Integration of the classical and RFLP linkage maps of the short arm of tomato chromosome 1

The classical map of the short arm of chromosome 1 of tomato (Lycopersicon esculentum) has been shown to contain inaccuracies while the RFLP map of this region is known to be generally accurate. Molecular analysis of populations derived from crosses between L. esculentum lines carrying chromosome 1 classical markers and L. pennellii has enabled us to produce an integrated classical and RFLP marker map of this region. New data concerning the linkage relationships between classical markers have also been combined with previous data to produce a new classical map of the short arm of chromosome 1. The orders of the classical markers on these two new maps are in almost complete agreement and are very different to that shown on the previous classical map.     

Molecular mapping of the centromeres of tomato chromosomes 7 and 9

The centromeres of two tomato chromosomes have been precisely localized on the molecular linkage map through dosage analysis of trisomic stocks. To map the centromeres of chromosomes 7 and 9, complementary telo-, secondary, and tertiary trisomic stocks were used to assign DNA markers to their respective chromosome arms and thus to localize the centromere at the junction of the short and long arms. It was found that both centromeres are situated within a cluster of cosegregating markers. In an attempt to order the markers within the centric clusters, genetic maps of the centromeric regions of chromosomes 7 and 9 were constructed from F₂ populations of 1620Lycopersicon esculentum × L. pennellii (E × P) plants and 1640L. esculentum × L. pimpinellifolium (E × PM) plants. Despite the large number of plants analyzed, very few recombination events were detected in the centric regions, indicating a significant suppression of recombination at this region of the chromosome. The fact that recombination suppression is equally strong in crosses between closely related (E × PM) and remotely related (E × P) parents suggests that centromeric suppression is not due to DNA sequence mismatches but to some other mechanism. The greatest number of centromeric markers was resolved in theL. esculentum × L. pennellii F₂ population. The centromere of chromosome 7 is surrounded by eight cosegregating markers: three on the short arm, five on the long arm. Similarly, the centric region of chromosome 9 contains ten cosegregating markers including one short arm marker and nine long arm markers. The localization of centromeres to precise intervals on the molecular linkage map represents the first step towards the characterization and ultimate isolation of tomato centromeres.     

Comparison of wheat physical maps with barley linkage maps for group 7 chromosomes

Comparative genetic maps among the Triticeae or Gramineae provide the possibility for combining the genetics, mapping information and molecular-marker resources between different species. Dense genetic linkage maps of wheat and barley, which have a common array of molecular markers, along with deletion-based chromosome maps of Triticum aestivum L. will facilitate the construction of an integrated molecular marker-based map for the Triticeae. A set of 21 cDNA and genomic DNA clones, which had previously been used to map barley chromosome 1 (7H), were used to physically map wheat chromosomes 7A, 7B and 7D. A comparative map was constructed to estimate the degree of linkage conservation and synteny of chromosome segments between the group 7 chromosomes of the two species. The results reveal extensive homoeologies between these chromosomes, and the first evidence for an interstitial inversion on the short arm of a barley chromosome compared to the wheat homoeologue has been obtained. In a cytogenetically-based physical map of group 7 chromosomes that contain restriction-fragment-length polymorphic DNA (RFLP) and random amplified polymorphic DNA (RAPD) markers, the marker density in the most distal third of the chromosome arms was two-times higher than in the proximal region. The recombination rate in the distal third of each arm appears to be 8–15 times greater than in the proximal third of each arm where recombination of wheat chromosomes is suppressed.     

Integration of the Classical and Molecular Linkage Maps of Tomato Chromosome 6

In the past, a classical map of the tomato genome has been established that is based on linkage data from intraspecific Lycopersicon esculentum crosses. In addition, a high density molecular linkage map has recently been constructed using a L. esculentum X L. pennellii cross. As the respective maps only partially match, they provide limited information about the relative positions of classical and molecular markers. In this paper we describe the construction of an integrated linkage map of tomato chromosome 6 that shows the position of cDNA-, genomic DNA- and RAPD markers relative to 10 classical markers. Integration was achieved by using a L. esculentum line containing an introgressed chromosome 6 from L. pennellii in crosses to a variety of L. esculentum marker lines. In addition, an improved version of the classical linkage map is presented that is based on a combined analysis of new linkage data for 16 morphological markers and literature data. Unlike the classical map currently in use, the revised map reveals clustering of markers into three major groups around the yv, m-2 and c loci, respectively. Although crossing-over rates are clearly different when comparing intraspecific L. esculentum crosses with L. esculentum X L. pennellii crosses, the clusters of morphological markers on the classical map coincide with clusters of genomic- and cDNA-markers on the molecular map constructed by Tanksley and coworkers.     

Re-orientation and integration of the classical and interspecific linkage maps of the long arm of tomato chromosome 7

To obtain reliable classical and integrated interspecies maps of the long arm of chromosome 7 of tomato, detailed mapping work was undertaken and several phenotypic and molecular markers were assigned loci on both maps to provide reliable cross-reference points. To maximise the value of the new maps, pair-wise segregation data for classical genetic markers from the literature were included, based on large segregating populations with readily scorable phenotypes. In addition, to increase confidence in these maps, introgression lines were used to confirm important map locations. The revised classical map is based on two- and three-point test-cross data from a number of F₂ and BC₁ mapping populations. The integrated interspecies map is based on F₂ mapping populations derived from crosses of Lycopersicon esculentum with Lycopersicon pennellii (LA716). The genetic analyses for both maps were performed using the computer package JoinMap. The revised composite classical map indicates that some of the map positions reported in the literature are incorrect. The linear order of the classical markers common to both the revised classical and integrated interspecies maps are in complete agreement. Production of the integrated interspecies map resulted in re-orientation of the existing molecular map. Received: 13 September 2000 / Accepted: 20 December 2000     

A consensus map of rye integrating mapping data from five mapping populations

A consensus map of rye (Secale cereale L.) was constructed using JoinMap 2.0 based on mapping data from five different mapping populations, including ‘UC90’ × ‘E-line’, ‘P87’ × ‘P105’, ‘I_0.1-line’ × ‘I_0.1-line’, ‘E-line’ × ‘R-line’, and ‘Ds2’ × ‘RxL10’. The integration of the five mapping populations resulted in a 779-cM map containing 501 markers with the number of markers per chromosome ranging from 57 on 1R to 86 on 4R. The linkage sizes ranged from 71.5 cM on 2R to 148.7 cM on 4R. A comparison of the individual maps to the consensus map revealed that the linear locus order was generally in good agreement between the various populations, but the 4R orientations were not consistent among the five individual maps. The 4R short arm and long arm assignments were switched between the two population maps involving the ‘E-line’ parent and the other three individual maps. Map comparisons also indicated that marker order variations exist among the five individual maps. However, the chromosome 5R showed very little marker order variation among the five maps. The consensus map not only integrated the linkage data from different maps, but also greatly increased the map resolution, thus, facilitating molecular breeding activities involving rye and triticale.     

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.     

Alignment of molecular and classical linkage maps of rice,Oryza sativa

Application of genetic linkage maps in plant genetics and breeding can be greatly facilitated by integrating the available classical and molecular genetic linkage maps. In rice, Oryza sativa L., the classical linkage map includes about 300 genes which correspond to various important morphological, physiological, biochemical and agronomic characteristics. The molecular maps consist of more than 500 DNA markers which cover most of the genome within relatively short intervals. Little effort has been made to integrate these two genetic maps. In this paper we report preliminary results of an ongoing research project aimed at the complete integration and alignment of the two linkage maps of rice. Six different F₂ populations segregating for various phenotypic and RFLP markers were used and a total of 12 morphological and physiological markers (Table 1) were mapped onto our recently constructed molecular map. Six linkage groups (i.e., chr. 1, 3, 7, 9, 11 and 12) on our RFLP map were aligned with the corresponding linkage groups on the classical map, and the previous alignment for chromosome 6 was further confirmed by RFLP mapping of an additional physiological marker on this chromosome. Results from this study, combined with our previous results, indicate that, for most chromosomes in rice, the RFLP map encompasses the classical map. The usefulness of an integrated genetic linkage map for rice genetics and breeding is discussed.Abbreviations RFLP restriction fragment length polymorphism - chr chromosome - cM centiMorgan     

Recombination around the Tm2a and Mi resistance genes in different crosses of Lycopersicon peruvianum

The amount of recombination in three different intraspecific crosses of the wild tomato species Lycopersicon peruvianum was investigated for the short arm of chromosome 6 that harbors the Mi nematode resistance gene and the centromeric region of chromosome 9 that contains the Tm2a virus resistance gene. These two genes have been introgressed into the cultivated tomato and are associated with a significant reduction in recombination in the respective region when crossed to other L. esculentum lines. For both regions and all crosses within L. peruvianum significantly more recombination (up to more than ten fold) was observed in the gametes derived from the female parent than in those from the male parent. In general, the differences were more pronounced for chromosome 6 than for chromosome 9. The amount of recombination in the three intraspecific L. peruvianum crosses was compared with the amount of recombination observed in the standard interspecific cross used for the construction of a saturated genetic map of tomato (L. esculentum x L. pennellii). In two of three cases for each region, more recombination was observed in the intraspecific crosses and in one case for each region significantly less recombination was found in the intraspecific cross when compared to the interspecific cross. Specifically for the Mi-carrying region, crosses within L. peruvianum exhibited up to 15-fold more recombination than crosses between resistant and susceptible L. esculentum lines, and such crosses will allow the fine mapping of this gene for the purpose of map-based cloning.     

An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations

Genetical maps of molecular markers in two very different F₁-derived doubled-haploid populations of Brassica oleracea are compared and the first integrated map described. The F₁ crosses were: Chinese kale×calabrese (var. alboglabra×var. italica) and cauliflower×Brussels sprout (var. botrytis×var. gemmifera). Integration of the two component maps using Joinmap v.2.0 was based on 105 common loci including RFLPs, AFLPs and microsatellites. This provided an effective method of producing a high-density consensus linkage map of the B. oleracea genome. Based on 547 markers mapping to nine linkage groups, the integrated map covers a total map length of 893 cM, with an average locus interval of 2.6 cM. Comparisons back to the component linkage maps revealed similar sequences of common markers, although significant differences in recombination frequency were observed between some pairs of homologous markers. Map integration resulted in an increased locus density and effective population size, providing a stronger framework for subsequent physical mapping and for precision mapping of QTLs using substitution lines. Received: 5 February 1999 / Accepted: 16 June 1999     

An RFLP linkage map of Lycopersicon peruvianum

In order to map genes determining resistance to bacterial canker in tomato, backcrosses were made between a resistant and a susceptible Lycopersicon peruvianum accession. The linkage study with RFLP markers yielded a genetic map of L. Peruvianum. This map was compared to that derived from a L. esculentum x L. pennellii F₂ population, based on 70 shared RFLP markers. The maps showed a good resemblance in both the order of markers and the length of the chromosomes, with the exception of just one relocated marker on chromosome 9. Because backcrosses were made with the F₁, either as the pollen parent or as the pistil parent, linkage maps from male and female meioses could be estimated. It was concluded that recombination at male meiosis was reduced, and that gametophytic selection for parental genotypes at more than one locus per chromosome might be partly responsible for the reduction of the estimated male map length.     

A genetic map of tomato based on BC(1) Lycopersicon esculentum x Solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes

F(1) hybrids between the cultivated tomato (Lycopersicon esculentum) and the wild nightshade Solanum lycopersicoides are male sterile and unilaterally incompatible, breeding barriers that impede further crosses to tomato. Meiosis is disrupted in 2x hybrids, with reduced chiasma formation and frequent univalents, but is normal in allotetraploid hybrids, indicating the genomes are homeologous. In this study, a partially male-fertile F(1) was backcrossed to tomato, producing the first BC(1) population suitable for genetic mapping from this cross. BC(1) plants were genotyped at marker loci to study the transmission of wild alleles and to measure rates of homeologous recombination. The pattern of segregation distortion, in favor of homozygotes on chromosomes 2 and 5 and heterozygotes on chromosomes 6 and 9, suggested linkage to a small number of loci under selection on each chromosome. Genome ratios nonetheless fit Mendelian expectations. Resulting genetic maps were essentially colinear with existing tomato maps but showed an overall reduction in recombination of approximately 27%. Recombination suppression was observed for all chromosomes except 9 and 12, affected both proximal and distal regions, and was most severe on chromosome 10 (70% reduction). Recombination between markers on the long arm of this chromosome was completely eliminated, suggesting a lack of colinearity between S. lycopersicoides and L. esculentum homeologues in this region. Results are discussed with respect to phylogenetic relationships between the species and their potential use for studies of homeologous pairing and recombination in a diploid plant genome.     

Development of a chromosomal arm map for wheat based on RFLP markers

Summary A chromosomal arm map has been developed for common wheat (Triticum aestivum L. em. Thell.) using aneuploid stocks to locate more than 800 restriction fragments corresponding to 210 low-copy DNA clones from barley cDNA, oat cDNA, and wheat genomic libraries. The number of restriction fragments per chromosome arm correlates moderately well with relative DNA content and length of somatic chromosomes. The chromosomal arm locations of loci detected with 6 different clones support an earlier hypothesis for the occurrence of a two-step translocation (4AL to 5AL, 5AL to 7BS, and 7BS to 4AL) in the ancestral wheat genomes. In addition, 1 clone revealed the presence of a 5AL segment translocated to 4AL. Anomalies in aneuploid stocks were also observed and can be explained by intrahomoeologous recombination and polymorphisms among the stocks. We view the development of this chromosomal arm map as a complement to, rather than as a substitute for, a conventional RFLP linkage map in wheat.Paper No. 802 of the Cornell Plant Breeding Series     

A cytogenetic map on the entire length of rye chromosome 1R,including one translocation breakpoint,three isozyme loci and four C-bands

Summary A cytogenetic map of the whole 1 R chromosome of rye has been made, with distances between adjacent markers shorter than 50% recombination. Included in the map are isozyme loci Gpi-R1, Mdh-R1 and Pgd2, the telomere C-bands of the short arm (ts1) and the long arm (tl1), two interstitial C-bands in the short arm proximal to the nuclear organizing region (NOR) (is1) and in the middle of the long arm (il1), respectively, and translocation T273W (Wageningen tester set). By means of electron microscope analysis of spread pachytene synaptonemal complexes, the breakpoint of this translocation was physically mapped in the short arm of 1R, proximal to NOR, and in the long arm of 5R (contrary to previous assumptions). The data indicated the marker order: ts1 — Gpi-R1 — is1 — T273W/Mdh-R1 — il1 — Pgd2 — tl1. A comparison between genetic and physical maps revealed that recombination is mainly restricted to the distal regions of both arms. For the translocation T273W, in heterozygotes no recombinants were observed between the translocation breakpoint and its two adjacently located markers (is1 and Mdh-R1), but recombination was not reduced in the distal regions of the chromosome. The segregations of several other isozyme and C-band markers also analyzed in the investigation presented here were consistent with observations of earlier authors concerning chromosome asignment and linkage relationships.     

Comparative genetic linkage map of Solanum sect. Juglandifolia: evidence of chromosomal rearrangements and overall synteny with the tomatoes and related nightshades

The two nightshades Solanum ochranthum and S. juglandifolium show genetic and morphological similarities to the tomatoes (Solanum sect. Lycopersicon), but are isolated from them by strong reproductive barriers. Their genetic relationships to tomato and other Solanum species were investigated using comparative genetic linkage maps obtained from an interspecific F₂ S. ochranthum × S. juglandifolium population. Sixty-six plants were screened using a total of 132 markers—CAPs, RFLPs and SSRs—previously mapped in tomato. Twelve linkage groups were identified, generally corresponding to the expected (syntenic) tomato chromosomes, with two exceptions. Chromosome 1 was composed of two linkage groups and chromosomes 8 and 12 were connected in one large linkage group, indicating a likely reciprocal translocation differentiating the two parental genomes. The total map length comprised 790 cM, representing a 42% reduction in recombination rate relative to the tomato reference map. Transmission ratio distortion affected one-third of the genome, with 13 putative TRD loci identified on 9 out of 12 chromosomes. Most regions were collinear with the tomato reference maps, including the long arm of chromosome 10, which is inverted relative to two other tomato-like nightshades, S. lycopersicoides and S. sitiens. The results support the status of S. ochranthum and S. juglandifolium as the nearest outgroup to the tomatoes and imply they are more closely related to cultivated tomato than predicted from crossing relationships, thus encouraging further attempts at hybridization and introgression between them.     

A YAC contig map of Arabidopsis thaliana chromosome 3

We have constructed a YAC contig map of Arabidopsis thaliana chromosome 3. From an estimated total size of 25 Mb, about 21 Mb were covered by 148 clones arranged into nine YAC contigs, which represented most of the low-copy regions of the chromosome. YAC clones were anchored with 259 molecular markers, including 111 for which linkage information was previously available. Most of the genetic map was included in the YAC coverage, and more than 60% of the genetic markers from the reference recombinant inbred line map were anchored, giving a high level of integration between the genetic and physical maps. The submetacentric structure of the chromosome was confirmed by physical data; 3R (the top arm of the linkage map) was about 12 Mb, and 3L (the bottom arm of the linkage map) was about 9 Mb. This YAC physical map will aid in chromosome walking experiments and provide a framework for large-scale DNA sequencing of chromosome 3.     

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

Background

Integration of molecular, genetic and cytological maps is still a challenge for most plant species. Recent progress in molecular and cytogenetic studies created a basis for developing integrated maps in cucumber (Cucumis sativus L.).

Results

In this study, eleven fosmid clones and three plasmids containing 45S rDNA, the centromeric satellite repeat Type III and the pericentriomeric repeat CsRP1 sequences respectively were hybridized to cucumber metaphase chromosomes to assign their cytological location on chromosome 2. Moreover, an integrated molecular cytogenetic map of cucumber chromosomes 2 was constructed by fluorescence in situ hybridization (FISH) mapping of 11 fosmid clones together with the cucumber centromere-specific Type III sequence on meiotic pachytene chromosomes. The cytogenetic map was fully integrated with genetic linkage map since each fosmid clone was anchored by a genetically mapped simple sequence repeat marker (SSR). The relationship between the genetic and physical distances along chromosome was analyzed.

Conclusions

Recombination was not evenly distributed along the physical length of chromosome 2. Suppression of recombination was found in centromeric and pericentromeric regions. Our results also indicated that the molecular markers composing the linkage map for chromosome 2 provided excellent coverage of the chromosome.     

Studies on the linkage map of chromosome 4 of the tomato and on the transmission of induced deficiencies

Various genetic and cytogenetic techniques were applied to an analysis of the linkage map of chromosome 4-a chromosome that is considered to be representative of the tomato complement. Loci have been approximated by standard F₂ linkage tests for 18 genes, including six on the short arm and 12 on the long arm, covering a map distance of 132 units (c.m.). The loci of four key markers were approximated on pachytene chromosomes by a study of radiation-induced deficiencies:clau near the end of the short arm,ful near the euchromatic-heterochromatic boundary of the short arm,ra near the same region on the long arm, ande in the middle of the long arm. Normal transmission for a presumedra deficiency suggests that this gene lies in the heterochromatin of 4L. According to tertiary trisomic segregation,w-4, known by linkage test to be proximal tora, resides on 4L, therefore probably also in the heterochromatic region. The centromere is consequently delimited to a region of 4 c.m. betweenful andw-4. The resultant maps reveal a very much lower crossover rate within heterochromatin—estimated at 0.8 c.m./μ—than for euchromatin—estimated at 4.8 c.m./μ for the short arm and 5.7 for the long arm. Also apparent is a strong tendency of the genes to concentrate toward the centromere of the genetic map and in the proximal sections of the euchromatin of the cytological map. Studies were made of the genetic transmission of various small deficiencies on chromosome 4 as well as a newly discovered deficiency fornv on chromosome 9, supporting the following conclusions. Regardless of their size, deficiendies of euchromatin are not transmitted. Deficiencies of heterochromatin are transmitted to a varying extent depending on their size. A presumed deficiency forra that is too small to be detected cytologically was transmitted without adverse effect on gametes. Somewhat larger deficiencies may be transmitted at reduced rates by female gametes and the largest at extremely low rates, even on the female side.     

Construction of an integrated consensus map of the apple genome based on four mapping populations

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1?=?Discovery × TN10-8, C2?=?Fiesta × Discovery, C3?=?Discovery × Prima, C4?=?Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female–male maps were built for each population using common female–male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (χ ²?=?16.53, df?=?16, p?=?0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female–male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.     

Genetic linkage between C-bands and storage protein genes in chromosome 1B of tetraploid wheat

Summary Genetic mapping of polymorphic C-bands allows direct comparisons between genetic and physical maps. Eleven C-bands and two seed storage protein genes on chromosome 1B, polymorphic between Langdon durum and four accessions of T. dicoccoides, were used to study the distribution of recombination along the entire length of the chromosome. Recombination in the short arm was almost completely restricted to the satellite, two-thirds of the arm's length from the centromere; the Gli-B1 gene was found to be tightly linked to the telomeric C-band. In the long arm, the distal 51.4% of the arm accounted for 88% of recombination; the proximal half of the arm accounted for the remaining 12%. While the amount of crossing-over differed significantly between the four T. dicoccoides 1B chromosomes, there were no significant differences in the relative distributions of crossing-over along the chromosome. Consequently, the genetic maps obtained from the four individual T. dicoccoides chromosomes were combined to yield a consensus map of 14 markers (including the centromere) for the chromosome.