Sucrose Phosphate Synthase Genes in Plants Belong to Three Different Families

We present phylogenetic analyses to demonstrate that there are three families of sucrose phosphate synthase (SPS) genes present in higher plants. Two data sets were examined, one consisting of full-length proteins and a second larger set that covered a highly conserved region including the 14-3-3 binding region and the UDPGlu active site. Analysis of both datasets showed a well supported separation of known genes into three families, designated A, B, and C. The genomic sequences of Arabidopsis thaliana include a member in each family: two genes on chromosome 5 belong to Family A, one gene on chromosome 1 to Family B, and one gene on chromosome 4 to Family C. Each of three Citrus genes belong to one of the three families. Intron/exon organization of the four Arabidopsis genes differed according to phylogenetic analysis, with members of the same family from different species having similar genomic organization of their SPS genes. The two Family A genes on Arabidopsis chromosome 5 appear to be due to a recent duplication. Analysis of published literature and ESTs indicated that functional differentiation of the families was not obvious, although B family members appear not to be expressed in roots. B family genes were cloned from two Actinidia species and southern analysis indicated the presence of a single gene family, which contrasts to the multiple members of Family A in Actinidia. Only two family C genes have been reported to date. Received: 17 April 2001 / Accepted: 27 August 2001     

Physical mapping of ribosomal DNA on several species of the subgenus Rosa

The localization of NORs by fluorescent in situ hybridization on metaphase spreads of five diploid (Rosa gigantea Coll., Rosa moschata Herrm., Rosa multiflora Thunb., Rosa rugosa Thunb. and Rosa sempervirens L., 2n=2x=14), one triploid (Rosa chinensis’semperflorens’ Koehne., 2n=3x=21) and one tetraploid (Rosa gallica ’versicolor’ L., 2n=4x=28) ancestral species of modern roses was studied. Two terminal hybridization signals were observed in all diploid species corresponding to a single NOR per genome in these species. Triploid R. chinensis showed three hybridization sites on the short arm of three morphologically similar chromosomes. Six hybridization sites, located at terminal positions of the short arms of three chromosome pairs, were observed in the tetraploid species. These signals corresponded to three pairs of NORs and all of them were located in chromosome pairs of different size. These observations, together with the analysis of meiotic pairing in PMCs, support the view that our specimen of R. chinensis is an autotriploid and that R. gallica’versicolor’ has an alloploidy nature. Received: 27 November 2000 / Accepted: 12 March 2001     

Deletion-based physical mapping of barley chromosome 7H

Chromosomal mutations in barley (Hordeum vulgare, 2n=2x=14, HH) chromosome 7H added to the common wheat (Triticum aestivum, 2n=6x=42, AABBDD) cultivar Chinese Spring were induced genetically by the gametocidal activity of certain alien chromosomes derived from wild species of the genus Aegilops. The rearranged barley chromosomes were characterized by C-banding, FISH and GISH. Twenty two deletion or translocation chromosomes in a hemizygous condition were selected for deletion mapping of 17 AFLP and 28 STS markers that are specific to 7H. Of the 22 breakpoints in chromosome 7H, seven involved the short arm (7HS), 12 the long arm (7HL) and three were in the centromeric region. The seven 7HS breakpoints separated all four 7HS-specific AFLP markers and split the 21 STS markers into six groups. One breakpoint occurred between two STS markers formerly occupying the same position in the genetic map. All seven 7HS breakpoints were separated from each other by either the AFLP or STS markers. The 12 breakpoints in 7HL divided the 13 7HL-specific AFLP markers into seven groups, and the seven STS markers into three groups. On the other hand, the 12 breakpoints in 7HL were divided into six groups by the AFLP markers and into two groups by the STS markers. This deletion-based map was in accordance with previously published genetic and physical maps using the same STS markers. The breakpoints, AFLP markers and STS markers were arrayed in a consistent order. Received: 5 February 2001 / Accepted: 19 February 2001     

Comparative mapping of cosmids and gene clones from a 1.6 Mb chromosomal region of Drosophila melanogaster in three species of the distantly related subgenus Drosophila

The successful hybridization of cosmid clones from Drosophila melanogaster (Sophophora subgenus) to the salivary gland chromosomes of other species as distantly related as those in the Drosophila subgenus attests their great potential for unravelling genome evolution. We have carried out, using 28 cosmids and 13 gene clones, a study of the organization of the D. melanogaster 95A-96A chromosomal region in three Drosophila subgenus species: D. repleta, D. buzzattii and D. virilis. These clones were first used to built an accurate map of this 1.6 Mb region of D. melanogaster chromosome 3R (Muller’s element E). Then, they were hybridized and mapped to the homologous chromosome 2 of the other three distantly related species. The studied region is disseminated over 13 different sites of chromosome 2 in the Drosophila subgenus species, which implies a minimum of 12 inversion breakpoints fixed between the two subgenera. Extrapolation to the entire chromosome gives 90 fixed inversions. The D. melanogaster Pp1-96A-Acr96Aa segment conserved in D. repleta and D. buzzatii is longer than previously thought and is also conserved in D. virilis. In addition, three other D. melanogaster segments conserved in the three Drosophila subgenus species were found. Finally, our data indicate significant statistical differences in the evolution rate of Muller’s element E among lineages, a result that agrees well with the previous cytogenetic data. Received: 22 July 1998; in revised form: 11 November 1998 / Accepted: 12 November 1998     

Molecular Phylogeny of Casuarinaceae Based on rbcL and matK Gene Sequences

rbcL (1310 bp) and matK (1014 bp), using 15 species representing the family. The study included analyses of Ticodendron (Ticodendraceae) and three species of Betulaceae as close relatives, and one species each of Juglandaceae and Myricaceae as outgroups. Analyses based on matK gene sequences, which provided a much better resolution than the analyses based on rbcL gene sequences alone, resulted in a single most parsimonious tree whose topology is almost identical with the strict consensus tree generated by the combined data set of rbcL and matK gene sequences. Results showed that Casuarinaceae are monophyletic, comprising four distinct genera, Allocasuarina, Casuarina, Ceuthostoma and Gymnostoma, which were not recognized until recently. Within the family, Gymnostoma is positioned at the most basal position and sister to the remainder. Within the remainder Ceuthostoma is sister to the Allocasuarina-Casuarina clade. Morphologically the basalmost position of Gymnostoma is supported by plesiomorphies such as exposed stomata in the shallow longitudinal furrows of the branchlets, a basic chromosome number x=8 and the gynoecium composed of two fertile, biovulate carpels. The three other genera, Allocasuarina, Casuarina, and Ceuthostoma, have invisible stomata in the deep longitudinal furrows of the branchlets, a higher basic chromosome number x=9 or 10–14 (unknown in Ceuthostoma), the gynoecium composed of one fertile and one sterile carpel with a single ovule (unknown in Ceuthostoma). The diversity of infructescence morphology found in the latter three genera suggests that they may have evolved in close association with the elaboration of fruit dispersal mechanisms. Received 14 September 2001/ Accepted in revised form 12 October 2001     

Karyological observations on Turbellaria Proseriata: karyometric analysis ofMonocelis fusca,M. lineata (Monocelididae) andParotoplana macrostyla (Otoplanidae)

A karyometric analysis of the chromosome set of the marine turbellariansMonocelis fusca, M. lineata andParotoplana macrostyla has been carried out. The karyotype of the twoMonocelis species investigated (2n=6) is formed by three pairs of small and similarly sized chromosomes: InM. fusca, chromosome 1 is metacentric, chromosome 2 acrocentric and chromosome 3 is subtelocentric.M. lineata also presents one pair of metacentric chromosomes (chromosome 2), while chromosomes 1 and 3 are submetacentric.P. macrostyla (2n=12) reveals two pairs of large metacentric and four pairs of small chromosomes, three of which are metacentric, whereas the last is subtelocentric.     

High-density physical maps reveal that the dominant male-sterile gene Ms3 is located in a genomic region of low recombination in wheat and is not amenable to map-based cloning

In wheat it is essential to know whether a gene is located in a high or low recombination region of the genome before initiating a map-based cloning approach. The objective of this study was to explore the potential feasibility of map-based cloning of the dominant male-sterile gene Ms3 of wheat. High-density physical maps of the short arms of the group-5 chromosomes (5AS, 5BS, and 5DS) of Triticum aestivum L. were constructed by mapping 40 DNA markers on a set of 17 homozygous deletion lines. One hundred RFLP loci were mapped: 35 on 5AS, 37 on 5BS, and 28 on 5DS. A consensus physical map was colinearly aligned with a consensus genetic map of the group-5 short arms. Sixteen of the 17 markers in the consensus genetic map encompass a genetic distance of 25 cM and correspond to the distal region (FL 0.56–0.97) of the consensus physical map. Two rice probes, RG463 and RG901, previously identified to be linked to markers CDO344 and CDO749 (group-5 short arm of wheat), respectively, in the genetic map of rice chromosome 12, map between FL 0.56 and 0.63 in the consensus map. Thus at least a part of the group-5 short arm is homoeologous to a region of chromosome 12 of rice. The genetic map of chromosome arm 5AS was constructed using a population of 139 BC₁ plants derived from a cross between the euploid wheat ”Chris” carrying a dominant male-sterile gene Ms3 and a disomic substitution line in which chromosome 5A of T. aestivum cv Chinese Spring was substituted by chromosome 5A from Triticum turgidum ssp. dicoccoides. The map has a genetic length of 53.4 cM with 11 DNA markers. The initial map showed that the gene Ms3 cosegregated with three markers, WG341, BCD1130 and CDO677. High-resolution mapping using an additional 509 BC₁ plants indicated that the marker WG341 was closely linked to Ms3 at a genetic distance of 0.8 cM. The Ms3 was mapped physically in the region spanning 40% of the arm length from the centromere of 5AS. Therefore, map-based cloning of the Ms3 is not feasible, although WG341 can be used as a useful tag for the Ms3 gene for breeding purposes. Received: 12 December 2000 / Accepted: 26 January 2001     

Speciation and chromosomal evolution of the palaearctic species of chironomids of the genus Sergentia Kieffer (Diptera, Chironomidae): Chromosome polymorphism in the populations of S. baueri Wülker et al., 1999, S. prima Proviz et al., 1997, and S. electa Proviz et al., 1999 from the Irkutsk reservoir

Chromosome polymorphism was studied in populations of three Palaearctic species of chironomids of the genus Sergentia Kieffer (Diptera, Chironomidae) from the Irkutsk reservoir: S. baueri Wülker et al., 1999, S. prima Proviz et al., 1997, and S. electa Proviz et al., 1999. It was found that in S. baueri heterozygous individuals constitute 72% of the population with 0.8 of inversion per individual. In total, three inversion sequences were detected. The most widespread was the inversion in regions 7–12 of the arm IIIR with the borders similar to those of the inversion in the Far East S. baueri populations and in populations of other species of the genus. In S. prima, heterozygotes constituted 60%, with the number of inversions per individual was 1.3. Seven inversion sequences were revealed, of which three were found in chromosome IV. In the S. electa population, only one inversion sequence was observed in chromosome III in 36% of larvae (0.4 of inversion per individual). The level of chromosome polymorphism in the populations of the Palaearctic species is comparable with that in the populations of endemic Sergentia from the Baikal Lake. Ten rearrangements were revealed in each of the two groups, but similar borders of chromosome regions were established only for two inversions. In the studied Sergentia species, chromosome IV has the most variable structure.     

CYTOLOGICAL STUDIES OF OEDOGONIUM. II. CHROMOSOME NUMBERS IN TWELVE SPECIES OF OEDOGONIUM

Mitotic chromosome counts are reported for 12 species of Oedogonium with the following distribution: two species with 13 chromosomes, two species with 16 chromosomes, five species with 17 chromosomes one species with 19 chromosomes, one species with 32 chromosomes, and one species with 38 + 1 chromosomes. Diploid strains of two species are illustrated and discussed. Cytological comparison of species establishes that there is great diversity in Oedogonium with relation to chromosome number, size, and morphology.     

Karyology of the genus Epidendrum (Orchidaceae: Laeliinae) with emphasis on subgenus Amphiglottium and chromosome number variability in Epidendrum secundum

Epidendrum is one of the largest Neotropical genera of Orchidaceae and comprises approximately 1500 species. Only 2.8% of these species have been studied cytologically, demonstrating chromosome numbers ranging from n = 12 in E. fulgens to n = 120 in E. cinnabarinum. The present work evaluated the evolution of the karyotypes of Epidendrum spp. based on data gathered from the literature and from analyses of the karyotypes of 16 Brazilian species (nine previously unpublished). The appearance of one karyotype with n = 12 with one larger chromosome pair in subgenus Amphiglottium appears to have occurred at the beginning of the divergence of this lineage, and x = 12 probably represents the basic number of this subgenus. Epidendrum secundum exhibits wide variation in chromosome numbers, with ten different cytotypes found in 22 Brazilian populations, seven of which were new counts: 2n = 30, 42, 50, 54, 56, 58 and 84. Most lineages of Epidendrum seem to have been secondarily derived from one ancestral stock with x = 20, as is seen in the majority of the present‐day representatives of the genus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 329–344.     

Hybrid origin of a B chromosome (PSR) in the parasitic wasp Nasonia vitripennis

Little is known about the origin and evolution of supernumerary (B) chromosomes. This study utilizes molecular markers to examine the evolutionary history and microstructural organization of the supernumerary paternal-sex-ratio (PSR) chromosome of the parasitic wasp Nasonia vitripennis. Copies of the retrotransposon NATE were previously isolated from PSR and the genomes of N. vitripennis and related wasp species. A phylogenetic analysis of sequences representing 29 elements from PSR and seven wasp species, coupled with a hybridization analysis of elements in genomic DNA provides evidence that PSR was recently transferred into N. vitripennis from a species in the genus Trichomalopsis. A linear region of the PSR chromosome was compared by Southern blot analysis with genomic DNA from N. vitripennis, Nasonia longicornis, Trichomalopsis americanus, and Trichomalopsis dubius. A region organized similarly to the region on PSR was not evident in any of the species, thus a progenitor region was not identified. However, the hybridizations revealed that this region of PSR is primarily composed of repetitive sequences that appear dispersed in these wasp genomes, and might represent additional mobile elements. At least three different dispersed repeats are present in the 18 kb region of PSR. The abundance of tandem and dispersed repetitive sequences in this relatively small region provides additional evidence for the degenerate structure of the PSR chromosome. Received: 19 December 1996; in revised form: 14 April 1997 / Accepted: 24 April 1997     

Genome Comparisons with Chromosomal and Molecular Markers for Three Closely Related Flax Species and Their Hybrids

Chromosome C-banding patterns were analyzed in three closely related flax species (Linum usitatissimumL., 2n = 30; L. angustifolium Huds., 2n = 30; and L. bienneMill., 2n = 30) and their hybrids. In each case, the karyotype included metacentrics, submetacentrics, and one or two satellite chromosomes. Chromosomes of the three flax species were similar in morphology, size (1–3 m), and C-banding pattern and slightly differed in size of heterochromatic regions. In all accessions, a large major site of ribosomal genes was revealed by hybridization in the pericentric region of a large metacentric. A minor 45S rDNA site was observed on a small chromosome in L. usitatissimum and L. bienne and on a medium-sized chromosome in L. angustifolium. Upon silver staining, a nucleolus-organizing region (NOR) was detected on a large chromosome in all species. InL. angustifolium, an Ag-NOR band was sometimes seen on a medium-sized chromosome. In the karyotypes of interspecific hybrids, silver-stained rDNA loci were observed on satellite chromosomes of both parental species. RAPD analysis with 22 primers revealed a high similarity of the three species. The greatest difference was observed between L. angustifolium and the other two species. The RAPD patterns of L. bienne and L. usitatissimum differed in fewer fragments. A dendrogram of genetic similarity was constructed for the three flax species on the basis of their RAPD patterns. Genome analysis with chromosome and molecular markers showed thatL. bienne must be considered as a subspecies of L. usitatissimum rather than a separate species. The three species were assumed to originate from a common ancestor, L. angustifoliumbeing closest to it.     

Use of recombinant inbred lines (RILs) to identify, locate and map major genes and quantitative trait loci involved with in vitro regeneration ability in Arabidopsis thaliana

The Landsberg erecta× Columbia recombinant inbred lines (RILs) of Arabidopsis have been used in order to identify and localize chromosome regions involved in the genetic control of the in vitro regeneration ability. Callus morphology (CM) and shoot regeneration (SR) traits have been considered for both leaf and root explants. The MAPMAKER analysis of leaf culture data has revealed at least one chromosome region involved with CM and several with SR, the 29–30 region of chromosome 1 being common for the two traits. Root explants did not segregate for CM but several QTLs have been detected for SR. The chromosome regions involved with leaf culture regeneration seem to be different from those of root cultures, although the regeneration of abnormal shoots in leaf explants share two chromosome regions with the regeneration of normal shoots in root cultures. Received: 19 April 2000 / Accepted: 12 May 2000     

Low incidence of polyploids and high uniformity of karyotypes displayed by Delphinium (Ranunculaceae) in the Hengduan Mountains region of south‐west China

The chromosome numbers and morphology in 92 populations belonging to 49 species and three varieties in the genus Delphinium L. (Ranunculaceae), mostly from the Hengduan Mountains region of south‐west China, were studied. Forty seven species and three varieties were diploid, with 2n = 16, one species was tetraploid, with 2n = 32, and one species had diploid and tetraploid cytotypes. Three species had B chromosomes, representing the first time the occurrence of B chromosomes has been reported in the genus. The karyotypes of all the diploid species were quite uniform, commonly bimodal, and usually consisted of one pair of large median‐centromeric (m), one pair of large submedian‐centromeric (sm), five pairs of medium‐sized subterminal‐centromeric (st), and one pair of smaller sm (rarely st) chromosomes. The low incidence of polyploids in Delphinium from the Hengduan Mountains region indicates that polyploidy has played a minor role in the speciation of this highly diversified genus in the region. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158 , 172–188.     

FISH mapping of the IGF2 gene in horse and donkey—detection of homoeology with HSA11

Three genomic subclones derived from a phage clone containing the equine IGF2 gene were used to FISH map the gene on horse (ECA) and donkey (EAS) metaphase chromosomes. The gene mapped on ECA 12q13 band and is the first locus mapped to this horse chromosome. In donkey the gene mapped very terminal on the long arm of one small submetacentric chromosome that shows almost identical DAPI-banding pattern with ECA12. This is the first locus mapped in donkey genome. Cross species chromosome painting of equine metaphase chromosomes with human Chromosome (Chr) 11-specific probe showed homoeology of this human chromosome with ECA12 and ECA7. The novel ECA12 comparative painting results are thus in accordance with the localization of the equine IGF2 gene. Comparison of the hitherto known physical locations of IGF2 in different species, viz. human, cattle, sheep, horse, and donkey, shows that this gene tends to maintain a terminal location on the chromosome arm. Received: 12 January 1997 / Accepted: 17 March 1997     

Chromosomal polymorphism of ribosomal genes in the genus Oryza

The genes encoding for 18S–5.8S–28S ribosomal RNA (rDNA) are both conserved and diversified. We used rDNA as probe in the fluorescent in situ hybridization (rDNA-FISH) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species. These included cultivated and wild species of rice, and four of them are tetraploids. Our results reveal polymorphism in the number of rDNA loci, in the number of rDNA repeats, and in their chromosomal positions among Oryza species. The numbers of rDNA loci varies from one to eight among Oryza species. The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza. The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions. In this study, we report two genome specific rDNA loci in the genus Oryza. One is specific to the BB genome, which was localized at the end of the short arm of chromosome 4. Another may be specific to the CC genome, which was localized in the proximal region of the short arm of chromosome 5. A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O. grandiglumis by rDNA-FISH. We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution. The possible mechanisms of cyto-evolution in tetraploid Oryza species are discussed.     

Chromosomal loci associated with endosperm hardness in a malting barley cross

A breeding objective for the malting barley industry is to produce lines with softer, plumper grain containing moderate protein content (9–12%) as they are more likely to imbibe water readily and contain more starch per grain, which in turn produces higher levels of malt extract. In a malting barley mapping population, ‘Arapiles’ × ‘Franklin’, the most significant and robust quantitative trait locus (QTL) for endosperm hardness was observed on the short arm of chromosome 1H, across three environments over two growing seasons. This accounted for 22.6% (Horsham 2000), 26.8% (Esperance 2001), and 12.0% (Tarranyurk 2001) of the genetic variance and significantly increased endosperm hardness by 2.06–3.03 SKCS hardness units. Interestingly, Arapiles and Franklin do not vary in Ha locus alleles. Therefore, this region, near the centromere on chromosome 1H, may be of great importance when aiming to manipulate endosperm hardness and malting quality. Interestingly, this region, close to the centromere on chromosome 1H, in our study, aligns with the region of the genome that includes the HvCslF9 and the HvGlb1 genes. Potentially, one or both of these genes could be considered to be candidate genes that influence endosperm hardness in the barley grain. Additional QTLs for endosperm hardness were detected on chromosomes 2H, 3H, 6H and 7H, confirming that the hardness trait in barley is complex and multigenic, similar to many malting quality traits of interest.     

Genetic analysis and FISH mapping of the Colourless non-ripening locus of tomato

Cnr (Colourless non-ripening) is a dominant pleiotropic ripening mutation of tomato (Lycopersicon esculentum) which has previously been mapped to the proximal region of tomato chromosome 2. We describe the fine mapping of the Cnr locus using both linkage analysis and fluorescence in situ hybridisation (FISH). Restriction fragment length polymorphism (RFLP)-, amplified restriction fragment polymorphism (AFLP)-, and cleaved amplified polymorphic sequence (CAPS)-based markers, linked to the Cnr locus were mapped onto the long arm of chromosome 2. Detailed linkage analysis indicated that the Cnr locus was likely to lie further away from the top of the long arm than previously thought. This was confirmed by FISH, which was applied to tomato pachytene chromosomes in order to gain an insight into the organisation of hetero- and euchromatin and its relationship to the physical and genetic distances in the Cnr region. Three molecular markers linked to Cnr were unambiguously located by FISH to the long arm of chromosome 2 using individual BAC probes containing these single-copy sequences. The physical order of the markers coincided with that established by genetic analysis. The two AFLP markers most-closely linked to the Cnr locus were located in the euchromatic region 2.7-cM apart. The physical distance between these markers was measured on the pachytene spreads and estimated to be approximately 900 kb, suggesting a bp:cM relationship in this region of chromosome 2 of about 330 kb/cM. This is less than half the average value of 750 kb/cM for the tomato genome. The relationship between genetic and physical distances on chromosome 2 is discussed. Received: 11 January 2001 / Accepted: 30 April 2001     

Phylogeography of a freshwater sculpin, Cottus nozawae, from the northeastern part of Honshu Island, Japan

 The fluvial sculpin, Cottus nozawae, is a coldwater-adapted fish distributed in Hokkaido Island and the northeastern part of Honshu Island (Tohoku District), Japan. Mitochondrial DNA (mtDNA) control region sequencing was used to investigate the geographic distribution of genetic variation and phylogeography of C. nozawae. Most populations possessed unique haplotypes, few being shared across river systems. Phylogenetic analysis of the sequences of the mtDNA control region and adjacent regions of C. nozawae revealed three distinct phylogenetic groups that differed by 3.05% to 3.11%, corresponding to distinct geographic regions, Hokkaido Island, northern Tohoku District, and Yamagata Prefecture (southwestern Tohoku District), respectively. The divergence times of three groups were estimated to be about 1.5 million years ago by applying a general rate for mtDNA, suggesting that the divergence among them might have occurred in the early Pleistocene. Divergence among the haplotypes within the group from the northern Tohoku District was also high (1.84%), no haplotypes being shared by local populations in different river systems in this region. Local populations from a single river system in this region comprise a distinct lineage that differed from other river systems. Such genetically divergent population structures among the different regions and river systems are considered to have resulted mainly from long-term isolation and restricted gene flow among river systems, probably promoted by the fluvial benthic life history and low dispersal ability of this species. Received: April 12, 2001 / Revised: December 1, 2001 / Accepted: December 19, 2001     

AFLP markers tightly linked to the aluminum-tolerance gene Alt3 in rye (Secale cereale L.)

Rye (Secale cereale L.) is considered to be the most aluminum (Al)-tolerant species among the Triticeae. It has been suggested that aluminum tolerance in rye is controlled by three major genes (Alt genes) located on rye chromosome arms 3RL, 4RL, and 6RS, respectively. Screening of an F₆ rye recombinant inbred line (RIL) population derived from the cross between an Al-tolerant rye (M39A-1–6) and an Al-sensitive rye (M77A-1) showed that a single gene controls aluminum tolerance in the population analyzed. In order to identify molecular markers tightly linked to the gene, we used a combination of amplified fragment length polymorphism (AFLP) and bulked segregant analysis techniques to evaluate the F₆ rye RIL population. We analyzed approximately 22,500 selectively amplified DNA fragments using 204 primer combinations and identified three AFLP markers tightly linked to the Alt gene. Two of these markers flanked the Alt locus at distance of 0.4 and 0.7 cM. Chromosomal localization using cloned AFLP and a restriction fragment length polymorphism (RFLP) marker indicated that the gene was on the long arm of rye chromosome 4R. The RFLP marker (BCD1230) co-segregated with the Alt gene. Since the gene is on chromosome 4R, the gene was designated as Alt3. These markers are being used as a starting point in the construction of a high resolution map of the Alt3 region in rye. Received: 29 March 2000 / Accepted: 9 July 2001