Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region

Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes

Nuclear transcription is not restricted to genes but occurs throughout the intergenic and noncoding space of eukaryotic genomes. The functional significance of this widespread noncoding transcription is mostly unknown. We show that Arabidopsis RNA polymerase IVb/Pol V, a multisubunit nuclear enzyme required for siRNA-mediated gene silencing of transposons and other repeats, transcribes intergenic and noncoding sequences, thereby facilitating heterochromatin formation and silencing of overlapping and adjacent genes. Pol IVb/Pol V transcription requires the chromatin-remodeling protein DRD1 but is independent of siRNA biogenesis. However, Pol IVb/Pol V transcription and siRNA production are both required to silence transposons, suggesting that Pol IVb/Pol V generates RNAs or chromatin structures that serve as scaffolds for siRNA-mediated heterochromatin-forming complexes. Pol IVb/Pol V function provides a solution to a paradox of epigenetic control: the need for transcription in order to transcriptionally silence the same region.

Molecular analysis of a large subtelomeric nucleotide-binding-site-leucine-rich-repeat family in two representative genotypes of the major gene pools of Phaseolus vulgaris

In common bean, the B4 disease resistance gene cluster is a complex cluster localized at the end of linkage group (LG) B4, containing at least three R specificities to the fungus Colletotrichum lindemuthianum. To investigate the evolution of this R cluster since the divergence of Andean and Mesoamerican gene pools, DNA sequences were characterized from two representative genotypes of the two major gene pools of common bean (BAT93: Mesoamerican; JaloEEP558: Andean). Sequences encoding 29 B4-CC nucleotide-binding-site-leucine-rich-repeat (B4-CNL) genes were determined-12 from JaloEEP558 and 17 from BAT93. Although sequence exchange events were identified, phylogenetic analyses revealed that they were not frequent enough to lead to homogenization of B4-CNL sequences within a haplotype. Genetic mapping based on pulsed-field gel electrophoresis separation confirmed that the B4-CNL family is a large family specific to one end of LG B4 and is present at two distinct blocks separated by 26 cM. Fluorescent in situ hybridization on meiotic pachytene chromosomes revealed that two B4-CNL blocks are located in the subtelomeric region of the short arm of chromosome 4 on both sides of a heterochromatic block (knob), suggesting that this peculiar genomic environment may favor the proliferation of a large R gene cluster.

Chromosomal phylogeny and karyotype evolution in x=7 crucifer species (Brassicaceae)

Karyotype evolution in species with identical chromosome number but belonging to distinct phylogenetic clades is a long-standing question of plant biology, intractable by conventional cytogenetic techniques. Here, we apply comparative chromosome painting (CCP) to reconstruct karyotype evolution in eight species with x=7 (2n=14, 28) chromosomes from six Brassicaceae tribes. CCP data allowed us to reconstruct an ancestral Proto-Calepineae Karyotype (PCK; n=7) shared by all x=7 species analyzed. The PCK has been preserved in the tribes Calepineae, Conringieae, and Noccaeeae, whereas karyotypes of Eutremeae, Isatideae, and Sisymbrieae are characterized by an additional translocation. The inferred chromosomal phylogeny provided compelling evidence for a monophyletic origin of the x=7 tribes. Moreover, chromosomal data along with previously published gene phylogenies strongly suggest the PCK to represent an ancestral karyotype of the tribe Brassiceae prior to its tribe-specific whole-genome triplication. As the PCK shares five chromosomes and conserved associations of genomic blocks with the putative Ancestral Crucifer Karyotype (n=8) of crucifer Lineage I, we propose that both karyotypes descended from a common ancestor. A tentative origin of the PCK via chromosome number reduction from n=8 to n=7 is outlined. Comparative chromosome maps of two important model species, Noccaea caerulescens and Thellungiella halophila, and complete karyotypes of two purported autotetraploid Calepineae species (2n=4x=28) were reconstructed by CCP.

Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements

Ongoing genomics projects of tomato (Solanum lycopersicum) and potato (S. tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, bacterial artificial chromosomes (BACs) can be positioned on pachytene complements by fluorescence in situ hybridization (FISH) on homeologous chromosomes of related species. Here we present results of such a cross-species multicolor cytogenetic mapping of tomato BACs on potato chromosomes 6 and vice versa. The experiments were performed under low hybridization stringency, while blocking with Cot-100 was essential in suppressing excessive hybridization of repeat signals in both within-species FISH and cross-species FISH of tomato BACs. In the short arm we detected a large paracentric inversion that covers the whole euchromatin part with breakpoints close to the telomeric heterochromatin and at the border of the short arm pericentromere. The long arm BACs revealed no deviation in the colinearity between tomato and potato. Further comparison between tomato cultivars Cherry VFNT and Heinz 1706 revealed colinearity of the tested tomato BACs, whereas one of the six potato clones (RH98-856-18) showed minor putative rearrangements within the inversion. Our results present cross-species multicolor BAC-FISH as a unique tool for comparative genetic studies across Solanum species.

Chromatin structure and physical mapping of chromosome 6 of potato and comparative analyses with tomato

Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 genetic marker-anchored bacterial artificial chromosome (BAC) clones on the pachytene chromosome 6 of potato. The FISH mapping results allowed us to define the genetic positions of the centromere and the pericentromeric heterochromatin and to relate chromatin structure to the distribution of recombination along the chromosome. A drastic reduction of recombination was associated with the pericentromeric heterochromatin that accounts for approximately 28% of the physical length of the pachytene chromosome. The pachytene chromosomes 6 of potato and tomato (S. lycopersicum) share a similar morphology. However, distinct differences of heterochromatin distribution were observed between the two chromosomes. FISH mapping of several potato BACs on tomato pachytene chromosome 6 revealed an overall colinearity between the two chromosomes. A chromosome inversion was observed in the euchromatic region of the short arms. These results show that the potato and tomato genomes contain more chromosomal rearrangements than those reported previously on the basis of comparative genetic linkage mapping.

Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes

Genetic evidence suggests that indole-3-butyric acid (IBA) is converted to the active auxin indole-3-acetic acid (IAA) by removal of two side-chain methylene units in a process similar to fatty acid beta-oxidation. Previous studies implicate peroxisomes as the site of IBA metabolism, although the enzymes that act in this process are still being identified. Here, we describe two IBA-response mutants, ibr1 and ibr10. Like the previously described ibr3 mutant, which disrupts a putative peroxisomal acyl-CoA oxidase/dehydrogenase, ibr1 and ibr10 display normal IAA responses and defective IBA responses. These defects include reduced root elongation inhibition, decreased lateral root initiation, and reduced IBA-responsive gene expression. However, peroxisomal energy-generating pathways necessary during early seedling development are unaffected in the mutants. Positional cloning of the genes responsible for the mutant defects reveals that IBR1 encodes a member of the short-chain dehydrogenase/reductase family and that IBR10 resembles enoyl-CoA hydratases/isomerases. Both enzymes contain C-terminal peroxisomal-targeting signals, consistent with IBA metabolism occurring in peroxisomes. We present a model in which IBR3, IBR10, and IBR1 may act sequentially in peroxisomal IBA beta-oxidation to IAA.

Integration of cytogenetic and genetic linkage maps unveils the physical architecture of tomato chromosome 2

We report the integration of the linkage map of tomato chromosome 2 with a high-density bacterial artificial chromosome fluorescence in situ hybridization (BAC-FISH)-based cytogenetic map. The euchromatic block of chromosome 2 resides between 13 and 142 cM and has a physical length of 48.12 microm, with 1 microm equivalent to 540 kb. BAC-FISH resolved a pair of loci that were 3.7-3.9 Mb apart and were not resolved on the linkage map. Most of the regions had crossover densities close to the mean of approximately 200 kb/cM. Relatively hot and cold spots of recombination were unevenly distributed along the chromosome. The distribution of centimorgan/micrometer values was similar to the previously reported recombination nodule distribution along the pachytene chromosome. FISH-based physical maps will play an important role in advanced genomics research for tomato, including map-based cloning of agronomically important traits and whole-genome sequencing.

Cytological investigation of Haplopappus gracilis (Nutt.) Gray: 5-methylcytosine-rich regions, fluorochrome banding and chromatin sensitivity to DNase I digestion

Haplopappus gracilis (Nutt.) Gray, one of the five known higher plants with a chromosome number of 2n = 4, was studied from a cytological point of view. The chromosome complement of this species was characterized by means of automated karyotype analysis. Moreover, the DNA methylation pattern and fluorochrome banding were determined and compared with cytological data present in the literature. DNA methylation distribution along metaphase chromosomes involved all chromosome territories evidenced by C-banding. Other methylated bands correlated positively with aceto-orcein-positive heterochromatic portions and/or with late replicating bands and/or fluorochrome bands. Some methylated bands showed differences between homologous chromosomes. These bands belonged partly to certain heterochromatic domains and partly to intercalary sites not defined by other standard banding techniques. Differences between the homologues were also indicated by our DNA content data obtained after DNase I digestion.

RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids

Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant A. thaliana and A. arenosa genomes that are homeologous in the allotetraploid. Here we report that RNAi of met1 reduced DNA methylation and altered the expression of approximately 200 genes, many of which encode transposons, predicted proteins, and centromeric and heterochromatic RNAs. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes, and an En/Spm-like transposon was reactivated in met1-RNAi A. suecica lines. Derepression of transposons, heterochromatic repeats, and centromeric small RNAs was primarily derived from the A. thaliana genome, and A. arenosa homeologous loci were less affected by methylation defects. A high level of A. thaliana centromeric small RNA accumulation was correlated with hypermethylation of A. thaliana centromeres. The greater effects of reduced DNA methylation on transposons and centromeric repeats in A. thaliana than in A. arenosa are consistent with the repression of many genes that are expressed at higher levels in A. thaliana than in A. arenosa in the resynthesized allotetraploids. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 remained in the resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810. At2g23810 was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that many A. thaliana genes are transcriptionally repressed in resynthesized allotetraploids, and a subset of A. thaliana loci including transposons and centromeric repeats are heavily methylated and subjected to homeologous genome-specific RNA-mediated DNA methylation in natural allopolyploids.

Cytological characterization of the tandem repetitive sequences and their methylation status in the Antirrhinum majus genome

Tandem repetitive sequences are DNA motifs common in the genomes of eukaryotic species and are often embedded in heterochromatic regions. In most eukaryotes, ribosomal genes, as well as centromeres and telomeres or subtelomeres, are associated with abundant tandem arrays of repetitive sequences and typically represent the final barriers to completion of whole-genome sequencing. The nature of these repeats makes it difficult to estimate their actual sizes. In this study, combining the two cytological techniques DNA fiber-FISH and pachytene chromosome FISH allowed us to characterize the tandem repeats distributed genome wide in Antirrhinum majus and identify four types of tandem repeats, 45S rDNA, 5S rDNA, CentA1, and CentA2, representing the major tandem repetitive components, which were estimated to have a total length of 18.50 Mb and account for 3.59% of the A. majus genome. FISH examination revealed that all the tandem repeats correspond to heterochromatic knobs along the pachytene chromosomes. Moreover, the methylation status of the tandem repeats was investigated in both somatic cells and pollen mother cells from anther tissues using an antibody against 5-methylcytosine combined with sequential FISH analyses. Our results showed that these repeats were hypomethylated in anther tissues, especially in the pollen mother cells at pachytene stage.

Quantitative trait loci mapping in five new large recombinant inbred line populations of Arabidopsis thaliana genotyped with consensus single-nucleotide polymorphism markers

Quantitative approaches conducted in a single mapping population are limited by the extent of genetic variation distinguishing the parental genotypes. To overcome this limitation and allow a more complete dissection of the genetic architecture of complex traits, we built an integrated set of 15 new large Arabidopsis thaliana recombinant inbred line (RIL) populations optimized for quantitative trait loci (QTL) mapping, having Columbia as a common parent crossed to distant accessions. Here we present 5 of these populations that were validated by investigating three traits: flowering time, rosette size, and seed production as an estimate of fitness. The large number of RILs in each population (between 319 and 377 lines) and the high density of evenly spaced genetic markers scored ensure high power and precision in QTL mapping even under a minimal phenotyping framework. Moreover, the use of common markers across the different maps allows a direct comparison of the QTL detected within the different RIL sets. In addition, we show that following a selective phenotyping strategy by performing QTL analyses on genotypically chosen subsets of 164 RILs (core populations) does not impair the power of detection of QTL with phenotypic contributions >7%.

The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

BACKGROUND

A series of Rps (resistance to Pytophthora sojae) genes have been protecting soybean from the root and stem rot disease caused by the Oomycete pathogen, Phytophthora sojae. Five Rps genes were mapped to the Rps1 locus located near the 28 cM map position on molecular linkage group N of the composite genetic soybean map. Among these five genes, Rps1-k was introgressed from the cultivar, Kingwa. Rps1-k has been providing stable and broad-spectrum Phytophthora resistance in the major soybean-producing regions of the United States. Rps1-k has been mapped and isolated. More than one functional Rps1-k gene was identified from the Rps1-k locus. The clustering feature at the Rps1-k locus might have facilitated the expansion of Rps1-k gene numbers and the generation of new recognition specificities. The Rps1-k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean.

RESULTS

Here the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1-k region are reported. A shotgun sequencing strategy was applied in sequencing the BAC contig. Sequence analysis predicted a few full-length genes including two Rps1-k genes, Rps1-k-1 and Rps1-k-2. Previously reported Rps1-k-3 from this genomic region 1 was evolved through intramolecular recombination between Rps1-k-1 and Rps1-k-2 in Escherichia coli. The majority of the predicted genes are truncated and therefore most likely they are nonfunctional. A member of a highly abundant retroelement, SIRE1, was identified from the Rps1-k region. The Rps1-k region is primarily composed of repetitive sequences. Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus.

CONCLUSION

These data indicate that the Rps1 locus is located in a gene-poor region. The abundance of repetitive sequences in the Rps1-k region suggested that the location of this locus is in or near a heterochromatic region. Poor recombination frequencies combined with presence of two functional Rps genes at this locus has been providing stable Phytophthora resistance in soybean.

Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development

To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

We used hybridization to the ATH1 gene expression array to interrogate genomic DNA diversity in 23 wild strains (accessions) of Arabidopsis thaliana (arabidopsis), in comparison with the reference strain Columbia (Col). At <1% false discovery rate, we detected 77,420 single-feature polymorphisms (SFPs) with distinct patterns of variation across the genome. Total and pair-wise diversity was higher near the centromeres and the heterochromatic knob region, but overall diversity was positively correlated with recombination rate (R(2) = 3.1%). The difference between total and pair-wise SFP diversity is a relative measure contrasting diversifying or frequency-dependent selection, similar to Tajima's D, and can be calibrated by the empirical genome-wide distribution. Each unique locus, centered on a gene, has a diversity and selection score that suggest a relative role in past evolutionary processes. Homologs of disease resistance (R) genes include members with especially high levels of diversity often showing frequency-dependent selection and occasionally evidence of a past selective sweep. Receptor-like and S-locus proteins also contained members with elevated levels of diversity and signatures of selection, whereas other gene families, bHLH, F-box, and RING finger proteins, showed more typical levels of diversity. SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http://signal.salk.edu/cgi-bin/AtSFP.

Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells

Chromocenters in Arabidopsis thaliana are discrete nuclear domains of mainly pericentric heterochromatin. They are characterized by the presence of repetitive sequences, methylated DNA and dimethylated histone H3K9. Here we show that dedifferentiation of specialized mesophyll cells into undifferentiated protoplasts is accompanied by the disruption of chromocenter structures. The dramatic reduction of heterochromatin involves the decondensation of all major repeat regions, also including the centromeric 180 bp tandem repeats. Only the 45S rDNA repeat remained in a partly compact state in most cells. Remarkably, the epigenetic indicators for heterochromatin, DNA methylation and H3K9 dimethylation, did not change upon decondensation. Furthermore, the decondensation of pericentric heterochromatin did not result in transcriptional reactivation of silent genomic elements. The decondensation process was reversible upon prolonged culturing. Strikingly, recondensation of heterochromatin into chromocenters is a stepwise process. Compaction of the tandemly arranged 45S rDNA regions occurs first, followed by the centromeric 180 bp and the 5S rDNA repeats and finally the dispersed repeats, including transposons. The sequence of reassembly seems to be correlated to the size of the repeat domains. Our results indicate that different types of pericentromeric repeats form different types of heterochromatin, which subsequently merge to form a chromocenter.

Rice as a model for centromere and heterochromatin research

Rice (Oryza sativa) has become an important model plant species in numerous research projects involving genome, molecular and evolutionary biology. In this review we describe the reasons why rice provides an excellent model system for centromere and heterochromatin research. In most multicellular eukaryotes, centromeres and heterochromatic domains contain long arrays of repetitive DNA elements that are recalcitrant to DNA sequencing. In contrast, three rice centromeres and the majority of the cytologically defined heterochromatin in the rice genome have been sequenced to high quality, providing an unparalleled resource compared to other model multicellular eukaryotes. Most importantly, active genes have been discovered in the functional domains of several rice centromeres. The centromeric genes and sequence resources provide an unprecedented opportunity to study function and evolution of centromeres and centromere-associated genes.

Recombination: an underappreciated factor in the evolution of plant genomes

Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.

Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research

Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic loci. FISH-based physical mapping provides a valuable complementary approach in genome sequencing and map-based cloning research. We expect that FISH will continue to play an important role in relating DNA sequence information to chromosome biology. FISH coupled with immunoassays will be increasingly used to study features of chromatin at the cytological level that control expression and regulation of genes.

Analysis of the subcellular localization, function, and proteolytic control of the Arabidopsis cyclin-dependent kinase inhibitor ICK1/KRP1

Recent studies have shown that cyclin-dependent kinase (CDK) inhibitors can have a tremendous impact on cell cycle progression in plants. In animals, CDK inhibitors are tightly regulated, especially by posttranslational mechanisms of which control of nuclear access and regulation of protein turnover are particularly important. Here we address the posttranslational regulation of INHIBITOR/INTERACTOR OF CDK 1 (ICK1)/KIP RELATED PROTEIN 1 (KRP1), an Arabidopsis (Arabidopsis thaliana) CDK inhibitor. We show that ICK1/KRP1 exerts its function in the nucleus and its presence in the nucleus is controlled by multiple nuclear localization signals as well as by nuclear export. In addition, we show that ICK1/KRP1 localizes to different subnuclear domains, i.e. in the nucleoplasm and to the chromocenters, hinting at specific actions within the nuclear compartment. Localization to the chromocenters is mediated by an N-terminal domain, in addition we find that this domain may be involved in cyclin binding. Further we demonstrate that ICK1/KRP1 is an unstable protein and degraded by the 26S proteasome in the nucleus. This degradation is mediated by at least two domains indicating the presence of at least two different pathways impinging on ICK1/KRP1 protein stability.

A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization

Recombinant populations were the basis for Mendel's first genetic experiments and continue to be key to the study of genes, heredity, and genetic variation today. Genotyping several hundred thousand loci in a single assay by hybridizing genomic DNA to oligonucleotide arrays provides a powerful technique to improve precision linkage mapping. The genotypes of two accessions of Arabidopsis were compared by using a 400,000 feature exon-specific oligonucleotide array. Around 16,000 single feature polymorphisms (SFPs) were detected in ~8,000 of the ~26,000 genes represented on the array. Allelic variation at these loci was measured in a recombinant inbred line population, which defined the location of 815 recombination breakpoints. The genetic linkage map had a total length of 422.5 cM, with 676 informative SFP markers representing intervals of ~0.6 cM. One hundred fifteen single gene intervals were identified. Recombination rate, SFP distribution, and segregation in this population are not uniform. Many genomic regions show a clustering of recombination events including significant hot spots. The precise haplotype structure of the recombinant population was defined with unprecedented accuracy and resolution. The resulting linkage map allows further refinement of the hundreds of quantitative trait loci identified in this well-studied population. Highly variable recombination rates along each chromosome and extensive segregation distortion were observed in the population.

A goal of many genetic studies is to discover the underlying genetic condition (the genotype) of a specific physical manifestation in an organism (the phenotype), such as diabetes in humans or leaf rust in cultivated wheat. A limitation to making such discoveries is the ability to resolve genotype. Gene arrays carry representations of the genome, called features, at high-density on a surface the size of a thumbnail. In this study, microarrays designed to measure gene expression were used to detect DNA sequence polymorphisms. DNA from two different Arabidopsis strains was hybridized to arrays representing nearly the entire coding region of the genome. Differences in hybridization intensity indicated differences in DNA sequence. The sequence differences, termed single feature polymorphisms, were then assayed in a population of 100 plants derived through inbreeding the progeny from the two parental strains. The precise location of the genetic recombination breakpoints was defined for each line. As a result, Singer et al. were able to generate one of the first very high-resolution genotyping data sets in a multicellular organism that allowed the construction of a high-resolution genetic map of Arabidopsis. This map will greatly facilitate attempts to make definitive associations between genotypes and phenotypes.

Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat

In this paper we describe a pair of novel Ty3/gypsy retrotransposons isolated from the dioecious plant Silene latifolia, consisting of a non-autonomous element Retand-1 (3.7 kb) and its autonomous partner Retand-2 (11.1 kb). These two elements have highly similar long terminal repeat (LTR) sequences but differ in the presence of the typical retroelement coding regions (gag-pol genes), most of which are missing in Retand-1. Moreover, Retand-2 contains two additional open reading frames in antisense orientation localized between the pol gene and right LTR. Retand transcripts were detected in all organs tested (leaves, flower buds and roots) which, together with the high sequence similarity of LTRs in individual elements, indicates their recent transpositional activity. The autonomous elements are similarly abundant (2,700 copies) as non-autonomous ones (2,100 copies) in S. latifolia genome. Retand elements are also present in other Silene species, mostly in subtelomeric heterochromatin regions of all chromosomes. The only exception is the subtelomere of the short arm of the Y chromosome in S. latifolia which is known to lack the terminal heterochromatin. An interesting feature of the Retand elements is the presence of a tandem repeat sequence, which is more amplified in the non-autonomous Retand-1.

History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement

We propose an evolutionary scenario that could have shaped the modern Arabidopsis thaliana genome, which began with the reduction in chromosome number from n=8 to n=5 in the past 4 million to 5 million years as a result of chromosome fusion. The scenario also includes three ancient polyploidizations: the most recent occurred in an early Brassicaceae with n=4 chromosomes 24 million to 40 million years ago. The two other polyploidizations occurred after the emergence of the Eudicots and the Angiosperms, respectively. Angiosperm evolution includes recurrent cycles of genome duplication and gene and chromosome reorganizations.

A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome

The detection of footprints of natural selection in genetic polymorphism data is fundamental to understanding the genetic basis of adaptation, and has important implications for human health. The standard approach has been to reject neutrality in favor of selection if the pattern of variation at a candidate locus was significantly different from the predictions of the standard neutral model. The problem is that the standard neutral model assumes more than just neutrality, and it is almost always possible to explain the data using an alternative neutral model with more complex demography. Today's wealth of genomic polymorphism data, however, makes it possible to dispense with models altogether by simply comparing the pattern observed at a candidate locus to the genomic pattern, and rejecting neutrality if the pattern is extreme. Here, we utilize this approach on a truly genomic scale, comparing a candidate locus to thousands of alleles throughout the Arabidopsis thaliana genome. We demonstrate that selection has acted to increase the frequency of early-flowering alleles at the vernalization requirement locus FRIGIDA. Selection seems to have occurred during the last several thousand years, possibly in response to the spread of agriculture. We introduce a novel test statistic based on haplotype sharing that embraces the problem of population structure, and so should be widely applicable.

The origin, meiotic behavior, and transmission of a novel minichromosome in Arabidopsis thaliana

A plant carrying a small extra chromosome was found in Landsberg erecta ecotype of Arabidopsis thaliana. Fluorescence in situ hybridization revealed that this minichromosome was derived from the short arm of chromosome 4. The size of this "mini4S" chromosome was estimated to be approximately 7.5 Mb on the basis of previously reported data and the amount of the centromeric major satellite (180-bp family) present, which was determined to be about 1 Mb, or about one third of that in the normal chromosome 4. No pairing between mini4S and its original chromosome 4 was observed at pachytene and metaphase I stages. The transmission of mini4S through pollen was limited, but about 30% of selfed progeny carried the mini4S chromosomes. The transmission rates considerably increased when the mini4S chromosomes were transferred to plants with a Columbia background by successive backcrosses. This suggests that the stability of the minichromosomes is controlled genetically by factors that can vary between ecotypes.

An integrated map of Oryza sativa L. chromosome 5

The developments of molecular marker-based genetic linkage maps are now routine. Physical maps based on contigs of large insert genomic clones have been established in several plant species. However, integration of genetic, physical, and cytological maps is still a challenge for most plant species. Here we present an integrated map of rice (Oryza sativa L.) chromosome 5, developed by fluorescence in situ hybridization mapping of 18 bacterial artificial chromosome (BAC) clones or PI-derived artificial chromosome (PAC) clones on meiotic pachytene chromosomes. Each BAC/PAC clone was anchored by a restriction fragment length polymorphism marker mapped to the rice genetic linkage map. This molecular cytogenetic map shows the genetic recombination and sequence information of a physical map, correlated to the cytological features of rice chromosome 5. Detailed comparisons of the distances between markers on genetic, cytological, and physical maps, revealed the distributions of recombination events and molecular organization of the chromosomal features of rice chromosome 5 at the pachytene stage. Discordance of distances between the markers was found among the different maps. Our results revealed that neither the recombination events nor the degree of chromatin condensation were evenly distributed along the entire length of chromosome 5. Detailed comparisons of the correlative positions of markers on the genetic, cytological, and physical maps of rice chromosome 5 provide insight into the molecular architecture of rice chromosome 5, in relation to its cytological features and recombination events on the genetic map. The prospective applications of such an integrated cytogenetic map are discussed.

High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9

High-resolution cytogenetic maps provide important biological information on genome organization and function, as they correlate genetic distance with cytological structures, and are an invaluable complement to physical sequence data. The most direct way to generate a cytogenetic map is to localize genetically mapped genes onto chromosomes by fluorescence in situ hybridization (FISH). Detection of single-copy genes on plant chromosomes has been difficult. In this study, we developed a squash FISH procedure allowing successful detection of single-copy genes on maize (Zea mays) pachytene chromosomes. Using this method, the shortest probe that can be detected is 3.1 kb, and two sequences separated by approximately 100 kb can be resolved. To show the robust nature of this protocol, we localized nine genetically mapped single-copy genes on chromosome 9 in one FISH experiment. Integration of existing information from genetic maps and the BAC contig-based physical map with the cytological structure of chromosome 9 provides a comprehensive cross-referenced cytogenetic map and shows the dramatic reduction of recombination in the pericentromeric heterochromatic region. To establish a feasible mapping system for maize, we also developed a probe cocktail for unambiguous identification of the 10 maize pachytene chromosomes. These results provide a starting point toward constructing a high-resolution integrated cytogenetic map of maize.

Dynamic evolution at pericentromeres

Pericentromeres are exceptional genomic regions: in animals they contain extensive segmental duplications implicated in gene creation, and in plants they sustain rearrangements and insertions uncommon in euchromatin. To examine the mechanisms and patterns of plant pericentromere evolution, we compared pericentromere sequence from four Brassicaceae species separated by <15 million years (Myr). This flowering plant family is ideal for studying relationships between genome reorganization and pericentromere evolution-its members have undergone recent polyploidization and hybridization, with close relatives changing in genome size and chromosome number. Through sequence and hybridization analyses, we examined regions from Arabidopsis arenosa, Capsella rubella, and Olimarabidopsis pumila that are homologous to Arabidopsis thaliana pericentromeres (peri-CENs) III and V, and used FISH to demonstrate they have been maintained near centromere satellite arrays in each species. Sequence analysis revealed a set of highly conserved genes, yet we discovered substantial differences in intergenic length and species-specific changes in sequence content and gene density. We discovered that A. thaliana has undergone recent, significant expansions within its pericentromeres, in some cases measuring hundreds of kilobases; these findings are in marked contrast to euchromatic segments in these species that exhibit only minor length changes. While plant pericentromeres do contain some duplications, we did not find evidence of extensive segmental duplications, as has been documented in primates. Our data support a model in which plant pericentromeres may experience selective pressures distinct from euchromatin, tolerating rapid, dynamic changes in structure and sequence content, including large insertions of mobile elements, 5S rDNA arrays and pseudogenes.

Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots"

Crossover (CO) is a key process for the accurate segregation of homologous chromosomes during the first meiotic division. In most eukaryotes, meiotic recombination is not homogeneous along the chromosomes, suggesting a tight control of the location of recombination events. We genotyped 71 single nucleotide polymorphisms (SNPs) covering the entire chromosome 4 of Arabidopsis thaliana on 702 F2 plants, representing 1404 meioses and allowing the detection of 1171 COs, to study CO localization in a higher plant. The genetic recombination rates varied along the chromosome from 0 cM/Mb near the centromere to 20 cM/Mb on the short arm next to the NOR region, with a chromosome average of 4.6 cM/Mb. Principal component analysis showed that CO rates negatively correlate with the G+C content (P = 3x10(-4)), in contrast to that reported in other eukaryotes. COs also significantly correlate with the density of single repeats and the CpG ratio, but not with genes, pseudogenes, transposable elements, or dispersed repeats. Chromosome 4 has, on average, 1.6 COs per meiosis, and these COs are subjected to interference. A detailed analysis of several regions having high CO rates revealed "hot spots" of meiotic recombination contained in small fragments of a few kilobases. Both the intensity and the density of these hot spots explain the variation of CO rates along the chromosome.

Physical organization of the major duplication onBrassica oleraceachromosome O6 revealed through fluorescence in situ hybridization withArabidopsisandBrassicaBAC probes

The close relationship between Brassica oleracea and Arabidopsis thaliana has been used to explore the genetic and physical collinearity of the two species, focusing on an inverted segmental chromosome duplication within linkage group O6 of B. oleracea. Genetic evidence suggests that these segments share a common origin with a region of Arabidopsis chromosome 1. Brassica oleracea and Arabidopsis bacterial artificial chromosome probes have been used for fluorescence in situ hybridization analysis of B. oleracea pachytene chromosomes to further characterize the inverted duplication. This has been highly effective in increasing the local resolution of the cytogenetic map. We have shown that the physical order of corresponding genetic markers is highly conserved between the duplicated regions in B. oleracea and the physical lengths of the regions at pachytene are similar, while the genetic distances are considerably different. The physical marker order is also well conserved between Arabidopsis and B. oleracea, with only one short inversion identified. Furthermore, the relative physical distances between the markers in one segment of B. oleracea and Arabidopsis have stayed approximately the same. The efficacy of using fluorescence in situ hybridization, together with other forms of physical and genetic mapping, for elucidating such issues relating to synteny is discussed.Key words: collinearity, cytogenetic map, pachytene chromosomes, Brassica, Arabidopsis.

Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis

Genome-wide 70-mer oligonucleotide microarrays of rice (Oryza sativa) and Arabidopsis thaliana were used to profile genome expression changes during light-regulated seedling development. We estimate that the expression of approximately 20% of the genome in both rice and Arabidopsis seedlings is regulated by white light. Qualitatively similar expression profiles from seedlings grown under different light qualities were observed in both species; however, a quantitatively weaker effect on genome expression was observed in rice. Most metabolic pathways exhibited qualitatively similar light regulation in both species with a few species-specific differences. Global comparison of expression profiles between rice and Arabidopsis reciprocal best-matched gene pairs revealed a higher correlation of genome expression patterns in constant light than in darkness, suggesting that the genome expression profile of photomorphogenesis is more conserved. Transcription factor gene expression under constant light exposure was poorly conserved between the two species, implying a faster-evolving rate of transcription factor gene expression in light-grown plants. Organ-specific expression profiles during seedling photomorphogenesis provide genome-level evidence for divergent light effects in different higher plant organs. Finally, overrepresentation of specific promoter motifs in root- and leaf-specific light-regulated genes in both species suggests that these cis-elements are important for gene expression responses to light.

The Arabidopsis genome: A foundation for plant research

The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about future developments in Arabidopsis research and its implications for crop science. The provision of large populations of gene disruption lines to the research community has greatly accelerated the impact of genomics on many areas of plant science. The tools and community organization required for plant integrative and systems biology approaches are now ready to accomplish the next big step in plant biology--the integration of knowledge and modeling of biological processes. In the future, plant science will continue to be enriched by the alignment of high-quality basic research (generally conducted in Arabidopsis), with strategic objectives in crop plants. The sequence and analysis of an increasing number of crop plant genomes enhance this alignment and provide new insights into genome evolution and crop plant domestication.

Cytogenetic mapping in maize

Cytogenetic maps depict the location and order of markers along chromosomes. Cytogenetic maps are important in genome research as they relate the genetic data and molecular sequences to the morphological features of chromosomes. In this paper, we discuss various methods used in cytogenetic mapping in maize, with special reference to fluorescence in situ hybridization (FISH) of single-copy sequences on meiotic pachytene chromosomes.

Ribosomal DNA heterochromatin in plants

The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamics.

DNA methylation and epigenetic inheritance during plant gametogenesis

In plants, newly acquired epigenetic states of transcriptional gene activity are readily transmitted to the progeny. This is in contrast to mammals, where only rare cases of transgenerational inheritance of new epigenetic traits have been reported (FASEB J 12:949-957, 1998; Nat Genet 23:314-318, 1999; Proc Natl Acad Sci U S A 100:2538-2543, 2003). Epigenetic inheritance in plants seems to rely on cytosine methylation maintained through meiosis and postmeiotic mitoses, giving rise to gametophytes. In particular, maintenance of CpG methylation ((m)CpG) appears to play a central role, guiding the distribution of other epigenetic signals such as histone H3 methylation and non-CpG DNA methylation. The evolutionarily conserved DNA methyltransferase MET1 is responsible for copying (m)CpG patterns through DNA replication in the gametophytic phase. The importance of gametophytic MET1 activity is illustrated by the phenotypes of met1 mutants that are severely compromised in the accuracy of epigenetic inheritance during gametogenesis. This includes elimination of imprinting at paternally silent loci such as FWA or MEDEA (MEA). The importance of DNA methylation in gametophytic imprinting has been reinforced by the discovery of DEMETER (DME), encoding putative DNA glycosylase involved in the removal of (m)C. DME opposes transcriptional silencing associated with imprinting activities of the MEA/FIE polycomb group complex.

Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile

Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102-bp tandem repeat with sequence identity to a previously characterized approximately 120-bp repeat (STR120). Fragments of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G. latifolia. These data present a picture of the repetitive fraction of the soybean genome that is highly concentrated in the pericentromeric regions, consisting of rapidly evolving tandem repeats with interspersed retroelements.

A novel approach to prepare extended DNA fibers in plants

BACKGROUND

The extended DNA fiber preparation procedure is still imperfect in plants due to the existence of a hard cell wall; thus, high quality of extended DNA fibers for fluorescence in situ hybridization (FISH) analysis is often difficult to be obtained rapidly and efficiently. In this study we have developed a fast and widely effective method to prepare DNA fibers from various plant species and the fibers are suitable for fiber FISH mapping.

METHODS

Fresh young leaves were chopped with a sharp sterile scalpel in a Petri dish that contained ice-cold nucleus isolation buffer followed by filtration through 33-mum nylon mesh. Nuclei were obtained by centrifuging the filtrates at high speed (16,000g) for 40 s. Nucleus lysis buffer (0.5% sodium dodecylsulfate, 5 mM ethylenediaminetetraacetic acid, 100 mM Tris, pH7.0) was added to nuclei on slides, and DNA fibers were dragged and extended with a clean coverslip.

RESULTS

The key of this method is that liquid nitrogen grinding of leaves is replaced by chopping with a blade in ice-cold nucleus isolation buffer. With the liquid nitrogen method, over- or under-grinding of leaves occurs more frequently, and DNA fibers with the desired quality are not obtained easily. In contrast, it is easier to release nuclei from cells in nucleus isolation buffer by chopping, which results in fewer nuclei being destroyed. Highly extended, intact, and long DNA fibers can be generated to a great probability with this method. In addition, this method is very simple and rapid, requiring only 20 min for the entire process, and is also safe because poisonous mercaptoethanol is replaced by dithiothreitol. The results of fiber-FISH with maize genomic DNA and 45S rDNA as probes showed that DNA fiber size as long as 1.96 Mb could be measured. The successful and reliable preparation of maize, wild rice, and barley DNA fibers suitable for FISH mapping proves that this technique is a widely effective approach for obtaining extended DNA fibers in plants.

CONCLUSIONS

A simple, rapid, safe, and widely effective method for getting extended DNA fibers has been developed in plants. (c) 2005 Wiley-Liss, Inc.

Variation in rDNA locus number and position among legume species and detection of 2 linked rDNA loci in the model Medicago truncatula by FISH

Within Fabaceae, legume species have a variable genome size, chromosome number, and ploidy level. The genome distribution of ribosomal genes, easily detectable by fluorescent in situ hybridization (FISH), is a good tool for anchoring physical and genetic comparative maps. The organisation of 45S rDNA and 5S loci was analysed by FISH in the 4 closely related species: Pisum sativum, Medicago truncatula, Medicago sativa (2 diploid taxa), and Lathyrus sativus. The 2 types of rDNA arrays displayed interspecific variation in locus number and location, but little intraspecific variation was detected. In the model legume, M. truncatula, the presence of 2 adjacent 45S rDNA loci was demonstrated, and the location of the rDNA loci was independent of the general evolution of the genome DNA. The different parameters relative to clustering of the rDNA loci in specific chromosome regions and the possible basis of rDNA instability are discussed.

Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana

Since the completion of the Arabidopsis thaliana genome sequence, there is an ongoing effort to annotate the genome as accurately as possible. Comparing genome sequences of related species complements the current annotation strategies by identifying genes and improving gene structure. A total of 595,321 Brassica oleracea shotgun reads were sequenced by TIGR (The Institute for Genome Research) and the collaboration of Washington University and Cold Spring Harbor. Vicogenta (a genome viewer based on GMOD and GBrowse) was created to view the current annotation and sequence alignments for Arabidopsis. Brassica reads were compared with the Arabidopsis genome and proteome databases using BLAST. Hypothetical genes and conserved unannotated regions on the short arm of chromosome 4 from Arabidopsis were experimentally verified using RT-PCR. We were able to improve the Arabidopsis annotation by identifying 25 genes that were missed, and confirming expression of 43 hypothetical genes in Arabidopsis. We were also able to detect conservation in genes whose transcription is normally suppressed due to methylation. We also examined how useful the O. sativa genome and ESTs from other species are, compared with Brassica, in improving the Arabidopsis annotation.

A gene expression map of Arabidopsis thaliana development

Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.

Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis

SU(VAR)3-9 like histone methyltransferases control heterochromatic domains in eukaryotes. In Arabidopsis, 10 SUVH genes encode SU(VAR)3-9 homologues where SUVH1, SUVH2 and SUVH4 (KRYPTONITE) represent distinct subgroups of SUVH genes. Loss of SUVH1 and SUVH4 causes weak reduction of heterochromatic histone H3K9 dimethylation, whereas in SUVH2 null plants mono- and dimethyl H3K9, mono- and dimethyl H3K27, and monomethyl H4K20, the histone methylation marks of Arabidopsis heterochromatin are significantly reduced. Like animal SU(VAR)3-9 proteins SUVH2 displays strong dosage-dependent effects. Loss of function suppresses, whereas overexpression enhances, gene silencing, causes ectopic heterochromatization and significant growth defects. Furthermore, modification of transgene silencing by SUVH2 is partially transmitted to the offspring plants. This epigenetic stability correlates with heritable changes in DNA methylation. Mutational dissection of SUVH2 indicates an implication of its N-terminus and YDG domain in directing DNA methylation to target sequences, a prerequisite for consecutive histone methylation. Gene silencing by SUVH2 depends on MET1 and DDM1, but not CMT3. In Arabidopsis, SUVH2 with its histone H3K9 and H4K20 methylation activity has a central role in heterochromatic gene silencing.

Recent development of image analysis methods in plant chromosome research

Image analysis methods have provided effective tools in chromosome research along with the development both in computer software and hardware. A chromosome image analyzing system, CHIAS, for plant chromosomes was developed in 1985 and was subsequently revised so that with CHIAS3 one can take advantage of Internet use for downloading the program. In this review, the recent developments of imaging methods in plant chromosome research for automating chromosome identification, constructing a map of a pachytene chromosome, and patterning of interphase nuclei are described.

A direct repeat sequence associated with the centromeric retrotransposons in wheat

A high-density BAC filter of Triticum monococcum was screened for the presence of a centromeric retrotransposon using the integrase region as a probe. Southern hybridization to the BAC digests using total genomic DNA probes of Triticum monococcum, Triticum aestivum, and Hordeum vulgare detected differentially hybridizing restriction fragments between wheat and barley. The fragments that hybridized to genomic DNA of wheat but not to that of barley were subcloned. Fluorescence in situ hybridization (FISH) analysis indicated that the clone pHind258 hybridized strongly to centromeric regions in wheat and rye and weakly to those in barley. The sequence of pHind258 was homologous to integrase and long terminal repeats of centromeric Ty3-gypsy retrotransposons of cereal species. Additionally, pHind258 has a pair of 192-bp direct repeats. FISH analysis indicated that the 192-bp repeat probe hybridized to centromeres of wheat and rye but not to those of barley. We found differential FISH signal intensities among wheat chromosomes using the 192-bp probe. In general, the A-genome chromosomes possess strong FISH signals, the B-genome chromosomes possess moderate signals, and the D-genome chromosomes possess weak signals. This was consistent with the estimated copy numbers of the 192-bp repeats in the ancestral species of hexaploid wheat.

Molecular cytogenetic maps of sorghum linkage groups 2 and 8

To integrate genetic, physical, and cytological perspectives of the Sorghum bicolor genome, we selected 40 landed bacterial artificial chromosome (BAC) clones that contain different linkage map markers, 21 from linkage group 2 (LG-02) and 19 from linkage group 8 (LG-08). Multi-BAC probe cocktails were constructed for each chromosome from the landed BACs, which were also preevaluated for FISH signal quality, relative position, and collective chromosome coverage. Comparison to the corresponding linkage map revealed full concordance of locus order between cytological and prior segregation analyses. The pericentromeric heterochromatin constituted a large quasi-uniform block in each bivalent and was especially large in the bivalent corresponding to LG-08. Centromere positions in LG-02 and LG-08 were progressively delimited using FISH to identify landed BACs for which the FISH signals visibly flanked the centromere. Alignment of linkage and cytological maps revealed that pericentromeric heterochromatin of these sorghum chromosomes is largely devoid of recombination, which is mostly relegated to the more distal regions, which are largely euchromatic. This suggests that the sorghum genome is thus even more amenable to physical mapping of genes and positional cloning than the C-value alone might suggest. As a prelude to positional cloning of the fertility restorer, Rf1, FISH of BAC clones flanking the Rf1 locus was used to delimit the chromosomal position of the gene. FISH of BACs that contain the most proximal linkage markers enabled localization of Rf1 to a approximately 0.4-Mbp euchromatic region of LG-08. Cytogenetic analyses of Rf1 and other trait loci will aid in assessing the feasibility of positional cloning and help formulate strategies required for cloning this and other agriculturally critical genes.

Genetic variation in epigenetic inheritance of ribosomal RNA gene methylation in Arabidopsis

We investigated the fidelity of epigenetic inheritance in crosses between three accessions of the flowering plant Arabidopsis thaliana (Canary Islands, Cape Verde Islands, and Columbia). Specifically, we examined the cytosine methylation content of the ribosomal RNA genes at the two nucleolus organizer regions (NOR2 and NOR4) in F1 and F2 hybrid individuals derived from reciprocal crosses between the high NOR methylation strain, Columbia, and the two other accessions, both of which have less NOR methylation. In crosses between the Columbia and Cape Verde Islands strains, the cytosine methylation content segregated as an additive Mendelian trait: the high NOR methylation state was tightly associated with the inheritance of the two Columbia-derived NOR loci. First-generation hybrid individuals between the Canary Islands and Columbia strains also showed a cytosine methylation content at the NORs intermediate between the parental values, consistent with the epigenetic inheritance of parental methylation patterns. Interestingly, mapping data from F2 individuals derived from a Canary Islands x Columbia cross revealed that NOR2 accounted for nearly all of the NOR methylation variation segregating in the population. NOR4 retains a significant effect on total NOR methylation content only through a complex epistatic interaction with NOR2. Our results indicate that the inheritance of differential cytosine methylation states at NOR loci can be modified by their genetic context, opening up the possibility of genetic dissection of epigenetic inheritance.

The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population

Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa x (A. roylei x A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.