RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye

One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat

Four hundred and seventy-eight microsatellite markers derived from expressed sequence tags (EST-SSRs) were screened among three mapping populations (W-7984xOpata 85, WOpop; LumaixHanxuan, LHpop; WenmaixShanhongmai, WSpop). The number of polymorphic EST-SSR primer pairs found in WOpop, LHpop and WSpop was 92, 58 and 29 respectively. A total of 101 EST-SSR loci amplified from 88 primer sets were distributed over the 20 chromosomes of the reference maps (no markers were located on chromosome 4B). These 101 mapped EST-SSR markers add to the existing 450 microsatellite loci previously mapped in bread wheat. Seventy-four of the 101 loci showed significant similarities to known genes, including 24 genes involved in metabolism, 4 in cellular structures, 9 in stress resistance, 12 in transcription, 2 in development, 2 transporters and 21 storage proteins. Besides gliadin and glutenin, most of the 53 genes with putative functions were mapped for the first time by EST-SSR markers in bread wheat. Sequence alignment of the mapped wheat EST-SSR loci allowed tentative assignment of functionality to the other members of grasses family. Colinearity combined with homology information offers an attractive approach to comparative genomics.

DNA markers in plant improvement: an overview

The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

A linkage map of meadow fescue ( Festuca pratensis Huds.) and comparative mapping with other Poaceae species

A genetic linkage map has been constructed for meadow fescue ( Festuca pratensis Huds.) (2n=2 x=14) using a full-sib family of a cross between a genotype from a Norwegian population (HF2) and a genotype from a Yugoslavian cultivar (B14). The two-way pseudo-testcross procedure has been used to develop separate maps for each parent, as well as a combined map. A total number of 550 loci have been mapped using homologous and heterologous RFLPs, AFLPs, isozymes and SSRs. The combined map consists of 466 markers, has a total length of 658.8 cM with an average marker density of 1.4 cM/marker. A high degree of orthology and colinearity was observed between meadow fescue and the Triticeae genome(s) for all linkage groups, and the individual linkage groups were designated 1F-7F in accordance with the orthologous Triticeae chromosomes. As expected, the meadow fescue linkage groups were highly orthologous and co-linear with Lolium, and with oat, maize and sorghum, generally in the same manner as the Triticeae chromosomes. It was shown that the evolutionary 4AL/5AL translocation, which characterises some of the Triticeae species, is not present in the meadow fescue genome. A putative insertion of a segment orthologous to Triticeae 2 at the top of 6F, similar to the rearrangement found in the wheat B and the rye R genome, was also observed. In addition, chromosome 4F is completely orthologous to rice chromosome 3 in contrast to the Triticeae where this rice chromosome is distributed over homoeologous group 4 and 5 chromosomes. The meadow fescue genome thus has a more ancestral configuration than any of the Triticeae genomes. The extended meadow fescue map reported here provides the opportunity for beneficial cross-species transfer of genetic knowledge, particularly from the complete genome sequence of rice.

Genetic mapping of Dn7, a rye gene conferring resistance to the Russian wheat aphid in wheat

The Russian wheat aphid is a significant pest problem in wheat and barley in North America. Genetic resistance in wheat is the most effective and economical means to control the damage caused by the aphid. Dn7 is a rye gene located on chromosome 1RS that confers resistance to the Russian wheat aphid. The gene was previously transferred from rye into a wheat background via a 1RS/1BL translocation. This study was conducted to genetically map Dn7 and to characterize the type of resistance the gene confers. The resistant line '94M370' was crossed with a susceptible wheat cultivar that also contains a pair of 1RS/1BL translocation chromosomes. The F(2) progeny from this cross segregated for resistance in a ratio of 3 resistant: 1 susceptible, indicating a single dominant gene. One-hundred and eleven RFLP markers previously mapped on wheat chromosomes 1A, 1B and 1D, barley chromosome 1H and rye chromosome 1R, were used to screen the parents for polymorphism. A genetic map containing six markers linked to Dn7, encompassing 28.2 cM, was constructed. The markers flanking Dn7 were Xbcd1434 and XksuD14, which mapped 1.4 cM and 7.4 cM from Dn7, respectively. Dn7 confers antixenosis, and provides a higher level of resistance than that provided by Dn4. The applications of Dn7 and the linked markers in wheat breeding are discussed.

Characterization of a gene from chromosome 1B encoding the large subunit of ADPglucose pyrophosphorylase from wheat: evolutionary divergence and differential expression of Agp2 genes between leaves and developing endosperm

A full-length genomic clone containing the gene encoding the large subunit of the ADPglucose pyrophosphorylase (Agp2), was isolated from a genomic library prepared from etiolated shoots of hexaploid wheat (Triticum aestivum L., cv, Chinese Spring). The coding region of this gene is identical to one of the cDNA clones previously isolated from a developing wheat grain cDNA library and is therefore an actively transcribed gene. The sequence represented by the cDNA spans 4.8 kb of the genomic clone and contains 15 introns. 2852 bp of DNA flanking the transcription start site of the gene was cloned upstream of the GUS (beta-glucuronidase) reporter gene. This Agp2::GUS construct and promoter deletions were used to study the pattern of reporter gene expression in both transgenic tobacco and wheat plants. Histochemical analysis of GUS expression in transgenic tobacco demonstrated that the reporter gene was expressed in guard cells of leaves and throughout the seed. In transgenic wheat, reporter gene expression was confined to the endosperm and aleurone with no expression in leaves. The cloned Agp2 gene was located to chromosome 1B by gene-specific PCR with nullisomic-tetrasomic lines. Northern analysis demonstrated that the Agp2 genes are differentially expressed in leaves and developing endosperm; while all three classes of Agp2 genes are transcribed in developing wheat grain endosperm, only one is transcribed in leaves. The differences between the Agp2 genes are discussed in relation to the evolution of hexaploid wheat.

Genetic analysis and genome mapping in Raphanus

The first genetic map of the Raphanus genome was developed based on meiosis in a hybrid between Raphanus sativus (cultivated radish) and Raphanus raphanistrum (wild radish). This hybrid was used to produce a BC1 population of 54 individuals and an F2 population of 85 individuals. A total of 236 marker loci were assayed in these populations using a set of 144 informative Brassica RFLP probes previously used for genetic mapping in other crucifer species. The genetic maps derived from the BC1 and F2 populations were perfectly collinear and were integrated to produce a robust Raphanus map. Cytological observations demonstrated strict bivalent pairing in the R. sativus x R. raphanistrum hybrids. Productive pairing along the length of each chromosome was confirmed by the identification of nine extensive linkage groups and the lack of clustering of marker loci. Indeed, the distributions of both marker loci and crossovers was more random than those reported for other crop species. The genetic markers and the reference map of Raphanus will be of considerable value for future trait mapping and marker-assisted breeding in this crop, as well as in the intergenomic transfer of Raphanus genes into Brassica crops. The future benefits of comparative mapping with Arabidopsis and Brassica species are also discussed.

The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms

Genes detected by wheat expressed sequence tags (ESTs) were mapped into chromosome bins delineated by breakpoints of 159 overlapping deletions. These data were used to assess the organizational and evolutionary aspects of wheat genomes. Relative gene density and recombination rate increased with the relative distance of a bin from the centromere. Single-gene loci present once in the wheat genomes were found predominantly in the proximal, low-recombination regions, while multigene loci tended to be more frequent in distal, high-recombination regions. One-quarter of all gene motifs within wheat genomes were represented by two or more duplicated loci (paralogous sets). For 40 such sets, ancestral loci and loci derived from them by duplication were identified. Loci derived by duplication were most frequently located in distal, high-recombination chromosome regions whereas ancestral loci were most frequently located proximal to them. It is suggested that recombination has played a central role in the evolution of wheat genome structure and that gradients of recombination rates along chromosome arms promote more rapid rates of genome evolution in distal, high-recombination regions than in proximal, low-recombination regions.

Development of PCR-based markers linked to dominant genes for male-fertility restoration in Pampa CMS of rye (Secale cereale L.)

Cytoplasmatic male sterility (CMS) is the basis for commercial hybrid seed production of rye. Nuclear restorer genes are indispensable for a complete restoration of fertility of the CMS lines. The drawbacks of current European restorer lines require the utilisation of new genetic resources that have been recently detected in an Iranian primitive rye population (IRAN IX) and an Argentinean landrace (Pico Gentario). The introgression of these effective restorer genes (Rfp1 and Rfp2, respectively) into breeding material can be facilitated by marker-assisted selection. Using two F(2) populations based on crosses between the non-restorer inbred line Lo6 and the restorer IRAN IX, as well as Pico Gentario, RAPDs and AFLPs were screened and led to a closely linked marker set for each of these genes. The conversion of the closest markers into fragment-specific sequence-characterised amplified region (SCAR) markers resulted in flanking ranges of 2.9 cM (Rfp1) and 5.2 cM (Rfp2). The application of these markers in backcross programmes is discussed.

Structural organization of the group-1 chromosomes of two bread wheat sister lines

Eureka and Renan are two French bread wheat cultivars derived from a 4-way cross. Using molecular markers (essentially RFLPs), we studied the structure of the group-1 chromosomes of these two genotypes, their parents and a doubled-haploid (DH) population derived from their F(1). Using the DH population (102 lines), a molecular map of the three homoeologous group-1 chromosomes was produced and compared with the map established on another intervarietal cross: Courtot x Chinese Spring (Cadalen et al. 1997). The polymorphic markers were mapped on the DH population and characterized on the four grand-parents, allowing us to compare the structural organization of the group-1 chromosomes of Eureka and Renan and determine their origin. These chromosomes were very different, except for small regions (1AL proximal and 1BL distal) which were identical.

New evidence for the synteny of rice chromosome 1 and barley chromosome 3H from rice expressed sequence tags

To provide improved access to the wealth of resources and genomic information that is presently being developed for rice a set of 88 rice expressed sequence tags (ESTs) previously mapped on rice chromosome 1 in the cross 'Nipponbare' × 'Kasalath' was used for comparative mapping in a cross of the barley cultivars 'Igri' and 'Franka'. As expected, most (89%) of the clones gave distinct banding patterns in barley of which about one-third was polymorphic between 'Igri' and 'Franka'. These polymorphisms were mapped, and most of these (56%) confirmed that rice chromosome 1 and barley chromosome 3H are syntenous. All single-copy markers identified conserved collinear positions, while markers with multiple copies did so in a few cases only. The markers that were not fitting in the collinear order were distributed randomly across the barley genome. The comparative maps of barley chromosome 3H and rice chromosome 1 comprise in total 26 common markers covering more than 95% of the genetic length of both chromosomes. A 30-fold reduction of recombination is seen around the barley centromere, and synteny may be interrupted in this region. However, the good overall synteny on a mesoscale (1–10 cM) justifies the use of rice as a platform for map-based cloning in barley.Key words: Oryza sativa, Hordeum vulgare, RFLP, synteny, comparative mapping.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative quasi-linkage

The main objectives of the study reported here were to construct a molecular map of wild emmer wheat, Triticum dicoccoides, to characterize the marker-related anatomy of the genome, and to evaluate segregation and recombination patterns upon crossing T. dicoccoides with its domesticated descendant Triticum durum (cultivar Langdon). The total map length exceeded 3000 cM and possibly covered the entire tetraploid genome (AABB). Clusters of molecular markers were observed on most of the 14 chromosomes. AFLP (amplified fragment length polymorphism) markers manifested a random distribution among homologous groups, but not among genomes and chromosomes. Genetic differentiation between T. dicoccoides and T. durum was attributed mainly to the B genome as revealed by AFLP markers. The segregation-distorted markers were mainly clustered on 4A, 5A, and 5B chromosomes. Homeoalleles, differentially conferring the vigor of gametes, might be responsible for the distortion on 5A and 5B chromosomes. Quasilinkage, deviation from free recombination between markers of nonhomologous chromosomes, was discovered. Massive negative interference was observed in most of the chromosomes (an excess of double crossovers in adjacent intervals relative to the expected rates on the assumption of no interference). The general pattern of distribution of islands of negative interference included near-centromeric location, spanning the centromere, and median/subterminal location. [An appendix describing the molecular marker loci is available as an online supplement at http://www.genome.org.]

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints

We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (</=1 Mb/cM) correspond to only 4.9% of the total barley genome and harbor 47.3% of the 429 markers of the studied RFLP map. The results for barley correspond well with those obtained by deletion mapping in wheat. This indicates that chromosomal regions characterized by similar recombination frequencies and marker densities are highly conserved between the genomes of barley and wheat. The findings for barley support the conclusions drawn from deletion mapping in wheat that for all plant genomes, notwithstanding their size, the marker-rich regions are all of similar gene density and recombination activity and, therefore, should be equally accessible to map-based cloning.

Physical mapping of wheat-Aegilops longissima breakpoints in mildew-resistant recombinant lines using FISH with highly repeated and low-copy DNA probes

Fluorescence in situ hybridization (FISH) with multiple probes, consisting of highly repeated DNA sequences (pSc119.2 and pAs1) and of a low-copy, 3BS-specific RFLP sequence (PSR907), enabled determination of the physical position of the wheat-alien breakpoints (BPs) along the 3BS and 3DS arms of common wheat recombinant lines. These lines harbour 3SlS Aegilops longissima segments containing the powdery mildew resistance gene Pm13. In all 3B recombinants, the wheat-Aegilops longissima physical BPs lie within the interval separating the two most distal of the three pSc119.2 3BS sites. In all such recombinants a telomeric segment, containing the most distal of the pSc119.2 3BS sites, was in fact replaced by a homoeologous Ae. longissima segment, marked by characteristic pSc119.2 hybridization sites. Employment of the PSR907 RFLP probe as a FISH marker allowed to resolve further the critical region in the various 3B recombinant lines. Three of them, like the control common wheat, exhibited between the two most distal pSc119.2 sites a single PSR907 FISH site, which was missing in a fourth recombinant line. The amount of alien chromatin can thus be estimated to represent around 20% of the recombinant arm in the three former lines and a maximum of 27% in the latter. A similar physical length was calculated for the alien segment contained in three 3D recombinants, all characterized by the presence of the Ae. longissima pSc119.2 sites distal to the nearly telomeric pAs1 sites of normal 3DS. Comparison between the FISH-based maps and previously developed RFLP maps of the 3BS-3SlS and 3DS-3SlS arms revealed substantial differences between physical and genetic map positions of the wheat-alien BPs and of molecular markers associated with the critical chromosomal portions.Key words: wheat-alien recombinants, chromosome engineering, fluorescence in situ hybridization, highly repeated and low-copy DNA probes, physical versus genetic maps.

RFLP mapping of a gene for hairy leaf sheath using a recombinant line from Hordeum vulgare L. ×Hordeum bulbosum L. cross

A gene conditioning hairy leaf sheath character, which was derived from Hordeum bulbosum and designated Hsb, was mapped using a cross between Hordeum vulgare and a H. vulgare/H. bulbosum recombinant line. The Hsb locus was tagged relative to eight RFLP markers detecting three loci on the distal part of chromosome 4HL. The map position suggests that Hsb of H. bulbosum is homoeologous to the gene Hp1 of rye (Secale cereale), which pleiotropically governs the traits hairy leaf sheath and hairy peduncle. It is proposed that the recombination break point between H. vulgare and H. bulbosum chromosomes occured at a position homoeologous compared with the 4L/5L translocation in Triticeae genomes, and may reflect a hot spot for chromosome breakage.Key words: Hordeum vulgare, Hordeum bulbosum, comparative mapping, hairy leaf sheath, RFLP.

The wheat peptidyl prolyl cis-trans-isomerase FKBP77 is heat induced and developmentally regulated

We isolated a cDNA encoding a 568-amino acid, heat-stress-induced peptidyl prolyl isomerase belonging to the FK506-binding-protein (FKBP) family. The open reading frame encodes for a peptidyl prolyl isomerase that possesses three FKBP-12-like domains, a putative tetratricopeptide motif, and a calmodulin-binding domain. Specific antibodies showed that the open reading frame encodes a heat-induced 77-kD protein, the wheat FKBP77 (wFKBP77), which exhibits 84% identity with the wFKBP73 and 42% identity with the human FKBP59. Because of the high similarity in sequence to wFKBP73, wFKBP77 was designated as the heat-induced isoform. The wFKBP77 mRNA steady-state level was 14-fold higher at 37 degreesC than at 25 degreesC. The wFKBP77 transcript abundance was the highest in mature embryos that had imbibed and 2-d-old green shoots exposed to 37 degreesC, and decreased to 6% in 6-d-old green shoots. The transcript level returned to the level detected at 25 degreesC after recovery of the embryos for 90 min at 25 degreesC. We compared wFKBP73 and wFKBP77 with the heat-shock proteins having cognate and heat-stress-induced counterparts.

Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley

The wheat genome is large, hexaploid, and contains a high amount of repetitive sequences. In order to isolate agronomically important genes from wheat by map-based cloning, a simpler model of the genome must be used for identifying candidate genes. The objective of this study was to comparatively map the genomic regions of two wheat leaf rust disease resistance loci, Lr1 and Lr10, in the putative model genomes of rice and barley. Two probes cosegregating with the Lr1 gene on chromosome 5DL of wheat were studied. The rice sequences corresponding to the two probes were isolated and mapped. The two probes mapped to two different rice chromosomes, indicating that the organization of the region orthologous to Lr1 is different in rice and wheat. In contrast, synteny was conserved between wheat and barley in this chromosomal region. The Lrk10 gene cosegregated with Lr10 on chromosome 1AS in wheat. The rice gene corresponding to Lrk10 was mapped on rice chromosome 1, where it occurred in many copies. This region on rice chromosome 1 corresponds to the distal part of the group 3S chromosomes in Triticeae. The synteny is conserved between rice chromosome 1 and the Triticeae group 3S chromosomes up to the telomere of the chromosomes. On group 3S chromosomes, we found a gene that is partially homologous to Lrk10. We conclude that in the genomic regions studied, there is limited and only partially useful synteny between wheat and rice. Therefore, barley should also be considered as a model genome for isolating the Lr1 and Lr10 genes from wheat.

Synteny with rice: analysis of barley malting quality QTLs and rpg4 chromosome regions

The barley (Hordeum vulgare L.) chromosome 1 centromere region contains two adjacent overlapping quantitative trait loci (QTLs) for malting quality traits, and the chromosome 7L subtelomere region contains the stem rust (causal agent Puccinia graminis f.sp. tritici) resistance gene rpg4. To facilitate the saturation mapping of these two target regions, a synteny-based approach was employed. Syntenic relationships between the barley target regions and the rice (Oryza sativa) genome were established through comparative mapping. The barley chromosome 1 centromere region was found to be syntenic with rice chromosome 8 and parts of rice chromosomes 3 and 10. A 6- to 15-fold difference in genetic distance between barley and rice in the syntenic region was observed, owing to the apparent suppressed recombination in the barley chromosome 1 centromere region. Barley chromosome 7L was found to be syntenic with rice chromosome 3. The establishment of synteny with rice in the two target regions allows well-established and characterized rice resources to be utilized in fine mapping and map-based cloning studies.Key words: genome synteny, quantitative trait loci, QTL, disease resistance gene, Triticeae.

A 120 kilobase resolution contig map of the rice genome

92% of the rice genome (4.3 x 10(8) bp, 2n = 24) was covered by 631 contigs of various length, which were generated by fingerprinting from a representative and genetically stable bacterial artificial chromosome (BAC) library of the Guang Lu Ai 4 (a O. Sativa variety) genome with the average insert of 120 kb in length. To form the contig map, 565 molecular markers of RFLP, STS, cDNA and anchor set derived from two O. Sativa varieties were by colony hybridization mapped to the contigs, which were then assigned to and ordered along the particular chromosomes according to the marker colinearity. Being highly conserved DNA sequences shared among the genomes of rice, barley, wheat, oat, maize, sorghum and sugar cane, 89 anchor markers mapped help to identify the rice genes through the information provided by the maps of relative genomes, and vice versa. Numerous repeated DNA sequences of various length were identified and mapped to the chromosomes. Physical distances have been determined for hundreds pairs of adjacent markers, which would facilitate the identification by map-based cloning the rice genes of interest. The accuracy of clone overlaps in contigs was further confirmed by the existence in contigs of well fit stacks of marker-lodged clones independently identified by hybridization. Large scale DNA sequencing of individual chromosomes could now be initiated simply by selecting and sequencing the minimally overlapped BAC clones of the contigs.

Public informatics resources for rice and other grasses

As an emerging model system, rice will benefit from an informatics infrastructure which organizes genome data and makes it available worldwide. RiceGenes and other Internet-accessible resources are evolving to meet these goals. Grass crops such as rice, maize, millet, sorghum and wheat are closely related but are represented by independent database projects; interlinking these resources would create a broad view of grass genetics and make it easier to compare data across genomes. The future success of grass informatics depends on the development of new comparative mapping displays as well as the participation of the research community in assembling and curating comparative map data.

Comparison and integration of four barley genetic maps

Barley (Hordeum vulgare L.) is one of the most extensively studied food crops in recent molecular research. More than 1000 molecular markers have been located on the barley genome by using five independent populations. For the present study, four segregation data sets, 'Proctor' × 'Nudinka', 'Igri' × 'Franka', 'Steptoe' × 'Morex', and 'Harrington' × TR306, were downloaded from the publicly available GrainGenes databank. Since 22% of the markers are common to at least two of the independent data sets, we were able to establish an integrated map using the computer package JOINMAP v2.0. The integrated map contains 898 markers, covers 1060 cM, and removes many large gaps present in the individual maps. Comparison of the integrated map with the individual maps revealed that the overall linear order of markers is in good agreement and that the integrated map is consistent with the component maps. No significant reordering of markers was found. This conservative property of the barley genome makes the integrated map reliable and successful. Except for chromosome 7 (5H), marker clustering was observed in the centromeric regions, probably owing to the centromeric suppression of recombination. Based on this integrated map, geneticists and breeders can choose their favourite markers in any region of interest of the barley genome. Key words : Hordeum vulgare, RFLP, integrated map.

Restriction fragment length polymorphism detected by cDNA and genomic DNA clones in Stylosanthes

A DNA isolation method suitable for genomic library construction and RFLP analyses of the forage legume Stylosanthes was developed. Probes isolated using this method were used to investigate the feasibility of constructing RFLP-based genetic maps in this genus. Two hundred and seventy-one PstI genomic DNA and 134 cDNA clones were analysed against four Stylosanthes accessions, including two tetraploids and two diploids, with the use of two restriction enzymes, DraI and HindIII. The proportion of clones which detected single-copy sequences from the PstI genomic library was higher than that from the cDNA library, but the percentage of clones which detected low-copy sequences was doubled in the latter. There was no significant difference in the level of RFLPs detected by gDNA and cDNA probes, although the level of polymorphism was lower in the diploids. A large proportion of RFLPs seemed to have resulted from mutation/base substitution events, and this was especially the case in diploids.

Comparative mapping in grasses. Oat relationships

The development of RFLP linkage maps in hexaploid and diploid oat allows us to study genetic relationships of these species at the DNA level. In this report, we present the extension of a previously developed diploid oat map (Avena atlantica x A. hirtula) and its molecular-genetic relationships with wheat, rice and maize. Examination of 92-99% of the length of the oat genome map with probes common to Triticeae species, rice or maize showed that 84, 79 and 71%, respectively, was conserved between these species and oat. Generally, the orders of loci among chromosomes homoelogous to oat chromosomes A and D were the most conserved and those of chromosomes homoeologous to oat chromosome G were the least conserved. Conservation was observed for blocks ranging from whole chromosomes 101 cM long to small segments 2.5 cM long containing two loci. Comparison of the homoeologous segments of Triticeae, rice and maize relative to oat indicated that certain regions have been maintained in all four species. The relative positions of major genes governing traits such as seed storage proteins and resistance to leaf rusts have been conserved between cultivated oat and Triticeae species. Also, the locations of three vernalization/or photoperiod response genes identified in hexaploid oat correspond to the locations of similar genes in homoeologous chromosomes of wheat, rice or maize. The locations of the centromeres for six of the seven oat chromosomes were estimated based on the homoeologous segments between oat and Triticeae chromosomes.

Comparative mapping in grasses. Wheat relationships

Conventionally, the genetics of species of the family Gramineae have been studied separately. Comparative mapping using DNA markers offers a method of combining the research efforts in each species. In this study, we developed consensus maps for members of the Triticeae tribe (Triticum aestivum, T. tauschii, and Hordeum spp.) and compared them to rice, maize and oat. The aneuploid stocks available in wheat are invaluable for comparative mapping because almost every DNA fragment can be allocated to a chromosome arm, thus preventing erroneous conclusions about probes that could not be mapped due to a lack of polymorphism between mapping parents. The orders of the markers detected by probes mapped in rice, maize and oat were conserved for 93, 92 and 94% of the length of Triticeae consensus maps, respectively. The chromosome segments duplicated within the maize genome by ancient polyploidization events were identified by homoeology of segments from two maize chromosomes to regions of one Triticeae chromosome. Homoeologous segments conserved across Triticeae species, rice, maize, and oat can be identified for each Triticeae chromosome. Putative orthologous loci for several simply inherited and quantitatively inherited traits in Gramineae species were identified.

Cytogenetic and molecular mapping of the wheat-Aegilops longissima chromatin breakpoints in powdery mildew-resistant introgression lines

The amount of alien chromatin introgressed in eight wheat/Ae. longissima Pm13 recombinant lines, involving breakpoints on the short arms of wheat chromosomes 3B and 3D, was evaluated by cytogenetic and molecular approaches. For each line the residual homologous synaptic ability of the recombinant chromosome in its proximal wheat and distal alien portion was estimated through meiotic analyses. Subsequently, telocentric and RFLP mapping were used to assess the genetic distance from the wheat centromere to the wheat/Ae. longissima breakpoints. One 3B recombinant line was distinguished from the other four by the chromosome pairing and telocentric mapping analyses. RFLP analysis succeeded in differentiating the remaining four lines into two groups. Chromosome pairing and telocentric mapping of the three 3D recombinant lines suggested that all had distinct breakpoints. However, the RFLP data could not discriminate between the two more proximal translocations. Physical locations for some RFLP loci were determined by a comparison of genotypes and C-banding karyotypes. This showed a considerable expansion of the genetic map compared to its physical length.

Multiple cDNAs of wheat voltage-dependent anion channels (VDAC): isolation, differential expression, mapping and evolution

The mitochondrial outer membrane of eukaryotic cells contains voltage-dependent anion channels (VDAC) also termed porins. Three cDNAs from wheat (Triticum aestivum) were isolated and sequenced (Tavdac 1-3). They share 65% similarity of their amino acid sequences, and therefore they probably represent isoforms. The deduced amino acid sequence of one of the cDNAs was found to be identical to the purified VDAC protein from wheat mitochondria [8]. Secondary structure analysis of the deduced amino acid sequences of the three vdac cDNAs revealed a characteristic alpha helix at their N-terminal and beta-barrel cylinders characteristic of VDAC channels. The Tavdac cDNAs are differentially expressed in meristematic tissues. The transcript levels of Tavdac 1 in all wheat tissues is at least 2.5-fold higher than Tavdac 2 and Tavdac 3. Tavdac 2 has a low level of expression in all floral tissues whereas Tavdac 3 is highly expressed in anthers. This is the first report on differential expression of vdac genes in plants. The Tavdac genes have been mapped on the wheat genome. Tavdac 1 is located on the long arm of chromosome 5, Tavdac 2 on the long arm of chromosome 1 and Tavdac 3 on the long arm of chromosome 3. A phylogenetic reconstruction indicates that vdac genes underwent numerous duplication events throughout their evolution. All duplications occurred after the separation of plants from animals and fungi, and no orthologous genes are shared among phyla. Within plants, some of the vdac gene duplications probably occurred before the monocotydelon-dicotydelon split.

Linkage relationships among stress-induced genes in wheat

Linkage relationships among genes responding to water-deficit, salt stress, and heat shock were investigated in diploid wheat, Triticum monococcum L. The position of these gene loci relative to closely linked markers and the centromeres is reported. It is proposed to continue to use the present T. monococcum mapping population and the genetic maps based thereon as a framework for future determination of relationships among other genes related to environmental stress in the tribe Triticeae.

Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination

The construction of comparative genetic maps of chromosomes 4A(m) and 5A(m) of Triticum monococcum and chromosomes of homoeologous groups 4, 5 and 7 of T. aestivum has provided insight into the evolution of these chromosomes. The structures of chromosomes 4A, 5A and 7B of modern-day hexaploid bread wheat can be explained by a 4AL/5AL translocation that occurred at the diploid level and is present both in T. monococcum and T. aestivum. Three further rearrangements, a 4AL/7BS translocation, a pericentric inversion and a paracentric inversion, have taken place in the tetraploid progenitor of hexaploid wheat. These structural rearrangements and the evolution of chromosomes 4A, 5A and 7B of bread wheat are discussed. The presence of the 4AL/5AL translocation in several Triticeae genomes raises two questions - which state is the more primitive, and is the translocation of mono- or poly-phylogenetic origin?The rearrangements that have occurred in chromosome 4A resulted in segments of both arms having different positions relative to the telomere, compared to 4A(m) and to 4B and 4D. Comparisons of map length in these regions indicate that genetic length is a function of distance from the telomere, with the distal regions showing the highest recombination.

Identification of molecular markers linked to the Agropyron elongatum-derived leaf rust resistance gene Lr24 in wheat

The objective of this study was to identify molecular markers linked to the wheat leaf rust resistance gene Lr24 derived from Agropyron elongatum (3DL/3Ag translocation). Two near isogenic lines (NILs), 'Arina' and Lr24/7 (*) "Arina", were screened for polymorphism at the DNA level with 115 RFLP probes. Twenty-one of these probes map to the homoeologous group 3. In addition, 360 RAPD primers were tested on the NILs. Six RFLP probes showed polymorphism between the NILs, and 11 RAPD primers detected one additional band in the resistant NIL. The genetic linkage of the polymorphic markers with Lr24 was tested on a segregating F2 population (150 plants) derived from a cross between the leaf rust resistant Lr24/7 (*) "Arina" and the susceptible spelt (Triticum spelta) variety 'Oberkulmer'. All 6 RFLP markers were completely linked to Lr24: one was inherited as a codominant marker (PSR1205), one was in coupling phase (PSR1203) and 4 were in repulsion phase (PSR388, PSR904, PSR931, PSR1067) with Lr24. The localization of these probes on chromosome 3D was confirmed by nulli-tetrasomic analysis. Distorted genotypic segregation was found for the Codominant RFLP marker PSR1205. This distortion can be explained by the occurrence of hemizygous plants. One of the 11 RAPD markers (OPJ-09) also showed complete linkage to theLr24 resistance gene. The polymorphic RAPD fragment was cloned and sequenced. Specific primers were synthesized, and they produced an amplification product only in the resistant plants. This specific marker allows a reliable and rapid screening of a large number of genotypes in practical breeding. Analysis of 6 additional lines containing Lr24 revealed that 3 lines have a smaller chromosomal segment of A. elongatum than lines derived from 'Agent', a commonly used gene donor for the Lr24 resistance gene.

RFLP mapping of the vernalization (Vrn1) and frost resistance (Fr1) genes on chromosome 5A of wheat

A population of single chromosome recombinant lines was developed from the cross between a frost-sensitive, vernalization-insensitive substitution line, 'Chinese Spring' (Triticum spelta 5A) and a frost-tolerant, vernalization-sensitive line, 'Chinese Spring' ('Cheyenne' 5A), and used to map the genes Vrn1 and Fr1 controlling vernalization requirement and frost tolerance, respectively, relative to RFLP markers located on this chromosome. The Vrn1 and Fr1 loci were located closely linked on the distal portion of the long arm of 5AL, but contrary to previous observations, recombination between them was found. Three RFLP markers, Xpsr426, Xcdo504 and Xwg644 were tightly linked to both. The location of Vrn1 suggests that it is homoeologous to other spring habit genes in related species, particularly the Sh2 locus on chromosome 7 (5H) of barley and the Sp1 locus on chromosome 5R of rye.

RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter × spring barley (Hordeum vulgare L.) cross

A genetic map of 92 RFLP loci and two storage protein loci was made using 94 doubled-haploid lines from a cross between the winter barley variety Igri and the spring variety Triumph. The markers were combined with data from two field experiments (one spring sown and one autumn (fall) sown) and a glasshouse experiment to locate a total of 13 genes (five major genes and eight quantitative trait loci (QTL)) controlling flowering time. Two photoperiod response genes were found; Ppd-H1 on chromosome 2(2H)S regulated flowering time under long days, while Ppd-H2 on chromosome 5(1H)L was detected only under short days. In the field experiments Ppd-H1 strongly affected flowering time from spring and autumn sowings, while Ppd-H2 was detected only in the autumn sowing. The glasshouse experiment also located two vernalization response genes, probably Sh and Sh2, on chromosomes 4(4H)L and 7(5H)L, respectively. The vernalization response genes had little effect on flowering time in the field. Variation in flowering time was also affected by nine additional genes, whose effects were not specifically dependent on photoperiod or vernalization. One was the denso dwarfing gene on chromosome 3(3H)L. The remaining eight were QTLs of smaller effect. One was located on chromosome 2(2H), one on 3(3H), one on 4(4H), one on 7(5H), two on 6(6H), and two on 1(7H). Model fitting showed that the 13 putative genes, and their interactions, could account for all the observed genetical variation from both spring and autumn sowings, giving a complete model for the control of flowering time in this cross.Key words: barley, Hordeum vulgare, flowering time, photoperiod, vernalization, mapping.

Conversion of a RAPD-generated PCR product, containing a novel dispersed repetitive element, into a fast and robust assay for the presence of rye chromatin in wheat

Bulk segregant analysis was used to obtain a random amplified polymorphic DNA (RAPD) marker specific for the rye chromosome arm of the 1BL.1RS translocation, which is common in many high-yielding bread wheat varieties. The RAPD-generated band was cloned and end-sequenced to allow the construction of a pair of oligonucleotide primers that PCR-amplify a DNA sequence only in the presence of rye chromatin. The amplified sequence shares a low level of homology to wheat and barley, as judged by the low strength of hybridization of the sequence to restriction digests of genomic DNA. Genetic analysis showed that the amplified sequence was present on every rye chromosome and not restricted to either the proximal or distal part of the 1RS arm. In situ hybridization studies using the amplified product as probe also showed that the sequence was dispersed throughout the rye genome, but that the copy number was greatly reduced, or the sequence was absent at both the centromere and the major sites of heterochromatin (telomere and nucleolar organizing region). The probe, using both Southern blot and in situ hybridization analyses, hybridized at a low level to wheat chromosomes, and no hybridizing restriction fragments could be located to individual wheat chromosomes from the restriction fragment length polymorphism (RFLP) profiles of wheat aneuploids. The disomic addition lines of rye chromosomes to wheat shared a similar RFLP profile to one another. The amplified sequence does not contain the RIS 1 sequence and therefore represents an as yet undescribed dispersed repetitive sequence. The specificity of the amplification primers is such that they will provide a useful tool for the rapid detection of rye chromatin in a wheat background. Additionally, the relatively low level of cross-hybridization to wheat chromatin should allow the sequence to be used to analyse the organization of rye euchromatin in interphase nuclei of wheat lines carrying chromosomes, chromosome segments or whole genomes derived from rye.

Predigestion of DNA template improves the level of polymorphism of random amplified polymorphic DNAs in wheat

Random amplified polymorphic DNA (RAPD) analysis in wheat has proven to be poor in its levels of both reproducibility and polymorphism. By digesting the template, prior to performing PCR, with frequently cutting restriction enzymes, the level of polymorphism was improved. RAPD profiles from certain primers were not affected by this pretreatment of the template, but other primers produced distinct profiles from each of several restriction enzymes assayed. Some polymorphisms were specific to one or more restriction digests, but none involved the simple loss of bands from the unrestricted template profile. Genotypic comparisons enabled the selection of primer-restriction enzyme combinations that enabled polymorphic and mappable patterns to be produced both between wheat varieties and between wheats with and without chromosomal segments deriving from related species.

Use of recombinant substitution lines in the construction of RFLP-based genetic maps of chromosomes 6A and 6B of tetraploid wheat (Triticum turgidum L.)

RFLP-based genetic maps of chromosomes 6A and 6B of Triticum turgidum have been constructed using data obtained by the study of Triticum turgidum var 'durum' cv 'Langdon'-T. t. var 'dicoccoides' recombinant substitution lines (RSLs) supplemented with data obtained from F3 families derived from 'Langdon' dicoccoides 6A and 6B disomic substitution lines. The average RFLP frequencies detected for the two chromosomes in a test of 45 DNA clones with six restriction enzymes were 56% and 53%, respectively, and a subset of 32 clones gave frequencies of 75% and 72%, respectively. Seventeen loci were mapped in 6A and 18 in 6B. With the possible exception of 5 loci in the centromeric region of 6A, all of the mapped 6A and 6B loci are located in the same arm as are homologous loci in hexaploid wheat, and the linear order of the loci is the same in the two chromosomes, except possibly close to the centromere. Major differences in genetic distances exist between homologous loci located in the proximal regions of the 6AL and 6BL linkage groups, however, the distances being much larger in the former than in the latter. The 6B maps that were constructed using data from both the RSL and the F2 populations and using data from the RSL population alone closely resemble one another, indicating that the 6B RSL population, composed of 85 lines, can be reliably used for genetic mapping. Additional studies must be conducted before the utility of the 6A RSL population, composed of 66 lines, can be adequately assessed.

Identification of homoeologous chromosomes in hexaploid oat (A. byzantina cv Kanota) using monosomics and RFLP analysis

The use of RFLP markers, together with a partial set of monosomics available in Avena byzantina cv Kanota, has enabled us to identify putative homoeologous chromosome sets in hexaploid Avena species (2n = 6x = 42, AACCDD). We first identified probes producing distinct three-band patterns on Southern blots that possibly reflect orthologous loci of the three genomes present in the hexaploid. Using monosomic analysis, 51 different restriction fragments that hybridized to 26 probes were localized to 12 different chromosomes for which monosomic stocks were available. These DNA restriction fragments were localized to specific monosomics using image analysis to quantify band intensity relative to other bands in the same lane. From these data, we have tentatively identified two complete homoeologous sets of three chromosomes each and two partial sets of two of the three chromosomes. The results indicate that RFLP dosage analysis is useful in the characterization of homoeologous chromosomes in hexaploid oat where nullisomics for many of the chromosomes are not available.Mention of a trademark or proprietary product does not constitute a guarantee or warranty by the USDA-ARS or the University of Minnesota and does not imply approval over other products that also may be suitable.

An RFLP-based genetic map of pearl millet (Pennisetum glaucum)

Analysis of a sample of diverse pearl millet genotypes with 200 genomic DNA probes revealed this crop species to be extremely polymorphic. Among these genotypes, 85% of probes detected polymorphism using only two restriction enzymes, with an average pair-wise polymorphism between all of the probe-enzyme combinations of 56%. Two crosses were employed to construct an RFLP-based genetic map. In an intervarietal F2 population, derived from a single F1 plant, 181 loci were placed on a linkage map. The total length of this map, which comprised seven linkage groups, was 303 cM and the average map distance between loci was about 2 cM, although a few intervals in excess of 10 cM were present at the ends of a few linkage groups. Very few clones, including those which hybridized to more than one copy, detected more than one locus in the pearl millet genome. The analysis was complicated initially because 83 of the 181 loci mapped to a single linkage group. Analysis of a second cross identified a probable translocation breakpoint in the middle of this large linkage group.

Estimation and test for linkage between markers: a comparison of lod score and χ (2) test in a linkage study of maritime pine (Pinus pinaster Ait.)

The first step in the construction of a linkage map involves the estimation and test for linkage between all possible pairs of markers. The lod score method is used in many linkage studies for the latter purpose. In contrast with classical statistical tests, this method does not rely on the choice of a first-type error level. We thus provide a comparison between the lod score and a χ (2) test on linkage data from a gymnosperm, the maritime pine. The lod score appears to be a very conservative test with the usual thresholds. Its severity depends on the type of data used.

A linkage map of rye

A linkage map of rye (Secale cereale L.) is presented which comprises 60 loci including RFLPs, RAPDs, isozyme, morphological and physiological markers. The genetics and linkage relationships of these markers were investigated in several inbred lines of rye. For the RFLP mapping a genomic library of PstI-digested DNA was constructed from which 50 size-selected clones were analysed. The portion of single-copy and multi-copy DNA and the frequency of polymorphic DNA was determined. The markers are unequally distributed over the seven chromosomes of rye. Many of them exhibit a distorted segregation. The main region of deviating segregation ratios could be localized near the self-incompatibility loci.

Identification and localization of molecular markers linked to the Lr9 leaf rust resistance gene of wheat

Near-isogenic lines (NILs) for the leaf rust resistance gene Lr9 were screened for polymorphisms at the molecular level. RAPD (random amplified polymorphic DNA) primers as well as RFLP (restriction fragment length polymorphism) markers were used. Out of 395 RAPD primers tested, three showed polymorphisms between NILs, i.e., an additional band was found in resistant lines. One of these polymorphic bands was cloned and sequenced. Specific primers were synthesized, and after amplification only resistant lines showed an amplified product. Thus, these primers define a sequence-tagged site that is specific for the translocated fragment carrying the Lr9 gene. A cross between a resistant NIL and the spelt (Triticum spelta) variety 'Oberkulmer' was made, and F2 plants were analyzed for genetic linkage. All three polymorphisms detected by the PCR (polymerase chain reaction) and one RFLP marker (cMWG684) showed complete linkage to the Lr9 gene in 156 and 133 plants analyzed, respectively. A second RFLP marker (PSR546) was closely linked (8±2.4 cM) to the Lr9 gene and the other four DNA markers. As this marker maps to the distal part of the long arm of chromosome 6B of wheat, Lr9 and the other DNA markers also map to the distal region of 6BL. All three PCR markers detected the Lr9 gene in independently derived breeding lines and varieties, thus proving their general applicability in wheat breeding programs.

Homoeologous relationships of rice, wheat and maize chromosomes

A set of cDNA clones, which had previously been mapped onto wheat chromosomes, was genetically mapped onto the chromosomes of rice. The resulting comparative maps make it possible to estimate the degree of linkage conservation between these two species. A number of chromosomal rearrangements, some of which must have involved interchromosomal translocations, differentiate the rice and wheat genomes. However, synteny of a large proportion of the loci appears to be conserved between the two species. The results of this study, combined with those from a recently published comparative map of the rice and maize genomes, suggest that rice, wheat and maize share extensive homoeologies in a number of regions in their genomes. Some chromosomes (e.g. chromosome 4 in rice, chromosomes 2 and 2S in wheat and maize, respectively) may have escaped major rearrangement since the divergence of these species from their last common ancestor. Comparative maps for rice, wheat and maize should make it possible to begin uniting the genetics of these species and allow for transfer of mapping information (including centromere positions) and molecular marker resources (e.g. RFLP probes) between species. In addition, such maps should shed light on the nature of chromosome evolution that accompanied the radiation of grasses in the early stages of plant diversification.

Intrachromosomal mapping of seven biochemical loci in barley, Hordeum vulgare

Seven biochemical loci, AmpA, Amy1, Amy2, Est-H5, Hor1, Hor2, and Wsp-H1, have been intrachromosomally mapped in the barley genome using a previously published RFLP-based genetic map. In all cases, the map locations confirmed prior chromosome assignments and agreed closely with the map positions of their homoeoloci in hexaploid wheat.