL populations co-located with several a priori candidate genes for seed oil composition. QTL for fatty acids 18:1, 18:2, 22:1, and fatty acids synthesized in plastids was identified in both Ler-0 × Sha and Ler-0 × Col-4 RIL populations, and QTL for 16:0 was identified in the Ler-0 × Sha and Ler-0 × No-0 RIL populations providing strong support for the importance of these QTL in determining seed oil composition. We identified melting point QTL in three RIL populations, and fatty acid QTL collocated with two of them, suggesting that the loci could be under selection for altering the melting point of seed oils to enhance adaptation and could be useful for breeding purposes. Nuclear-cytoplasmic interactions and epistasis were rare. Analysis of the genetic correlations between these loci and other fatty acids indicated that these correlations would tend to strongly enhance selection for desirable fatty acids.     

Incompatibility between Flac, R386, and F:pSC101 recombinant plasmids: the specificity of F incompatibility genes.

The specificity of F incompatibility genes (inc⁺) has been studied with the Flac and R386 plasmids, members of the IncFI incompatibility group. Recently, two inc⁺ regions, incA (46.4–49.3F) and incB (43.1–46.4F) were identified by cloning these F sequences onto pSC101 and subsequently demonstrating incompatibility of the recombinants with Flac. It is shown here that the FincA⁺ recombinant is incompatible with both Flac and R386 while the FincB⁺ recombinant is incompatible only with Flac. Also, a plasmid mutant is described that has reduced incompatibility against Flac and R386. The mutation is located on the BamHI restriction fragment that contains the FincA region. These genetic findings are consistent with the deduction of Palchaudhuri and Maas, based on heteroduplex analysis of IncFI plasmids, that placed the IncFI determinant in the 46.4–48.6F region. The findings also indicate that the FincB⁺ gene product, which has been implicated in negative control of F copy number, is specific for the F replicon.     

Genetics and Lineage-Specific Evolution of a Lethal Hybrid Incompatibility Between Drosophila mauritiana and Its Sibling Species

The Dobzhansky–Muller model posits that intrinsic postzygotic reproductive isolation—the sterility or lethality of species hybrids—results from the evolution of incompatible epistatic interactions between species: favorable or neutral alleles that become fixed in the genetic background of one species can cause sterility or lethality in the genetic background of another species. The kind of hybrid incompatibility that evolves between two species, however, depends on the particular evolutionary history of the causative substitutions. An allele that is functionally derived in one species can be incompatible with an allele that is functionally derived in the other species (a derived-derived hybrid incompatibility). But an allele that is functionally derived in one species can also be incompatible with an allele that has retained the ancestral state in the other species (a derived-ancestral hybrid incompatibility). The relative abundance of such derived-derived vs. derived-ancestral hybrid incompatibilities is unknown. Here, we characterize the genetics and evolutionary history of a lethal hybrid incompatibility between Drosophila mauritiana and its two sibling species, D. sechellia and D. simulans. We show that a hybrid lethality factor(s) in the pericentric heterochromatin of the D. mauritiana X chromosome, hybrid lethal on the X (hlx), is incompatible with a factor(s) in the same small autosomal region from both D. sechellia and D. simulans, Suppressor of hlx [Su(hlx)]. By combining genetic and phylogenetic information, we infer that hlx-Su(hlx) hybrid lethality is likely caused by a derived-ancestral incompatibility, a hypothesis that can be tested directly when the genes are identified.     

DELLA蛋白缺失对拟南芥干旱胁迫耐受性的影响

为探索DELLA蛋白缺失对拟南芥耐旱能力的影响,对拟南芥野生型Ler和DELLA蛋白缺失突变体della进行干旱处理,测定存活率、萌发率、离体叶片的失水率、脯氨酸、可溶性糖和丙二醛含量,并对发挥植物细胞脱水保护功能的胚胎晚期丰富蛋白编码基因LEA和ABA应答基因LOX3、COR15b、COR413的表达量进行了检测。结果表明:(1)干旱21d后复水,della突变体的存活率明显高于野生型Ler;(2)della突变体在含甘露醇的固体培养基上的萌发率显著高于Ler;(3)della突变体离体叶片的失水速率明显低于Ler;(4)干旱胁迫后,della突变体脯氨酸、可溶性糖和丙二醛含量的积累低于Ler;(5)干旱胁迫后,della突变体的LEA基因上调表达程度高于Ler,而ABA应答基因上调表达程度低于Ler。研究表明,DELLA蛋白的缺失有助于提高植物抗旱能力。     

Effect of gibberellin on <Emphasis Type="Italic">Arabidopsis</Emphasis> growth,development, and hormonal balance under green and blue light

The role of gibberellins in plant morphology under selective light was studied. A comparison of the effects of green and blue light on growth, development, and hormonal balance was performed for two Arabidopsis thaliana (L.) Heynh. (ecotype Landsberg erecta lines: wild type Ler and its ga4-1 mutant with suppressed GA_4/1 synthesis. The absence of active GA_4/1 from ga4-1 mutant determined its retarded growth, slowed passing through developmental phases, suppressed apical dominance, and reduced seed productivity. The retarded growth and development of the mutant was related to changed hormonal balance in them as compared to wild-type line: IAA content and the IAA/ABA ratio were declined, zeatin riboside and ABA accumulated. Green light retarded stem elongation and branching, reduced leaf specific surface density and plant seed productivity, and retarded plant transition to reproduction to a greater degree at GA_4/1 deficit (ga4-1) than at its normal content (Ler).