Genetic basis of adaptation: flowering time in Arabidopsis thaliana

 We have mapped QTLs (quantitative trait loci) for an adaptive trait, flowering time, in a selfing annual, Arabidopsis thaliana. To obtain a mapping population we made a cross between an early-summer, annual strain, Li-5, and an individual from a late over-wintering natural population, Naantali. From the backcross to Li-5 298 progeny were grown, of which 93 of the most extreme individuals were genotyped. The data were analysed with both interval mapping and composite interval mapping methods to reveal one major and six minor QTLs, with at least one QTL on each of the five chromosomes. The QTL on chromosome 4 was a major one with an effect of 17.3 days on flowering time and explaining 53.4% of the total variance. The others had effects of at most 6.5 days, and they accounted for only small portions of the variance. Epistasis was indicated between one pair of the QTLs. The result of finding one major QTL and little epistasis agrees with previous studies on flowering time in Arabidopsis thaliana and other species. That several QTLs were found was expected considering the large number of possible candidate loci. In the light of the suggested genetic models of gene action at the candidate loci, epistasis was to be expected. The data showed that major QTLs for adaptive traits can be detected in non-domesticated species. Received: 15 January 1997/Accepted: 21 February 1997     

Events during the first four rounds of mitosis establish three developmental domains in the syncytial endosperm of Arabidopsis thaliana

Summary. Endosperm begins development as a single fertilized cell that undergoes many rounds of mitosis without cytokinesis resulting in a syncytium. The multinucleate cytoplasm is organized by nucleus-based radial microtubule systems into nuclear-cytoplasmic domains. When microtubules are organized into mitotic spindles, the integrity of the common cytoplasm is maintained by an unaltered network of filamentous actin. The first four rounds of mitosis result in the establishment of three developmental domains within the common cytoplasm. The spindles of the first two rounds of mitosis are oriented parallel to the long axis of the central cell, resulting in four nuclear-cytoplasmic domains in a filamentous arrangement. A switch in spindle orientation occurs in the third round of mitosis; all four spindles are oriented perpendicular to the long axis resulting in eight nuclear-cytoplasmic domains arranged in two adjacent files. Whereas the first three rounds of mitosis are synchronous, the fourth occurs as a wave of successive mitoses that begins at the micropylar pole. By the 16-nuclei stage, differences in nuclear shape, cytoskeletal arrays, and cytoplasmic characteristics mark the differentiation of the syncytium into micropylar, central, and chalazal developmental chambers. Nuclei in the micropylar chamber are fusiform and sheathed by parallel microtubules that flare from their tips, while those in the central and chalazal chambers are spherical. Nuclei in the central chamber are surrounded by radial microtubule systems, while those in the chalaza are enmeshed in a reticulum of microtubules. Whereas the cytoplasm in both micropylar and chalazal chambers is dense and nearly nonvacuolate, the syncytium in the central chamber consists of a single layer of evenly spaced nuclear-cytoplasmic domains surrounding a large central vacuole.Correspondence and reprints: Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-2451, U.S.A.Present address: Department of Plant Sciences, University of Arizona, Tucson, Arizona, U.S.A.     

Megasporogenesis in Arabidopsis thaliana L.: an ultrastructural study

 In this study, megasporogenesis of the plant model Arabidopsis thaliana was investigated by electron microscopy for the first time. The data described here could constitute a reference for future investigations of Arabidopsis mutants. During the beginning of meiosis the megaspore mother cell shows a polarity created by unequal distribution of organelles in the cytoplasm. Plastids accumulate in the chalazal region and long parallel saccules of endoplasmic reticulum, small vacuoles and some dictyosomes are found in the micropylar region. Plasmodesmata are abundant in the chalazal cell wall. The nucleus is almost centrally localized and contains a prominent excentric nucleolus and numerous typical synaptonemal complexes. After the second division of meiosis the four megaspores are separated by thin cell walls crossed by numerous plasmodesmata and do not show significant cellular organization. The young functional megaspore is characterized by a large nucleus and a large granular nucleolus. The cytoplasm is very electron dense due to the abundance of free ribosomes and contains the following randomly distributed organelles: mitochondria, a few short saccules of endoplasmic reticulum, dictyosomes and undifferentiated plastids. However, there is no apparent polarity, except for the distribution of some small vacuoles which are more abundant in the micropylar region of the cell. The degenerating megaspores are extremely electron dense and do not show any substructure. Received: 30 July 1998 / Revision accepted: 3 February 1999     

DEAD-box基因家族在拟南芥生长发育中的作用

在RNA代谢过程中,需要许多蛋白和核酸的参与,其中一类蛋白就是RNA解旋酶。RNA解旋酶通过水解ATP获得能量来参与RNA代谢的多个方面,包括核内转录、pre-mRNA的剪切、核糖体发生、核质运输、蛋白质翻译、RNA降解、细胞器内基因的表达。DEAD-box蛋白家族是RNA解旋酶中最大的亚家族,它具有9个保守结构域,因motifyⅡ的保守氨基酸序列Asp-Glu-Ala-Asp(DEAD)而命名。该家族在酵母、拟南芥(Arabidopsis thaliana Heynh.)和人类基因组中都有较多的家庭成员。近年来,研究者对拟南芥DEAD-box蛋白家族的结构和功能进行了一些研究,本文着重总结DEAD-box基因家族对拟南芥生长发育的影响。     

Switch (swi1), an Arabidopsis thaliana mutant affected in the female meiotic switch

In this paper, we describe a novel plant mutant affected exclusively in the female mitosis-meiosis switch. The major effect of the swi1 mutation in Arabidopsis thaliana L. is to delay megasporogenesis events by inserting additional mitotic divisions of the mega- sporocyte. As a result of this delay, megagametogenesis is also affected. The absence of cellular polarity in the megasporocytes was also observed. Ovule ontogenesis is not affected by the mutation. The swi1 mutant is particularly interesting for studying sporophyt-gametophyte interactions. The swi1 mutation, obtained from a T-DNA tagging experiment, is monogenic recessive and mapped on chromosome five, at 16 cM from the yellow inflorescence marker. Received: 29 June 1999 / Revision accepted: 3 August 1999     

Estimating genetic diversity of Arabidopsis thaliana ecotypes with amplified fragment length polymorphisms (AFLP)

The extensive natural variation of Arabidopsis thaliana ecotypes is being increasingly exploited as a source of variants of genes which control (agronomically) important traits. We have subjected 19 different Arabidopsis thaliana ecotypes to an analysis using the anplified fragment length polymorphism (AFLP) technique in order to estimate their genetic diversity. The genetic diversity was estimated applying the method of Nei and Li (1979) and a modified version of it and using 471 informative polymorphisms. The data obtained revealed that within this small set of ecotypes a group of three ecotypes and a further single ecotype exhibit considerable genetic diversity in comparison to the others. These ecotypes clustered at positions significantly separated from the bulk of the ecotypes in the generated similarity plots. The analysis demonstrated the usefulness of the AFLP method for determinating intraspecies genetic diversity as exemplified with Arabidopsis thaliana ecotypes. Results are discussed and compared with data obtained with other methods. Received: 18 June 1999 / Accepted: 28 July 1999     

High-frequency linkage of co-expressing T-DNA in transgenic Arabidopsis thaliana transformed by vacuum-infiltration of Agrobacterium tumefaciens

The efficiency of co-expression and linkage of distinct T-DNAs present in separate Agrobacterium tumefaciens was analysed in Arabidopsis thaliana transformed by the vacuum infiltration method. Co-expression was monitored by the synthesis of three bacterial proteins involved in the production of polyhydroxybutyrate (PHB) in the plastids. Out of 80 kanamycin- resistant transgenic plants analysed, 13 plants were co-transformed with the two distinct T-DNAs and produced PHB. Of those, 7 lines had a kanamycin-resistance segregation ratio consistent with the presence of a single functional insert. Genetic linkage between the distinct T-DNAs was demonstrated for all 13 PHB-producing lines, while physical linkage between the distinct T-DNAs was shown for 12 out of 13 lines. T-DNAs were frequently linked in an inverted orientation about the left borders. Transformation of A. thaliana by the co-infiltration of two A. tumefaciens containing distinct T-DNAs is, thus, an efficient approach for the integration and expression of several transgenes at a single locus. This approach will facilitate the creation and study of novel metabolic pathways requiring the expression of numerous transgenes. Received: 7 May 1999 / Accepted: 28 July 1999     

fist: an Arabidopsis mutant with altered cell division planes and radial pattern disruption during embryogenesis

A T-DNA-tagged, embryo-defective Arabidopsis thaliana mutant, fist, was identified and shown to exhibit defects in nuclear positioning and cell division orientation beginning at the four-cell stage of the embryo proper. Cell division orientation was randomised, with each embryo exhibiting a different pattern. Periclinal divisions did not occur after the eight-cell embryo proper stage and fist embryos lacked a histologically distinct protoderm layer. Terminal embryos resembled globular-stage embryos, but were a disorganised mass containing 30–100 cells. Some terminal embryos (5%) developed xylem-like elements in outer surface cells, indicating that the fist mutation affects radial pattern. A soybean β-conglycinin seed storage protein gene promoter, active in wild-type embryos from heart stage to maturity, was also active in terminal fist embryos despite their disorganised globular state. This indicated that some pathways of cellular differentiation in fist embryos proceed independently of both organised division plane orientation and normal morphogenesis. Endosperm morphogenesis in seeds containing terminal fist embryos was arrested at one of three distinct developmental stages and appeared unlinked to fist embryo morphogenesis. The β-conglycinin seed storage protein gene promoter, normally active in cellularised wild-type endosperm, was inactive in fist endosperm, indicating abnormal development of fist endosperm at the biochemical level. These data indicate that the fist mutation, either directly or indirectly, results in defects in cell division orientation during the early stages of Arabidopsis embryo development. Other aspects of the fist phenotype, such as defects in endosperm development and radial pattern formation, may be related to abnormal cell division orientation or may occur as pleiotropic effects of the fist mutation. Received: 15 July 1997 / Accepted: 9 September 1997     

Hairy root production in Arabidopsis thaliana: cotransformation with a promoter-trap vector results in complex T-DNA integration patterns

 In comparison with the production of transgenic plants, the generation of hairy roots has the advantage that more independent transgenic lines can be produced in a shorter period of time. Therefore, we wanted to combine this approach with the promoter-trapping strategy to identify nematode-induced plant promoters. For the efficient production and culture of transgenic hairy root lines of Arabidopsis thaliana, the standard Agrobacterium rhizogenes transformation procedure was modified to avoid rapid callusing of the hairy roots. An average of 0.72 independent kanamycin-resistant (Km^R) roots were obtained per leaf piece. However, a much lower frequency of reporter gene activation was obtained than expected from experiments with the same vectors in Agrobacterium tumefaciens: of more than 700 independent Km^R hairy roots tested, only 8 were β-glucuronidase (GUS) positive. DNA hybridization was done on ten hairy root lines, of which one had a single truncated T-DNA and the others multiple copies of T-DNA that led to complex hybridization patterns. In a parallel analysis of A. thaliana plants transformed with the same vectors using A. tumefaciens, relatively simple T-DNA integration patterns were obtained. The low occurrence of GUS-positive hairy root lines in our experiments could be explained by the multiple T-DNA copies, especially in inverted array, that result in high frequencies of gene inactivation. Received: 11 August 1998 / Revision received: 17 February 1999 / Accepted: 18 March 1999     

Indole acetonitrile-sensitivity of transgenic tobacco containing Arabidopsis thaliana nitrilase genes

 The Arabidopsis thaliana genome has four nitrilase (nitrile aminohydrolase, EC 3.5.5.1) genes (NIT1 to NIT4). These nitrilases catalyze hydrolysis of indole-3-acetonitrile (IAN) to indole-3-acetic acid (IAA). Growth of A. thaliana is inhibited by IAN probably due to hydrolysis of IAN to IAA, while the tobacco (Nicotiana tabacum) genome has only NIT4 homologs and is resistant to IAN. In this study, we introduced A. thaliana NIT1 to NIT4 into tobacco. Introduction of NIT1, NIT2 or NIT3 into tobacco conferred growth inhibition by IAN. NIT2 transgenic plants were highly sensitive to IAN, and NIT1 and NIT3 transgenic plants were moderately sensitive. On the other hand, NIT4 transgenic plants were less sensitive to IAN, although some morphological changes in the roots were observed as the wild-type tobacco. These findings suggest that the ability of transgenic tobacco to convert IAN to IAA in vivo is markedly different among transgenes of NIT1 to NIT4. Received: 22 November 1999 / Revision received: 28 January 2000 / Accepted: 4 February 2000     

Protophloem differentiation in early Arabidopsis thaliana development

During Arabidopsis embryogenesis, procambial cells undergo coordinated, asymmetric cell divisions, giving rise to vascular precursor cells (protophloem and protoxylem precursors). After germination, these cells terminally differentiate into specialized conducting cells, referred to as protophloem and protoxylem cells. Few readily identifiable markers of the onset of specification and differentiation are available, hampering the molecular genetic analysis of protophloem development. Confocal microscopy was used to investigate the patterning and differentiation of phloem cells during early plant development. Longitudinal divisions of phloem initials allowed the identification of protophloem precursor cells and adjacent metaphloem initials along the length of the plant. During germination, protophloem differentiation was observed at two independent locations, in the cotyledons and the hypocotyl. In both locations, differentiation was concomitant with cell elongation. We identified five gene-trap lines (PD1-PD5) with marker gene expression in immature protophloem elements. The spatio-temporal marker expression pattern of the lines divides them into two groups. The early specification markers PD4 and PD5 were expressed in developing organs before procambium formation and then became restricted to phloem initial cells. The protophloem precursor markers PD1-PD3 were expressed in differentiating protophloem cells at different stages of their development. All markers were expressed transiently and iteratively during the differentiation of protophloem in newly formed organs. Flanking genes were identified for four out of five gene-trap insertion lines. The possible function of these genes with respect to phloem differentiation is discussed.     

Length polymorphism and allele structure of trinucleotide microsatellites in natural accessions of Arabidopsis thaliana

 The objective of this work was to assess the degree of trinucleotide microsatellite length polymorphism in the selfing species Arabidopsis thaliana. PCR amplifications of 12 microsatellite loci among 49 natural populations revealed between one to eight length variants (alleles) for each locus. The average number of alleles per locus was four and the average genetic diversity index was 0.43. Divergence between length variants was investigated at the nucleotide level. Several observations emerge from the sequence data: (1) for most loci, length polymorphism results only from variations in the number of trinucleotide repeats; (2) for a few others, some variability was noted in the flanking sequences; (3) for compound and interrupted loci containing two arrays of trinucleotide repeats, length variations preferentially affect the longest one. Five of the Arabidopsis thaliana accessions were clearly composed of two sublines. In 2 other accessions, some heterozygous individual plants, probably resulting from recent outcrosses, were found. A phylogenetic tree constructed on the basis of trinucleotide microsatellite allelic diversity shows that genetic relationships among the accessions are not correlated with their geographic origin. Received: 4 November 1997 / Accepted: 3 March 1998     

Heteroblasty in Arabidopsis thaliana (L.) Heynh

 Heteroblasty in Arabidopsis thaliana was analyzed in a variety of plants with mutations in leaf morphology using a tissue-specific β-glucuronidase gene marker. Some mutants exhibited their mutant phenotypes specifically in foliage leaves. The phenotypes associated with the foliage-leaf-specific mutations were also found to be induced ectopically in cotyledons in the presence of the lec1 mutation. Moreover, the features of an emf1lec1 double mutant showed that cotyledons can be partially converted into carpelloids. When heteroblastic traits were examined in foliage leaves in the presence of certain mutations or natural deviations by histochemical analysis of the expression of the tissue-specific marker gene, it was found that ectopic expression of the developmental program for the first foliage leaves in lec1 cotyledons seemed to affect the heteroblastic features of the first set of foliage leaves, while foliage leaves beyond the third position appeared normal. Similarly, in wild-type plants, discrepancies in heteroblastic features, relative to standard features, of foliage leaves at early positions seemed to be eliminated in foliage leaves at later positions. These results suggest that heteroblasty in foliage leaves might be affected in part by the heteroblastic stage of the preceding foliage leaves but is finally controlled autonomously at each leaf position. Received: 9 July 1999 / Accepted: 17 August 1999     

Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa

In higher plants, circadian rhythms are highly relevant to a wide range of biological processes. To such circadian rhythms, the clock (oscillator) is central, and recent intensive studies on the model higher plant Arabidopsis thaliana have begun to shed light on the molecular mechanisms underlying the functions of the central clock. Such representative clock-associated genes of A. thaliana are the homologous CCA1 and LHY genes, and five PRR genes that belong to a small family of pseudo-response regulators including TOC1. Others are GI, ZTL, ELF3, ELF4, LUX/PCL1, etc. In this context, a simple question arose as to whether or not the molecular picture of the model Arabidopsis clock is conserved in other higher plants. Here we made an effort to answer the question with special reference to Oryza sativa, providing experimental evidence that this model monocot also has a set of highly conserved clock-associated genes, such as those designated as OsCCA1, OsPRR-series including OsTOC1/OsPRR1, OsZTLs, OsPCL1 as well as OsGI. These results will provide us with insight into the general roles of plant circadian clocks, such as those for the photoperiodic control of flowering time that has a strong impact on the reproduction and yield in many higher plants.     

Polarization predicts the pattern of cellularization in cereal endosperm

Summary The endosperm of cereal grains develops as a multinucleate mass of wall-less cytoplasm (syncytium) that lines the periphery of the central cell before becoming cellular. The pattern of initial wall formation is precisely oriented and is followed by a round of precisely oriented formative cell division that gives rise to initials for the two tissues of endosperm. The initial anticlinal walls form at boundaries of nuclear-cytoplasmic domains (NCDs) defined by radial microtubules emanating from nuclei in the syncytium. Polarized growth of the NCDs in axes perpendicular to the embryo sac wall and centripetal elongation of the anticlinal walls results in a single layer of open ended alveoli overtopped by the remaining syncytial cytoplasm. This arboreal stage, so named because the elongate nucleate columns of cytoplasm resemble an orchard of trees, predicts the division polarity of the imminent formative division. Mitosis occurs as a wave which, like polarization, moves in both directions from ventral to dorsal. Spindles are oriented parallel to the long axis of the alveoli and cell plates give rise to periclinal walls. The outer daughter nuclei (aleurone initials) are thus completely enclosed by walls and the inner nuclei (starchy endosperm initials) are in alveoli adjacent to the central vacuole.     

Blue light-dependent nuclear positioning in Arabidopsis thaliana leaf cells

The plant nucleus changes its intracellular position not only upon cell division and cell growth but also in response to environmental stimuli such as light. We found that the nucleus takes different intracellular positions depending on blue light in Arabidopsis thaliana leaf cells. Under dark conditions, nuclei in mesophyll cells were positioned at the center of the bottom of cells (dark position). Under blue light at 100 mumol m(-2) s(-1), in contrast, nuclei were located along the anticlinal walls (light position). The nuclear positioning from the dark position to the light position was fully induced within a few hours of blue light illumination, and it was a reversible response. The response was also observed in epidermal cells, which have no chloroplasts, suggesting that the nucleus has the potential actively to change its position without chloroplasts. Light-dependent nuclear positioning was induced specifically by blue light at >50 mumol m(-2) s(-1). Furthermore, the response to blue light was induced in phot1 but not in phot2 and phot1phot2 mutants. Unexpectedly, we also found that nuclei as well as chloroplasts in phot2 and phot1phot2 mutants took unusual intracellular positions under both dark and light conditions. The lack of the response and the unusual positioning of nuclei and chloroplasts in the phot2 mutant were recovered by externally introducing the PHOT2 gene into the mutant. These results indicate that phot2 mediates the blue light-dependent nuclear positioning and the proper positioning of nuclei and chloroplasts. This is the first characterization of light-dependent nuclear positioning in spermatophytes.     

Development and disintegration of phragmoplasts in living cultured cells of a GFP::TUA6 transgenic Arabidopsis thaliana plant

Summary.  Cultured suspension cells of Arabidopsis thaliana that stably express a green-fluorescent protein–α-tubulin 6 fusion protein were used to follow the development and disintegration of phragmoplasts. The development and disintegration of phragmoplasts in the living cultured cells could be successively observed by detecting the green-fluorescent protein fluorescence of the microtubules. In the early telophase spindle, where two kinetochore groups and two daughter chromosome groups had completely separated from one another, fluorescence appeared in the interzone between the two chromosome groups. The fluorescent region was gradually condensed at the previous equator and increased in fluorescence intensity, and finally it formed the initial phragmoplast. The initial phragmoplast moved from the cell center towards the cell periphery, and it lost fluorescence at its center and became double rings in shape. The expansion orientation of the phragmoplast was not always the same as that of the future new cell wall before it came in contact with the cell wall. The phragmoplast did not usually come in contact with the cell wall simultaneously with its entire length. A portion of the phragmoplast which was earlier in contact with the cell wall disappeared earlier than other portions of the phragmoplast. The duration of contact between any portions of the phragmoplast and the plasma membrane of the cell wall was 15–30 min. The fluorescence intensity of the cytoplasm did not seem to be elevated by the disintegration of the strongly fluorescent phragmoplast. Received August 8, 2002; accepted September 25, 2002; published online March 11, 2003     

Fast and reliable genotype validation using microsatellite markers in Arabidopsis thaliana

 In this paper we show how rogue genotypes in the parental stocks or contaminants among the crossed progeny of Arabidopsis thaliana can be readily identified and excluded from the breeding process using microsatellite markers derived from a small quantity of intact leaf tissue which has been alkali-treated. This method is fast and cost effective as it does not require DNA extraction, is highly reliable, and is less damaging to small plants where only limited quantities of plant tissue are available. Furthermore, a large number of samples can be processed in 1 day, facilitating the identification process prior to selfing or crossing the plants. In addition, the procedure could potentially be automated since no centrifugation is required. Received: 2 April 1998 / Accepted: 31 May 1998