A method for producing synaptonemal complex complements in lily and mouse

A whole-mount procedure for producing pachytene synaptonemal complex complements of Lilium longiflorum was developed. The method involves swelling of the meiotic nuclei followed by nonionic detergent lysis of the nuclear envelope. This technique adequately spreads out the long lily chromosomes while producing only minimal distortion of the chromosomal axes. The ultrastructure of the synaptonemal complex is normal, and the chromatin remains closely associated with the synaptonemal complex. The procedure also was used successfully to produce pachytene synaptonemal complex preparations of mouse chromosomes. In the mouse, the centromeric heterochromatin remains associated with the synaptonemal complex, but the euchromatin is more widely dispersed.     

Pachytene pairing and metaphase I configurations in a tetraploid somatic Lycopersicon esculentum x L. peruvianum hybrid.

In the tetraploid somatic hybrid between the diploid Lycopersicon species L. esculentum (tomato) and L. peruvianum, synaptonemal complexes formed quadrivalents in 73 of the 120 sets of four chromosomes (60.8%) in 10 cells studied in detail at pachytene. Of these, 43 had one pairing partner exchange, 22 had two, and 8 had three, very close to a Poisson distribution. The points of pairing partner exchange were concentrated at the middle of the two arms. The frequency per arm corresponded with physical arm length. There was a sharp drop around the centromere, and pericentric heterochromatin had a slightly lower probability of being involved in pairing partner exchange than euchromatin. The chromosomes align before pairing and there are several points of pairing initiation, with concentrations at or near the ends and the centromere. From zygotene to late pachytene the quadrivalent frequency decreased considerably. At late pachytene it was lower than expected with the observed high frequency of pairing partner exchange. Pairing affinity between species was only slightly lower than affinity within species, in spite of considerable genetic differentiation. The frequency of recombination nodules increased from early to late zygotene and then decreased strongly to full pachytene. There is a highly significant negative correlation between percent pairing and SC length. At metaphase I the frequency of quadrivalents was 0.444, and branched quadrivalents were rare, probably caused by interference and restriction of chiasma formation to distal euchromatin. Metaphase I quadrivalent frequency is a relatively good indication of pairing affinity in this material.     

Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome

Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for approximately 90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin-the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently-well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.     

FISH to meiotic pachytene chromosomes of tomato locates the root-knot nematode resistance gene Mi-1 and the acid phosphatase gene Aps-1 near the junction of euchromatin and pericentromeric heterochromatin of chromosome arms 6S and 6L, respectively

 The root-knot nematode resistance gene Mi-1 in tomato has long been thought to be located in the pericentromeric heterochromatin region of the long arm of chromosome 6 because of its very tight genetic linkage (approx. 1 cM) to the markers Aps-1 (Acid phosphatase 1) and yv (yellow virescent). Using Mi-BAC clones and an Aps-1 YAC clone in fluorescence in situ hybridisation (FISH) to pachytene chromosomes we now provide direct physical evidence showing that Mi-1 is located at the border of the euchromatin and heterochromatin regions in the short arm (6S) and Aps-1 in the pericentromeric heterochromatin of the long arm (6L) close to the euchromatin. Taking into account both the estimated DNA content of hetero- and euchromatin regions and the compactness of the tomato chromosomes at pachytene (2 Mb/μm), our data suggest that Mi-1 and Aps-1 are at least 40 Mb apart, a base pair-to-centiMorgan relationship that is more than 50-fold higher than the average value of 750 kb/cM of the tomato genome. An integrated cytogenetic-molecular map of chromosome 6 is presented that provides a framework for physical mapping. Received: 24 July 1998 / Accepted: 14 August 1998     

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6

Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.     

QTL analysis of morphological traits in a tomato recombinant inbred line population.

Quantitative trait loci (QTLs) influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RILs) derived from a cross of the cultivated tomato Lycopersicon esculentum with a related wild species, Lycopersicon cheesmanii. One hundred and thirty-two RFLP loci spaced throughout the tomato genome were used as DNA probes on genomic DNA from 97 RIL families. Morphological traits, including plant height, plant fresh mass, number of branches, number of nodes, first flower-bearing node, and leaf length, were evaluated in two controlled environment trials in 1992 and 1993. QTLs were detected via regression analyses at multiple marker loci for each morphological trait. A total of 41 markers were significantly associated with the traits examined. Large additive effects were measured at many of these loci. QTLs for multiple traits were detected on chromosomes 3 (TG74) and 4 (CT188), suggesting the possible association of these chromosome segments with genes controlling growth and development in tomato. These chromosomal regions were also associated with multiple morphological traits in a L. esculentum x Lycopersicon pennellii cross. A total of 13% of the QTLs identified for traits common to both studies occupied similar map positions.     

DNA amounts and chromatin compactness in Vicia

2C DNA amounts and areas of chromatin were determined with a M 86 Vickers microdensitometer in 56 species of Vicia (x=5, 6, 7), exhibiting large differences in chromosome size. There were significant differences between the species both in DNA content and chromatin area. The nuclear DNA amounts range from 3.85 to 27.07 pg. DNA distribution appears discontinuous; species cluster into distinct groups and the average nuclear DNA amount separating each successive pair is approximately the same (2.23 pg). The compaction of DNA in interphase nuclei increases with increasing DNA amount, which is, at least partly, due to a disproportionate increase in the heterochromatin relative to the euchromatin component of DNA. Comparisons of DNA readings at various stages of the cell cycle show that the DNA amounts are underestimated by microdensitometry in nuclei with high DNA density. Estimation of relative DNA content and area of individual chromosomes were made in twelve species. The results show that changes in DNA content within chromosomes affect the degree of metaphase coiling in an orderly fashion.     

The 1.688 repetitive DNA of Drosophila: concerted evolution at different genomic scales and association with genes

Concerted evolution leading to homogenization of tandemly repeated DNA arrays is widespread and important for genome evolution. We investigated the range and nature of the process at chromosomal and array levels using the 1.688 tandem repeats of Drosophila melanogaster where large arrays are present in the heterochromatin of chromosomes 2, 3, and X, and short arrays are found in the euchromatin of the same chromosomes. Analysis of 326 euchromatic and heterochromatic repeats from 52 arrays showed that the homogenization of 1.688 repeats occurred differentially for distinct genomic regions, from euchromatin to heterochromatin and from local arrays to chromosomes. We further found that most euchromatic arrays are either close to, or are within introns of, genes. The short size of euchromatic arrays (one to five repeats) could be selectively constrained by their role as gene regulators, a situation similar to the so-called "tuning knobs."     

Location and variation of the constitutive heterochromatin in Petunia hybrida

The location of heterochromatin in the chromosomes of Petunia hybrida (2n=14) is presented. C-banded mitotic metaphase chromosomes and carmine-stained pachytene bivalents have been studied. It is shown that the heterochromatin is predominantly located near the centromeres and at the secondary constrictions of the satellite chromosomes. The distribution of chromomeres in pachytene bivalents also reveals that heterochromatin is not restricted to distinct blocks, as is the case in tomato, but occurs in smaller chromomeres which gradually decrease in size towards the ends. Conspicuous telomeres have not been observed. Both C-banding technique and pachytene analysis demonstrate large variation of heterochromatin between different lines of Petunia. The study of pachytene morphology has been hampered by a high degree of non-specific stickiness of the bivalents. Both techniques prove to be unsuitable tools for large-scale chromosome identification of Petunia lines.     

Centric-fusion translocation and whole-arm heterochromatin in the karyotype of the blue fox (Alopex lagopus L.): synaptonemal complex analysis.

Conventional observations of mitotic chromosomes from two male blue foxes, revealing a centric-fusion translocation and whole-arm heterochromatin, were verified by synaptonemal complex analysis. This analysis revealed that the centric fusion had been preceded by a conspicuous loss of chromosome material in the two one-armed chromosomes involved, but the chromosomal origin of the centric-fusion kinetochore could not be established. The nontranslocated chromosomes of the trivalent, which in all cells but one were in cis configuration, had reached by early pachytene a stage in which almost complete homologous pairing and nonhomologous association or pairing of the free ends of the chromosomes could be observed. In later stages, complete pairing of the nontranslocated chromosomes with the corresponding arms of the centric-fusion translocation was seen occasionally. One to six autosomal bivalents demonstrated unpaired heterochromatic arms in early pachytene, and the heterochromatic chromosome arms were sometimes unpaired even in late pachytene. Some of them showed a distinct size heteromorphism in late zygotene and early pachytene. In most late-pachytene cells, however, the heteromorphic chromosomes were completely length-adjusted. Only a small fraction of the cells showed pairing interference between nonhomologous chromosomes.     

Chromosome pairing and potential for intergeneric recombination in some hypotetraploid somatic hybrids of Lycopersicon esculentum (+) Solanum tuberosum.

Three somatic hybrids resulting from protoplast fusions of a diploid kanamycin-resistant line of tomato (Lycopersicon esculentum) and a dihaploid hygromycin-resistant transformant of a monohaploid potato (Solanum tuberosum) line were used for a cytogenetic study on chromosome pairing and meiotic recombination. Chromosome counts in root-tip meristem cells revealed two hypotetraploids with chromosome complements of 2n = 46 and one with 2n = 47. Electron microscope analyses of synaptonemal complex spreads of hypotonically burst protoplasts at mid prophase I showed abundant exchanges of pairing partners in multivalents involving as many as eight chromosomes. In the cells at late pachytene recombination nodules were found in multivalents on both sides of pairing partner exchanges, indicating recombination at both homologous and homoeologous sites. Light microscope observations of pollen mother cells at late diakinesis and metaphase I also revealed multivalents, though their occurrence in low frequencies betrays the reduction of multivalent number and complexity. Precocious separation of half bivalents at metaphase I and lagging of univalents at anaphase I were observed frequently. Bridges, which may result from an apparent inversion loop found in the synaptonemal complexes of a mid prophase I nucleus, were also quite common at anaphase I, though the expected accompanying fragments could be detected in only a few cells. Most striking were the high frequencies of first division restitution in preparations at metaphase II/anaphase II, giving rise to unreduced gametes. In spite of the expected high numbers of balanced haploid and diploid gametes, male fertility, as revealed by pollen staining, was found to be negligible.     

Sequence and Analysis of the Tomato JOINTLESS Locus

A 119-kb bacterial artificial chromosome from the JOINTLESS locus on the tomato (Lycopersicon esculentum) chromosome 11 contained 15 putative genes. Repetitive sequences in this region include one copia-like LTR retrotransposon, 13 simple sequence repeats, three copies of a novel type III foldback transposon, and four putative short DNA repeats. Database searches showed that the foldback transposon and the short DNA repeats seemed to be associated preferably with genes. The predicted tomato genes were compared with the complete Arabidopsis genome. Eleven out of 15 tomato open reading frames were found to be colinear with segments on five Arabidopsis bacterial artificial chromosome/P1-derived artificial chromosome clones. The synteny patterns, however, did not reveal duplicated segments in Arabidopsis, where over half of the genome is duplicated. Our analysis indicated that the microsynteny between the tomato and Arabidopsis genomes was still conserved at a very small scale but was complicated by the large number of gene families in the Arabidopsis genome.     

Comparative linkage map of the Solanum lycopersicoides and S. sitiens genomes and their differentiation from tomato.

The wild nightshades Solanum lycopersicoides and Solanum sitiens are closely affiliated with the tomatoes (Lycopersicon spp.). Intergeneric hybridization with cultivated tomato (Lycopersicon esculentum) is impeded by strong reproductive barriers including hybrid sterility and suppressed recombination. Conservation of genome structure between these nightshades and tomato was studied by construction of a genetic map from F2 S. sitiens x S. lycopersicoides and comparison with existing maps of tomato. Owing to self-incompatibility of the F1, two hybrid plants were crossed to obtain a population of 82 F2 individuals. Using 166 previously mapped RFLP markers and 5 restriction enzymes, 101 loci polymorphic in the S. sitiens x S. lycopersicoides population were identified. Analysis of linkage between the markers resulted in a map with 12 linkage groups covering 1192 cM and one unlinked marker. Recombination rates were similar to those observed in tomato; however, significant segregation distortion was observed for markers on 7 out of the 12 chromosomes. All chromosomes were colinear with the tomato map, except for chromosome 10, where a paracentric inversion on the long arm was detected. In this region, S. sitiens and S. lycopersicoides share the same chromosomal configuration previously reported for potato (S. tuberosum) and pepper (Capsicum), suggesting that of tomato is derived. The 10L inversion explains the lack of recombination detected among homeologous chromosomes of intergeneric hybrids in this region. On this basis, we recognize two principle genomes, designated L for the Lycopersicon spp., and S for S. lycopersicoides and S. sitiens, the first examples of structural differentiation between tomato and its cross-compatible wild relatives.     

Karyotype and nuclear DNA content of hexa-, octo-, and duodecaploid lines of Bromus subgen. Ceratochloa

The subgenus Ceratochloa of the genus Bromus includes a number of closely related allopolyploid forms or species that present a difficult taxonomic problem. The present work combines data concerning chromosome length, heterochromatin distribution and nuclear genome size of different 6x, 8x and 12x accessions in this subgenus. Special attention is paid to the karyotype structure and genomic constitution of duodecaploid plants recently found in South America. Hexaploid lineages possess six almost indistinguishable genomes and a nuclear DNA content between 12.72 pg and 15.10 pg (mean 1Cx value = 2.32 pg), whereas octoploid lineages contain the same six genomes (AABBCC) plus two that are characterized by longer chromosomes and a greater DNA content (1Cx = 4.47 pg). Two duodecaploid accessions found in South America resemble each other and apparently differ from the North American duodecaploid B. arizonicus as regards chromosome size and nuclear DNA content (40.00 and 40.50 pg vs. 27.59 pg). These observations suggest that the South American duodecaploids represent a separate evolutionary lineage of the B. subgenus Ceratochloa, unrecognized heretofore.     

Genomic in situ hybridization analysis of a trigenomic hybrid involving Solanum and Lycopersicon species.

A 4x potato (+) tomato fusion hybrid (2n = 4x = 48) was successfully backcrossed with a diploid Lycopersicon pennellii (2n = 2x = 24). Genomic in situ hybridization (GISH) on somatic and meiotic chromosomes confirmed that the progenies were triploids (2n = 3x = 36) and possessed three different genomes: potato, tomato, and L. pennellii. Therefore, they have been called trigenomic hybrids. Total genomic probes of both Lycopersicon species were found to hybridize mutually, whereas the potato genome was clearly differentiated. During metaphase I, bivalents were formed predominantly between tomato and L. pennellii chromosomes and the univalents of potato chromosomes were most common. Trivalents in all cases included homoeologous chromosomes of potato, tomato, and L. pennellii. However, the triploids were totally sterile as determined from extensive crossing. On chromosome doubling of triploids by shoot regeneration from callus, hexaploids (2n = 6x = 72) were obtained. Despite exhibiting clear allohexaploid behaviour by forming 36 bivalents at meiosis, these were also completely sterile like their triploid counterparts. In spite of this drawback, the prospects of chromosome pairing between potato L. pennellii and Solanum genomes does open the possibilities for bringing the two genera close.     

QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato.

Quantitative trait loci (QTLs) for resistance to Phytophthora infestans (late blight) were mapped in tomato. Reciprocal backcross populations derived from cultivated Lycopersicon esculentum x wild Lycopersicon hirsutum (BC-E, backcross to L. esculentum; BC-H, backcross to L. hirsutum) were phenotyped in three types of replicated disease assays (detached-leaflet, whole-plant, and field). Linkage maps were constructed for each BC population with RFLPs. Resistance QTLs were identified on all 12 tomato chromosomes using composite interval mapping. Six QTLs in BC-E (lb1a, lb2a, lb3, lb4, lb5b, and lb11b) and two QTLs in BC-H (lb5ab and lb6ab) were most consistently detected in replicated experiments or across assay methods. Lycopersicon hirsutum alleles conferred resistance at all QTLs except lb2a. Resistance QTLs coincided with QTLs for inoculum droplet dispersal on leaves, a trait in L. hirsutum that may contribute to resistance, and dispersal was mainly associated with leaf resistance. Some P. infestans resistance QTLs detected in tomato coincided with chromosomal locations of previously mapped R genes and QTLs for resistance to P. infestans in potato, suggesting functional conservation of resistance within the Solanaceae.     

Electron microscopy of meiosis in Drosophila melanogaster females

Complete reconstruction of the synaptonemal complex in 12 pachytene (defined here as that stage in which the synaptonemal complex is continuous throughout the bivalents) nuclei from one wild-type germarium has permitted the following observations. 1) Drosophila melanogaster bivalents at pachytene exhibit a chromocentral arrangement; the pericentric heterochromatin of all bivalents lies in one region of the nucleus, the chromocenter. Telomeric ends do not appear to abutt the nuclear envelope. 2) Synaptonemal complex is present in the pericentric heterochromatin; however, it is morphologically distinct from that present in the euchromatic portion of the bivalents. 3) Length of the synaptonemal complex of the bivalent arms is greatest at early pachytene; the synaptonemal complex then becomes progressively shorter. Minimum length is approximately one-half of the maximum. 4) Decrease in length of synaptonemal complex is accompanied by an increase in thickness. Reconstruction of 20 pachytene nuclei from an additional 8 germaria suggests that these observations are typical. Correlations between these cytological observations and genetic observations (e.g., patterns of crossing-over) are discussed.     

The chromosomes of tufted deer (Elaphodus cephalophus)

Mitotic and meiotic chromosome preparations of the tufted deer (Elaphodus cephalophus) were studied to elucidate the sex-chromosomal polymorphism evidenced by this species. Females had 2n = 46 or 47 chromosomes, whereas males had 2n = 47 or 48 chromosomes. An X;autosome translocation was identified by synaptonemal complex analysis of spermatocytes at pachytene and confirmed by the presence of a trivalent at diakinesis/metaphase I. The present work, in combination with earlier observations by others, indicates that E. cephalophus possesses a varied X-chromosome morphology involving an X;autosome translocation and addition of varying amounts of heterochromatin. It is speculated that sex-chromosome polymorphism may be responsible for the observed differences in diploid chromosome number of tufted deer.     

Kinetochores of grasshoppers with Robertsonian chromosome fusions

The pachytene karyotypes of three grasshopper species with 2 and 3 Robertsonian fusions were constructed from electron micrographs of serially sectioned spermatocyte nuclei. Tracings of the synaptonemal complexes permitted identification of each bivalent and its centromeric region. Chromosomes with the centromere in a terminal position have a knob of centric heterochromatin on the synaptonemal complex where it ends at the nuclear envelope. In Chorthippus and in Chloealtis the submetacentric Robertsonian fusion chromosomes each have a single centric knob in the appropriate place. In Neopodismopsis each of the 2 submetacentric chromosomes have a centric knob which is double in size and structure. In spermatogonial metaphases the submetacentric chromosomes of Neopodismopsis have 70–80 microtubules per kinetochore while the telocentric chromosomes have 30–40 tubules per kinetochore. These observations are correlated with evidence from light microscopy that Robertsonian fusions may produce mono- or dicentric chromosomes.