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M Koornneef

Publications and source records attributed to M Koornneef.

At least 19 recordsLinked to original sources
PubMed2000

Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics.

The definition of gene functions requires the phenotypic characterization of genetic variants. Currently, such functional analysis of Arabidopsis genes is based largely on laboratory-induced mutants that are selected in forward and reverse genetic studies. An alternative complementary source of genetic variation is available: the naturally occurring variation among accessions. The multigenic nature of most of this variation has limited its application until now. However, the use of genetic methods developed to map quantitative trait loci, in combination with the characteristics and resources available for molecular biology in Arabidopsis, allow this variation to be exploited up to the molecular level. Here, we describe the current tools available for the forward genetic analysis of this variation, and review the recent progress in the detection and mapping of loci and the cloning of large-effect genes.

Arabidopsis↗
PubMed2000

Influence of the testa on seed dormancy, germination, and longevity in Arabidopsis.

The testa of higher plant seeds protects the embryo against adverse environmental conditions. Its role is assumed mainly by controlling germination through dormancy imposition and by limiting the detrimental activity of physical and biological agents during seed storage. To analyze the function of the testa in the model plant Arabidopsis, we compared mutants affected in testa pigmentation and/or structure for dormancy, germination, and storability. The seeds of most mutants exhibited reduced dormancy. Moreover, unlike wild-type testas, mutant testas were permeable to tetrazolium salts. These altered dormancy and tetrazolium uptake properties were related to defects in the pigmentation of the endothelium and its neighboring crushed parenchymatic layers, as determined by vanillin staining and microscopic observations. Structural aberrations such as missing layers or a modified epidermal layer in specific mutants also affected dormancy levels and permeability to tetrazolium. Both structural and pigmentation mutants deteriorated faster than the wild types during natural aging at room temperature, with structural mutants being the most strongly affected.

Arabidopsis↗
PubMed2000

Gibberellin requirement for Arabidopsis seed germination is determined both by testa characteristics and embryonic abscisic acid.

The mechanisms imposing a gibberellin (GA) requirement to promote the germination of dormant and non-dormant Arabidopsis seeds were analyzed using the GA-deficient mutant ga1, several seed coat pigmentation and structure mutants, and the abscisic acid (ABA)-deficient mutant aba1. Testa mutants, which exhibit reduced seed dormancy, were not resistant to GA biosynthesis inhibitors such as tetcyclacis and paclobutrazol, contrarily to what was found before for other non-dormant mutants in Arabidopsis. However, testa mutants were more sensitive to exogenous GAs than the wild-types in the presence of the inhibitors or when transferred to a GA-deficient background. The germination capacity of the ga1-1 mutant could be integrally restored, without the help of exogenous GAs, by removing the envelopes or by transferring the mutation to a tt background (tt4 and ttg1). The double mutants still required light and chilling for dormancy breaking, which may indicate that both agents can have an effect independently of GA biosynthesis. The ABA biosynthesis inhibitor norflurazon was partially efficient in releasing the dormancy of wild-type and mutant seeds. These results suggest that GAs are required to overcome the germination constraints imposed both by the seed coat and ABA-related embryo dormancy.

Abscisic Acid↗
PubMed1999

Natural allelic variation at seed size loci in relation to other life history traits of Arabidopsis thaliana.

We have analyzed two Arabidopsis strains differing in the mean seed size and seed number they produced. The accession Cape Verde Islands (Cvi) yielded on average about 40% fewer seeds than the laboratory strain Landsberg erecta (Ler), but Cvi seeds were almost twice as heavy. Maternal and nonmaternal genetic factors were involved in the seed size variation, and interactions between both types of factors presumably occurred. The Ler/Cvi seed size difference increased through seed development from ovule maturation until seed desiccation, suggesting that multiple processes of seed development were affected. In addition, it involved changes in the final cell number and cell size of the seed coat and the embryo. Cell number variation was controlled mainly by maternal factors, whereas nonmaternal allelic variation mostly affected cell size. By using a recombinant inbred line population derived from Ler and Cvi, we mapped quantitative trait loci (QTLs) affecting 12 life history traits related to seed size, fruit size, seed number, and plant resources. Five of the seed size QTLs colocated with QTLs for other traits, suggesting that they control seed size via maternal components affecting ovule number and/or carpel development, ovule development, or reproductive resource allocation in the mother plant. The six remaining putative seed size QTLs did not show a significant effect on any other trait, suggesting that this allelic variation may be involved specifically in seed development processes.

Alleles↗
PubMed1999

Characterization of the gene encoding the apoprotein of phytochrome B2 in tomato, and identification of molecular lesions in two mutant alleles.

The structure of the gene encoding the apoprotein of tomato phytochrome B2 (PHYB2) has been determined from genomic and cDNA sequences. The coding region is organized into four exons, like almost every other angiosperm phytochrome (phy). The deduced phyB2 apoprotein (PHYB2) consists of 1121 amino acids, with 82, 74 and 70% identity to tomato PHYB1, Arabidopsis PHYB, and Arabidopsis PHYD, respectively. In order to facilitate the identification of new mutants, we constructed a double mutant that is deficient in phyA and phyB1. When grown in white light, this mutant becomes only slightly taller than wild type and is similar in phenotype to the monogenic phyB1-deficient mutant. This double mutant has been used as the parent line for mutagenesis with gamma radiation. Several recessive mutants with long hypocotyls and reduced anthocyanin content were selected under white light and screened for mutations in PHYB2, PHYE and PHYF. Two of the triple-mutant lines, designated 55H and 70F, had elongated hypocotyls and fruit trusses, and pale immature fruits. Both belong to the same complementation group and both were found to have defects in PHYB2. Line 70F was found by Northern analysis to have a slightly larger PHYB2 transcript. Part or all of the intron between the second and third exons was found to be retained following RT-PCR of PHYB2 mRNA from line 70F. Three base substitutions were detected near the donor splice site for this intron, including a change from the consensus /GT to /GA at the 5' end of this intron. In every case, the C-terminal 164 amino acids of PHYB2 were replaced by 59 nonsense amino acids followed by a stop codon. Sequencing of PHYB2 from 55H revealed a single-nucleotide deletion near the end of the third exon, resulting in one incorrect codon followed immediately by a stop codon. The predicted mutant apoprotein in 55H is 90 residues shorter than wild-type PHYB2.

Alleles↗
PubMed1999

Importance of the B2 domain of the Arabidopsis ABI3 protein for Em and 2S albumin gene regulation.

Genetic and molecular studies have shown that the Arabidopsis ABSCISIC ACID-INSENSITIVE3 (ABI3) protein plays a prominent role in the control of seed maturation. The ABI3 protein and its orthologues from various other plant species share four domains of high sequence identity, including three basic domains designated as B1, B2 and B3. The leaky abi3-1 mutation is a single amino acid substitution within the B3 domain. A new abi3 allele, abi3-7, was generated by mutagenizing abi3-1 seeds. The abi3-7 line contains, in addition to the abi3-1 mutation, a point mutation that converts residue Ala-458 into Thr within the B2 domain of the ABI3 protein. This Ala residue is absolutely conserved in all known ABI3 orthologues. Abi3-7 seeds display reductions in dormancy and in sensitivity to abscisic acid which are intermediate between those of the leaky abi3-1 and of the severe abi3-4 and abi3-5 mutants. Accumulation and distribution of At2S1 and At2S2 albumin mRNA as well as of AtEm1 and AtEm6 late embryogenesis-abundant proteins and mRNA have been analyzed. Both At2S1 and At2S2 mRNA are reduced in abi3-7, but distribution of At2S2 is spatially restricted. Accumulation of AtEm6 protein is more sensitive to abi3-7 mutation than AtEm1. However both mRNAs are considerably reduced in this mutant. Their distribution is also differentially affected. These results provide genetic evidence for the importance of the conserved B2 domain for ABI3 function in vivo.

2S Albumins, Plant↗
PubMed1999

The BANYULS gene encodes a DFR-like protein and is a marker of early seed coat development.

Mutations in the BANYULS (BAN) gene lead to precocious accumulation of anthocyanins in immature seed coat in Arabidopsis. The ban -1 allele has been isolated from a collection of T-DNA transformants and found to be tagged by the integrative molecule. The sequencing of wild-type and two independent mutant alleles confirmed the identity of the gene. Analysis of the full-length cDNA sequence revealed an open reading frame encoding a 342 amino acid protein which shared strong similarities with DFR and other enzymes of the phenylpropanoid biosynthesis pathway. BAN expression was restricted to the endothelium of immature seeds at the pre-globular to early globular stages of development as predicted from the maternal inheritance of the phenotype, and therefore represents a marker for early differentiation and development of the seed coat. BAN is probably involved in a metabolic channelling between the production of anthocyanins and pro-anthocyanidins in the seed coat.

Alleles↗
PubMed1999

Natural allelic variation identifies new genes in the Arabidopsis circadian system.

We have analysed the circadian rhythm of Arabidopsis thaliana leaf movements in the accession Cvi from the Cape Verde Islands, and in the commonly used laboratory strains Columbia (Col) and Landsberg (erecta) (Ler), which originated in Northern Europe. The parental lines have similar rhythmic periods, but the progeny of crosses among them reveal extensive variation for this trait. An analysis of 48 Ler/Cvi recombinant inbred lines (RILs) and a further 30 Ler/Col RILs allowed us to locate four putative quantitative trait loci (QTLs) that control the period of the circadian clock. Near-isogenic lines (NILs) that contain a QTL in a small, defined chromo- somal region allowed us to confirm the phenotypic effect and to map the positions of three period QTLs, designated ESPRESSO, NON TROPPO and RALENTANDO. Quantitative trait loci at the locations of RALENTANDO and of a fourth QTL, ANDANTE, were identified in both Ler/Cvi and Ler/Col RIL populations. Some QTLs for circadian period are closely linked to loci that control flowering time, including FLC. We show that flc mutations shorten the circadian period such that the known allelic variation in the MADS-box gene FLC can account for the ANDANTE QTL. The QTLs ESPRESSO and RALENTANDO identify new genes that regulate the Arabidopsis circadian system in nature, one of which may be the flowering-time gene GIGANTEA.

Alleles↗
PubMed1999

ANTHOCYANINLESS2, a homeobox gene affecting anthocyanin distribution and root development in Arabidopsis.

The ANTHOCYANINLESS2 (ANL2) gene was isolated from Arabidopsis by using the maize Enhancer-Inhibitor transposon tagging system. Sequencing of the ANL2 gene showed that it encodes a homeodomain protein belonging to the HD-GLABRA2 group. As we report here, this homeobox gene is involved in the accumulation of anthocyanin and in root development. Histological observations of the anl2 mutant revealed that the accumulation of anthocyanin was greatly suppressed in subepidermal cells but only slightly reduced in epidermal cells. Furthermore, the primary roots of the anl2 mutant showed an aberrant cellular organization. We discuss a possible role of ANL2 in the accumulation of anthocyanin and cellular organization of the primary root.

Amino Acid Sequence↗
PubMed1999

The early-flowering mutant efs is involved in the autonomous promotion pathway of Arabidopsis thaliana.

The transition to flowering is a crucial moment in a plant's life cycle of which the mechanism has only been partly revealed. In a screen for early flowering, after mutagenesis of the late-flowering fwa mutant of Arabidopsis thaliana, the early flowering in short days (efs) mutant was identified. Under long-day light conditions, the recessive monogenic efs mutant flowers at the same time as wild type but, under short-day conditions, the mutant flowers much earlier. In addition to its early-flowering phenotype, efs has several pleiotropic effects such as a reduction in plant size, fertility and apical dominance. Double mutant analysis with several late-flowering mutants from the autonomous promotion (fca and fve) and the photoperiod promotion (co, fwa and gi) pathways of flowering showed that efs reduces the flowering time of all these mutants. However, efs is completely epistatic to fca and fve but additive to co, fwa and gi, indicating that EFS is an inhibitor of flowering specifically involved in the autonomous promotion pathway. A vernalisation treatment does not further reduce the flowering time of the efs mutant, suggesting that vernalisation promotes flowering through EFS. By comparing the length of the juvenile and adult phases of vegetative growth for wild-type, efs and the double mutant plants, it is apparent that efs mainly reduces the length of the adult phase.

Arabidopsis↗
PubMed1998

Arabidopsis thaliana: a model plant for genome analysis.

Arabidopsis thaliana is a small plant in the mustard family that has become the model system of choice for research in plant biology. Significant advances in understanding plant growth and development have been made by focusing on the molecular genetics of this simple angiosperm. The 120-megabase genome of Arabidopsis is organized into five chromosomes and contains an estimated 20,000 genes. More than 30 megabases of annotated genomic sequence has already been deposited in GenBank by a consortium of laboratories in Europe, Japan, and the United States. The entire genome is scheduled to be sequenced by the end of the year 2000. Reaching this milestone should enhance the value of Arabidopsis as a model for plant biology and the analysis of complex organisms in general.

Arabidopsis↗
PubMed1998

Paracentromeric sequences on tomato chromosome 6 show homology to human satellite III and to the mammalian CENP-B binding box.

In order to isolate centromeric sequences from tomato (Lycopersicon esculentum) chromosome 6, a large-scale RAPD screen was performed. Among 1500 polymorphic RAPD markers tested, 100 were identified as chromosome 6-specific, using a L. esculentum substitution line carrying chromosome 6 from L. pennellii. Fifty-seven of these markers proved to originate from L. pennellii, and of these, 13 were genetically mapped between the morphological markers yellow virescent (yv) and thiaminless (tl), which flank the centromere. These markers could be assigned to three genetic loci, with 11 of the markers mapping to a single locus. Further resolution of this cluster was achieved using radiation-induced deletions that removed yv or tl but not the centromere. Seven markers were shown to be located outside all of the deletions. These seven markers and three of the other markers of the cluster were cloned and sequenced. Five of the clones are present as single-copy or low-copy-number sequences and five represent middle repetitive sequences. Three sequences show homology to the mammalian CENP-B binding box; clone AG12 contains two of these boxes and also shows homology to human satellite III.

Autoantigens↗
PubMed1998

Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population.

An amplified fragment polymorphism (AFLP) based linkage map has been generated for a new Landsberg erecta/ Cape Verde Islands (Ler/Cvi) recombinant inbred line (RIL) population. A total of 321 molecular PCR based markers and the erecta mutation were mapped. AFLP markers were also analysed in the Landsberg erecta/Columbia (Ler/Col) RIL population (Lister and Dean, 1993) and 395 AFLP markers have been integrated into the previous Arabidopsis molecular map of 122 RFLPs, CAPSs and SSLPs. This enabled the evaluation of the efficiency and robustness of AFLP technology for linkage analyses in Arabidopsis. AFLP markers were found throughout the linkage map. The two RIL maps could be integrated through 49 common markers which all mapped at similar positions. Comparison of both maps led to the conclusion that segregating bands from a common parent can be compared between different populations, and that AFLP bands of similar molecular size, amplified with the same primer combination in two different ecotypes, are likely to correspond to the same locus. AFLPs were found clustering around the centromeric regions, and the authors have established the map position of the centromere of chromosome 3 by a quantitative analysis of AFLP bands using trisomic plants. AFLP markers were also used to estimate the polymorphism rate among the three ecotypes. The larger polymorphism rate found between Ler and Cvi compared to Ler and Col will mean that the new RIL population will provide a useful material to map DNA polymorphisms and quantitative trait loci.

Arabidopsis↗
PubMed1998

Properties of proteins and the glassy matrix in maturation-defective mutant seeds of Arabidopsis thaliana.

In situ Fourier transform infrared microspectroscopy was used to study the heat stability of proteins and hydrogen bonding interactions in dry maturation-defective mutant seeds of Arabidopsis thaliana. alpha-Helical, turn and beta-sheet conformations were the major protein secondary structures in all of these seeds. On heating, intermolecular extended beta-sheet structures, typical of protein denaturation, were formed in abscisic acid-insensitive (abi3) and leafy cotyledon (lec) mutant seeds. Proteins in dry wild-type seeds did not denature up to 150 degrees C, but those in dry desiccation-sensitive, lec1-1, lec1-3 and abi3-5 seeds did at 68, 89 and 87 degrees C, respectively. In the desiccation-tolerant abi3-7 and abi3-1 seeds, denaturation commenced above 120 and 135 degrees C, respectively. Seeds of the aba1-1 abi3-1 double mutant showed signs of denaturation already upon drying. The molecular packing in the seeds was studied by observing the shift in the position of the OH-stretching vibration band with temperature. The maximal rate of change of this band with temperature was much higher in the desiccation-sensitive abi3-5, aba1-1 abi3-1, lec1-1, and lec1-3 mutant seeds than in the desiccation-tolerant wild-type, abi3-1, abi3-7, and lec2-1 seeds. We interpret this to mean that the molecular packing density is higher in dry desiccation-tolerant than in dry desiccation-sensitive seeds, which is associated with a higher or lower protein denaturation temperature, respectively. The results are discussed in relation to the physiological and biochemical characteristics of these mutant seeds.

Arabidopsis↗
PubMed1998

Genetic interactions among late-flowering mutants of Arabidopsis.

Flowering time in Arabidopsis is controlled by a large number of genes, identified by induced mutations. Forty-two double mutants involving 10 of these loci were obtained and analyzed for their flowering behavior under long-day conditions, with and without vernalization, and under short-day conditions. The genetic interactions between the various mutants proved to be complex, although a major epistatic group (called group A) could be identified corresponding to the mutants, which are relatively insensitive to vernalization and daylength. In contrast, the genetic behavior of the mutants much more responsive to these environmental factors (group B) is more complex. The vernalization responsiveness of the group B mutants did not compensate for the lateness of the group A mutants. This indicated that these genes do not control vernalization sensitivity as such, but provide a factor that becomes limiting in short days. The classification of these mutants in different physiological groups is discussed in relation to the detected genetic interactions, and based on these interactions a more detailed model of their role in flowering initiation is proposed.

Arabidopsis↗
PubMed1998

Somatic embryogenesis in Arabidopsis thaliana is facilitated by mutations in genes repressing meristematic cell divisions.

Embryogenesis in plants can commence from cells other than the fertilized egg cell. Embryogenesis initiated from somatic cells in vitro is an attractive system for studying early embryonic stages when they are accessible to experimental manipulation. Somatic embryogenesis in Arabidopsis offers the additional advantage that many zygotic embryo mutants can be studied under in vitro conditions. Two systems are available. The first employs immature zygotic embryos as starting material, yielding continuously growing embryogenic cultures in liquid medium. This is possible in at least 11 ecotypes. A second, more efficient and reproducible system, employing the primordia timing mutant (pt allelic to hpt, cop2, and amp1), was established. A significant advantage of the pt mutant is that intact seeds, germinated in 2,4-dichlorophenoxyacetic acid (2, 4-D) containing liquid medium, give rise to stable embryonic cell cultures, circumventing tedious hand dissection of immature zygotic embryos. pt zygotic embryos are first distinguishable from wild type at early heart stage by a broader embryonic shoot apical meristem (SAM). In culture, embryogenic clusters originate from the enlarged SAMs. pt somatic embryos had all characteristic embryo pattern elements seen in zygotic embryos, but with higher and more variable numbers of cells. Embryogenic cell cultures were also established from seedling, of other mutants with enlarged SAMs, such as clavata (clv). pt clv double mutants showed additive effects on SAM size and an even higher frequency of seedlings producing embryogenic cell lines. pt clv double mutant plants had very short fasciated inflorescence stems and additive effects on the number of rosette leaves. This suggests that the PT and CLV genes act in independent pathways that control SAM size. An increased population of noncommitted SAM cells may be responsible for facilitated establishment of somatic embryogenesis in Arabidopsis.

Arabidopsis↗
PubMed1998

Analysis of natural allelic variation at flowering time loci in the Landsberg erecta and Cape Verde Islands ecotypes of Arabidopsis thaliana.

We have analyzed the flowering behavior of two Arabidopsis ecotypes: the laboratory strain Landsberg erecta (Ler) and an ecotype from the tropical Cape Verde Islands (Cvi). They differ little in their flowering phenotypes and in their responses to photoperiod length changes and to vernalization treatment. However, segregating populations derived from crosses between them showed a much larger variation. An approach of quantitative trait locus (QTL) mapping in recombinant inbred lines (RILs) grown under three environments differing in day-length and/or vernalization treatment has been used to detect and locate flowering loci. Four main QTLs were identified, designated early day-length insensitive (EDI), flowering F, G, and H (FLF, FLG, and FLH, respectively), to which most of the flowering behavior differences could be attributed. To further characterize the individual loci, near isogenic lines were constructed by introgressing Cvi early alleles of EDI and FLH into the Ler genetic background. EDI-Cvi alleles produce earliness under both long- and short-day photoperiods, rendering Ler plants almost day-length neutral. In addition, RILs were selected to analyze FLF and FLG. These loci interact epistatically and RILs carrying late alleles at FLF and FLG were very responsive to vernalization and showed an increased response to photoperiod length changes. The possible role of these loci for the control of flowering is discussed in the context of the current Arabidopsis model.

Alleles↗