Potential and limits to unravel the genetic architecture and predict the variation of Fusarium head blight resistance in European winter wheat (Triticum aestivum L.)

Genome-wide mapping approaches in diverse populations are powerful tools to unravel the genetic architecture of complex traits. The main goals of our study were to investigate the potential and limits to unravel the genetic architecture and to identify the factors determining the accuracy of prediction of the genotypic variation of Fusarium head blight (FHB) resistance in wheat (Triticum aestivum L.) based on data collected with a diverse panel of 372 European varieties. The wheat lines were phenotyped in multi-location field trials for FHB resistance and genotyped with 782 simple sequence repeat (SSR) markers, and 9k and 90k single-nucleotide polymorphism (SNP) arrays. We applied genome-wide association mapping in combination with fivefold cross-validations and observed surprisingly high accuracies of prediction for marker-assisted selection based on the detected quantitative trait loci (QTLs). Using a random sample of markers not selected for marker-trait associations revealed only a slight decrease in prediction accuracy compared with marker-based selection exploiting the QTL information. The same picture was confirmed in a simulation study, suggesting that relatedness is a main driver of the accuracy of prediction in marker-assisted selection of FHB resistance. When the accuracy of prediction of three genomic selection models was contrasted for the three marker data sets, no significant differences in accuracies among marker platforms and genomic selection models were observed. Marker density impacted the accuracy of prediction only marginally. Consequently, genomic selection of FHB resistance can be implemented most cost-efficiently based on low- to medium-density SNP arrays.

Assessment of genetic diversity among Syrian durum (Triticum turgidum ssp. durum) and bread wheat (Triticum aestivum L.) using SSR markers

Genetic diversity among 49 wheat varieties (37 durum and 12 bread wheat) was assayed using 32 microsatellites representing 34 loci covering almost the whole wheat genome. The polymorphic information content (PIC) across the tested loci ranged from 0 to 0.88 with average values of 0.57 and 0.65 for durum and bread wheat respectively. B genome had the highest mean number of alleles (10.91) followed by A genome (8.3) whereas D genome had the lowest number (4.73). The correlation between PIC and allele number was significant in all genome groups accounting for 0.87, 074 and 0.84 for A, B and D genomes respectively, and over all genomes, the correlation was higher in tetraploid (0.8) than in hexaploid wheat varieties (0.5). The cluster analysis discriminated all varieties and clearly divided the two ploidy levels into two separate clusters that reflect the differences in genetic diversity within each cluster. This study demonstrates that microsatellites markers have unique advantages compared to other molecular and biochemical fingerprinting techniques in revealing the genetic diversity in Syrian wheat varieties that is crucial for wheat improvement.

A high density barley microsatellite consensus map with 775 SSR loci

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

Transferability of wheat microsatellites to diploid Aegilops species and determination of chromosomal localizations of microsatellites in the S genome

Overall, 253 genomic wheat (Triticum aestivum) microsatellite markers were studied for their transferability to the diploid species Aegilops speltoides, Aegilops longissima, and Aegilops searsii, representing the S genome. In total, 88% of all the analyzed primer pairs of markers derived from the B genome of hexaploid wheat amplified DNA fragments in the genomes of the studied species. The transferability of simple sequence repeat (SSR) markers of the T. aestivum A and D genomes totaled 74%. Triticum aestivum-Ae. speltoides, T. aestivum-Ae. longissima, and T. aestivum-Ae. searsii chromosome addition lines allowed us to determine the chromosomal localizations of 103 microsatellite markers in the Aegilops genomes. The majority of them were localized to homoeologous chromosomes in the genome of Aegilops. Several instances of nonhomoeologous localization of T. aestivum SSR markers in the Aegilops genome were considered to be either amplification of other loci or putative translocations. The results of microsatellite analysis were used to study phylogenetic relationships among the 3 species of the Sitopsis section (Ae. speltoides, Ae. longissima, and Ae. searsii) and T. aestivum. The dendrogram obtained generally reflects the current views on phylogenetic relationships among these species.

Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley

Hordeum vulgare subsp. spontaneum, the wild progenitor of barley, is a potential source of useful genetic variation for barley breeding programs. The objective of this study was to map quantitative trait loci (QTLs) in an advanced backcross population of barley. A total of 207 BC3 lines were developed using the 2-rowed German spring cultivar Hordeum vulgare subsp. vulgare 'Brenda' as a recurrent parent and the H. vulgare subsp. spontaneum accession HS584 as a donor parent. The lines were genotyped by 108 simple-sequence repeat (SSR) markers and evaluated in field tests for the measurement of grain yield and its components, such as ear length, spikelet number per spike, grain number per spike, spike number, and 1000-grain mass, as well as heading date and plant height. A total of 100 QTLs were detected. Ten QTLs with increasing effects were found for ear length, spikelet number, and grain number per spike. Three QTLs contributed by HS584 were found to significantly decrease days to heading across all years at 2 locations. In addition, 2 QTLs from HS584 on chromosomes 2H and 3H were associated with resistance to leaf rust. Based on genotypic data obtained from this population, 55 introgression lines carrying 1 or 2 donor segments were selected to develop a set of doubled-haploid lines, which will be used to reconfirm and investigate the effects of 100 QTLs for future genetic studies.

Comparative mapping of genes for glume colouration and pubescence in hexaploid wheat (Triticum aestivum L.)

Microsatellite markers were used to map the major genes Bg (determining black glume colour), Rg1 and Rg3 (red glume), and a locus determining smokey-grey coloured glume to the distal ends of the short arms of the homoeologous group 1 chromosomes, proximally (or closely linked) to Xgwm1223 and distal to Xgwm0033. On this basis, we propose that these genes represent a set of homoeoloci, designated Rg-A1, Rg-B1, and Rg-D1. Rg3 and Bg appear to be variant alleles of Rg-A1. Both Rg3 and Bg are closely linked with the major glume pubescence gene Hg. Similarly, the hexaploid wheat smokey-grey glume gene and Rg2 represent alleles at Rg-D1. The microsatellite markers linked to the Rg genes were used to analyse a phenotypically and genotypically characterized set of Siberian spring wheats. A coincidence between the presence of the 264-bp allele of Xgwm0136 and Rg-A1b (Rg3) was observed; so Xgwm0136 can probably be used as a diagnostic marker for this gene.

Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.)

Using a cDNA array-based functional genomics approach in barley, several candidate genes for malting quality including serine carboxypeptidase I (Cxp1) were previously identified (Potokina et al. in Mol Breed 14:153, 2004). The gene was mapped as a single nucleotide polymorphism (SNP) marker on chromosome 3H using the Steptoe (feeding grade)xMorex (malting grade) mapping population. Subsequently, the relative level of Cxp1 expression was determined by real-time RT-PCR for each of the 134 progeny lines and mapped as a quantitative trait. Only one quantitative trait locus (QTL) could be identified that significantly influenced the level of the Cxp1 expression. The expressed QTL maps to the same region on chromosome 3H as does the structural gene and corresponds to a QTL for "diastatic power," one among several traits measured to assess malting quality. An analysis of 90 barley cultivars sampled from a worldwide collection revealed six SNPs at the Cxp1 locus, three of which display complete linkage disequilibrium and define two haplotypes. The Cxp1 expression level in a set of barley accessions showing haplotype I was significantly higher than that of accessions displaying haplotype II. The data provide evidence that (1) the expression of Cxp1 is regulated in cis and that (2) the level of diastatic power in the barley seed is influenced by the level of Cxp1 expression.

Rationalising germplasm collections: a case study for wheat

In total 70 genebank accessions comprising 50 hexaploid, 12 tetraploid and 8 diploid wheats of the Gatersleben collection were selected based on the screening of the passport data for identical cultivar names or accession numbers of the donor genebanks. Twelve potential duplicate groups consisting of three to nine accessions with identical names/numbers were selected and analysed with DNA markers (microsatellites). A bootstrap approach based on re-sampling of both microsatellite markers and alleles within marker loci was used to test for homogeneity. Although several homogeneous groups were identified it became clear that cultivar name identity alone did not allow the determination of duplicates. A combination of SSR-analysis followed by the bootstrap method and database survey considering the botanical classification and other data (origin, growth habit and donor) available is recommended in order to determine duplicates. A procedure for the identification of duplicates and their further handling in ex situ genebanks is discussed.

Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley

Advanced backcross (AB)-quantitative trait locus (QTL) analysis has been successfully applied for detecting and transferring QTLs from unadapted germplasm into elite breeding lines in various plant species. Here, we describe the application of a modified AB breeding scheme to spring barley. A BC3-doubled haploid (DH) population consisting of 181 lines derived from the German spring barley cultivar 'Brenda' (Hordeum vulgare subsp. vulgare) as the recurrent parent and the wild species line 'HS213' (H. vulgare subsp. spontaneum) as the donor line was evaluated for yield and its components as well as malting quality traits. A set of 60 microsatellite markers was used to genotype the population, and phenotypic data were collected at two locations in Germany in continuous years. Altogether, 25 significant QTLs were detected by single-marker regression analysis and interval mapping. Most positive QTLs originated from the recurrent parent 'Brenda'. A QTL, Qhd2.1, on chromosome 2HS from 'Brenda' explained 18.3% and 20.7% of the phenotypic variation for yield and heading date, respectively. Due to the small percentage of donor-parent genome of 6.25%, the BC3-DH lines could be directly used for the extraction of near-isogenic lines (NILs) for Qhd2.1. Consequently, it was possible to determine the precise location of the locus hd2.1 within a region of 6.5 cM, using an F2 population consisting of 234 individuals developed from a cross between an NIL containing a defined donor segment at this locus and 'Brenda'. The location of this QTL was consistent with the presence of a major photoperiod response gene, Ppd-H1, previously reported in this region, which is associated with pleiotropic effects on yield components. In summary, the analysis of a BC3-DH population in barley provides a compromise between the analysis of QTLs by means of an AB scheme and the generation of defined substitution lines. Several lines carrying defined different donor segments for only one single chromosome or trait in the genetic background of 'Brenda' could be selected for further genetic studies.

Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (Triticum aestivum L.)

We report here the second advanced backcross quantitative trait locus (AB-QTL) analysis carried out in winter wheat. Seven agronomic traits were studied in a BC2F1 population derived from a cross between the German winter wheat variety Flair and the synthetic wheat line XX86 developed in Japan. We selected 111 BC2F1 lines and genotyped these with 197 microsatellite markers. Field data for seven agronomic traits were collected from corresponding BC2F3 families that were grown at up to six locations in Germany. QTL analyses for yield and yield components were performed using single-marker regression and interval mapping. A total of 57 putative QTLs derived from XX86 were detected, of which 24 (42.1%) were found to have a positive effect from the synthetic wheat XX86. These favourable QQTLs were mainly associated with thousand-grain weight and grain weight per ear. Many QTLs for correlated traits were mapped in similar chromosomal regions. The AB-QTL data obtained in the present study are discussed and compared with results from previous QTL analyses.

Genetic diversity in cultivated plants-loss or stability?

Human activities like urbanisation, the replacement of traditional agriculture systems by modern industrial methods or the introduction of modern high-yielding varieties may pose a danger to the biological diversity. Using microsatellite markers, we analysed samples of cultivated wheat ( Triticum aestivum L.) collected over an interval of 40-50 years in four comparable geographical regions of Europe and Asia. No significant differences in both the total number of alleles per locus and in the PIC values were detected when the material collected in the repeated collection missions in all four regions were compared. About two-thirds of the alleles were common to both collection periods, while one-third represented collection mission-specific alleles. These findings demonstrate that an allele flow took place during the adaptation of traditional agriculture to modern systems, whereas the level of genetic diversity was not significantly influenced.

Molecular studies on genetic integrity of open-pollinating species rye (Secale cereale L.) after long-term genebank maintenance

The genetic integrity of six accessions represented by 14 sub-populations of the open-pollinating species rye ( Secale cereale L.) was investigated. Seeds available from a herbarium collection (first regeneration) and from the cold store (most recent regeneration) were multiplied two to fourteen times and fingerprinted using microsatellite markers. Four accessions had significantly different allele frequencies. These were multiplied seven to thirteen times. Nearly 50% of the alleles discovered in the original samples were not found in the material present in the cold store. However alleles were detected in the most recently propagated sub-populations, that were not observed in the investigated plants of the original one. The change in allele frequencies is a continuous process. Reasons for the occurrence of genetic changes and consequences for managing open pollinating species maintained in ex situ genebanks are discussed.

Development and genetic mapping of 127 new microsatellite markers in barley

To enhance the marker density of existing genetic maps of barley ( Hordeum vulgare L.), a new set of microsatellite markers containing dinucleotide motifs was developed from genomic clones. Out of 254 primer pairs tested, a total of 167 primer pairs were classifed as functional in a panel of six barley cultivars and three H. spontaneum accessions, and of those, 127 primer pairs resulting in 133 loci were either mapped or located onto chromosomes. The polymorphism information content (PIC) ranged from 0.05 to 0.94 with an average of 0.60. The number of alleles per locus varied from 1 to 9. On average, 3.9 alleles per primer pair were observed. The RFLP frameworks of two previously published linkage maps were used to locate a total of 115 new microsatellite loci on at least one mapping population. The chromosomal assignment of 48 mapped loci was corroborated on a set of wheat-barley chromosome addition lines; 18 additional loci which were not polymorphic in the mapping populations were assigned to chromosomes by this method. The microsatellites were located on all seven linkage groups with four significant clusters in the centromeric regions of 2H, 3H, 6H and 7H. These newly developed microsatellites improve the density of existing barley microsatellite maps and can be used in genetic studies and breeding research.

Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat ( Triticum aestivum L.)

Advanced backcross QTL (AB-QTL) analysis was used to identify quantitative trait loci (QTLs) for yield and yield components in a BC(2)F(2) population derived from a cross between the German winter wheat variety 'Prinz' and the synthetic wheat line W-7984 developed by CIMMYT. Two hundred and ten microsatellite markers were employed to genotype 72 pre-selected BC(2)F(2) plants and phenotypic data were collected for five agronomic traits from corresponding BC(2)F(3) families that were grown at four locations in Germany. Using single-marker regression and interval mapping, a total of 40 putative QTLs derived from W-7984 were detected, of which 11 were for yield, 16 for yield components, eight for ear emergence time and five for plant height. For 24 (60.0%) of them, alleles from the synthetic wheat W-7984 were associated with a positive effect on agronomic traits, despite the fact that synthetic wheat was overall inferior with respect to agronomic appearance and performance. The present study indicated that favorable QTL alleles could be transferred from wild relatives of wheat into an elite wheat variety for improvement of quantitative trait loci like yield by the advanced backcross QTL strategy and molecular breeding. To our knowledge, the results presented here were the first report on AB-QTL analysis in wheat.

Microsatellite mapping of the powdery mildew resistance gene Pm5e in common wheat (Triticum aestivum L.)

Powdery mildew, caused by Erysiphe graminis DM f. sp. tritici (Em. Marchal), is one of the most important diseases of common wheat world-wide. Chinese wheat variety 'Fuzhuang 30' carries the powdery mildew resistance gene Pm5e and has proven to be a valuable resistance source of powdery mildew for wheat breeding. Microsatellite markers were employed to identify the gene Pm5e in a F(2) progeny from the cross 'Nongda 15' (susceptible) x 'Fuzhuang 30' (resistant). The gene Pm5e was mapped in the distal region of chromosome 7BL. Seven microsatellite markers were found to be linked to the gene Pm5e, of which two codominant markers Xgwm783 and Xgwm1267 were relatively close to Pm5e with a linkage distance of 11.0 cM and 6.6 cM, respectively. It is possible to use the 136-bp allele of Xgwm1267 in 'Fuzhuang 30' for marker-assisted selection during the wheat resistance breeding process for facilitation of gene pyramiding. The mapping information in the present study provides a starting point for fine mapping of the Pm5 locus and map-based cloning to clarify the molecular structure and function of the different alleles at the Pm5 locus. A microsatellite linkage map of chromosome 7B was constructed with 20 microsatellite loci, nine on the short arm and 11 on the long arm. This information will be very useful for further mapping of agronomically important genes of interest on chromosome 7B.

Inheritance of microsatellite alleles in pedigrees of Latvian barley varieties and related European ancestors

Genetic diversity and inheritance of 65 microsatellite (SSR) loci were studied in a set of 37 barley varieties involved in the pedigrees of seven Latvian barley varieties: Abava, Agra, Balga, Imula, Linga, Priekulu 1 and Stendes. Cluster analysis divided all the varieties into two large groups according to their geographic distribution. Moravian, Swedish and Danish varieties clustered separately from varieties from Norway and Finland. The pattern of subgroups of both European and Latvian varieties was in accordance with their pedigree information. Graphical genotypes of microsatellite alleles of all seven barley chromosomes were determined for all the 37 varieties studied. Parental inheritance and transmission of microsatellite alleles through the generations of the pedigrees were analysed. The results confirmed the importance and informative value of microsatellite markers for genetic studies in barley and their utility for barley breeding and other applications in fundamental and applied barley genetics.

Genetic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel

This study investigated allele size constraints and clustering, and genetic effects on microsatellite (simple sequence repeat, SSR) diversity at 28 loci comprising seven types of tandem repeated dinucleotide motifs in a natural population of wild emmer wheat, Triticum dicoccoides, from a shade vs sun microsite in Yehudiyya, northeast of the Sea of Galilee, Israel. It was found that allele distribution at SSR loci is clustered and constrained with lower or higher boundary. This may imply that SSR have functional significance and natural constraints. Genetic factors, involving genome, chromosome, motif, and locus significantly affected SSR diversity. Genome B appeared to have a larger average repeat number (ARN), but lower variance in repeat number (sigma(ARN)(2)), and smaller number of alleles per locus than genome A. SSRs with compound motifs showed larger ARN than those with perfect motifs. The effects of replication slippage and recombinational effects (eg, unequal crossing over) on SSR diversity varied with SSR motifs. Ecological stresses (sun vs shade) may affect mutational mechanisms, influencing the level of SSR diversity by both processes.

QTL analysis for grain protein content using SSR markers and validation studies using NILs in bread wheat

QTL interval mapping for grain protein content (GPC) in bread wheat was conducted for the first time, using a framework map based on a mapping population, which was available in the form of 100 recombinant inbred lines (RILs). The data on GPC for QTL mapping was recorded by growing the RILs in five different environments representing three wheat growing locations from Northern India; one of these locations was repeated for 3 years. Distribution of GPC values followed normal distributions in all the environments, which could be explained by significant g x e interactions observed through analyses of variances, which also gave significant effects due to genotypes and environments. Thirteen (13) QTLs were identified in individual environments following three methods (single-marker analysis or SMA, simple interval mapping or SIM and composite interval mapping or CIM) and using LOD scores that ranged from 2.5 to 6.5. Threshold LOD scores (ranging from 3.05 to 3.57), worked out and used in each case, however, detected only seven of the above 13 QTLs. Only four (QGpc.ccsu-2B.1; QGpc.ccsu-2D.1; QGpc.ccsu-3D.1 and QGpc.ccsu-7A.1) of these QTLs were identified either in more than one location or following one more method other than CIM; another QTL (QGpc.ccsu-3D.2), which was identified using means for all the environments, was also considered to be important. These five QTLs have been recommended for marker-assisted selection (MAS). The QTLs identified as above were also validated using ten NILs derived from three crosses. Five of the ten NILs possessed 38 introgressed segments from 16 chromosomes and carried 42 of the 173 markers that were mapped. All the seven QTLs were associated with one or more of the markers carried by the above introgressed segments, thus validating the corresponding markers. More markers associated with many more QTLs to be identified should become available in the future by effective MAS for GPC improvement.

[Molecular analysis of leaf-rust resistant introgression lines obtained by crossing hexaploid wheat Triticum aestivum with tetraploid wheat Triticum timopheevii]

Twenty-four Triticum eastivum x T. timopheevii hybrid lines developed on the basis of five varieties of common wheat and resistant to leaf rust were analyzed by the use of microsatellite markers specific for hexaploid common wheat T. aestivum. Investigation of intervarietal polymorphism of the markers showed that the number of alleles per locus ranged from 1 to 4, depending on the marker (2.5 on average). In T. timopheevii, amplification fragments are produced by 80, 55, and 30% of primers specific to the A, B, and D common wheat genomes, respectively. Microsatellite analysis revealed two major areas of introgression of the T. timopheevii genome: chromosomes of homoeological groups 2 and 5. Translocations were detected in the 2A and 2B chromosomes simultaneously in 11 lines of 24. The length of the translocated fragment in the 2B chromosome was virtually identical in all hybrid lines and did not depend on the parental wheat variety. In 15 lines developed on the basis of the Saratovskaya 29, Irtyshanka, and Tselinnaya 20, changes occurred in the telomeric region of the long arm of the 5A chromosome. Analysis with markers specific to the D genome suggested that introgressions of the T. timopheevii genome occurred in chromosomes of the D genome. However, the location of these markers on T. timopheevii chromosomes is unknown. Our data suggest that the genes for leaf-rust resistance transferred from T. timopheevii to T. aestivum are located chromosomes of homoeological group 2.

Construction and analysis of a microsatellite-based database of European wheat varieties

A database of 502 recent European wheat varieties, mainly of winter type, was constructed using 19 wheat microsatellites and one secalin-specific marker. All datapoints were generated in at least two laboratories using different techniques for fragment analysis. An overall level of >99.5% accuracy was achieved. The 199 alleles detected allowed discrimination between all of the varieties except duplicates, and varieties derived from identical parents. Approximately 25% of the varieties showed some heterogeneities, with the highest level of heterogeneity in south-eastern European material. The highest genetic diversity and the highest number of rare alleles were found in varieties from southern Europe. The relative allele frequencies varied for most microsatellites in different geographical regions.

Development of a set of Triticum aestivum-Aegilops tauschii introgression lines

New wheat introgression lines were obtained which contain different segments of individual chromosomes of Aegilops tauschii in the Triticum aestivum cv. 'Chinese Spring' background. The introgression lines were developed to examine various subsets of alleles from the wild grass in the genetic background of common wheat. As starting point substitution lines of 'Chinese Spring' in which single chromosomes of the D genome had been replaced by homologous chromosomes of a synthetic wheat were used. Synthetic wheat had been obtained earlier from a cross between the tetraploid emmer (genomes AABB) and wild grass Aegilops tauschii (genome DD). The seven wheat chromosome substitution lines carrying different chromosomes of Ae. tauschii were crossed twice to T. aestivum cv. 'Chinese Spring' and 259 BC1-progeny plants were analysed. Phenotypic evaluation was carried out for different traits such as plant height, spikelet number, peduncle length, flowering time, spike length, tiller number, grain weight per ear, fertility and thousand kernel weight. Genotypic analysis was performed using a set of 65 microsatellite markers previously mapped on the chromosomes of the D genome of wheat. During this analysis recombinant lines carrying different segments of Ae. tauschii chromosomes were detected. Plants containing small introgressions of the alien genetic material were selfed to get homozygous lines and plants carrying large pieces of the donor chromosome were backcrossed again to get smaller introgressions. Further microsatellite analysis of selected BC1F2-progeny plants resulted in detection of a first set of 36 homozygous lines carrying different pieces of Ae. tauschii genome.

Climatic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel

Microsatellite (SSR) diversity at 28 loci comprising seven types of tandem dinucleotide repeated motifs was analyzed in 105 individual plants of wild emmer wheat, Triticum dicoccoides, from a microsite in Yehudiyya, northeast of the Sea of Galilee, Israel. The study area was less than 1000 m(2) and involved 12 paired plots distributed in a mosaic pattern. Each experiment involved very close (a few meters apart), but sharply divergent, microclimatic niches in the open park forest of Tabor oak: (1) sun, between trees, and (2) shade, under tree canopy. Significant microclimatic divergence characterized many loci displaying asymmetric and non-random distribution of repeat numbers. Niche-specific and niche-unique alleles and linkage disequilibria were found in the two sub-populations. Microsatellite diversity at both single- and two-locus levels is affected by microclimatic environment. The evidence reflects effects of ecological stresses and natural selection on SSR diversity, resulting presumably in adaptive structures.

Molecular mapping, phenotypic expression and geographical distribution of genes determining anthocyanin pigmentation of coleoptiles in wheat ( Triticum aestivumL.)

Three major gene loci determining the anthocyanin pigmentation of coleoptiles were mapped on the short arms of chromosomes 7A, 7B and 7D, respectively. All three genes map about 15 to 20 cM distal from the centromere and, therefore, it may be concluded that they are members of a homoeologous series and should be designated Rc-A1, Rc-B1 and Rc-D1, respectively. Further homoeologous loci exist in Triticum durum, Triticum tauschii, and most probably in Secale cereale and Hordeum vulgare. By analyzing a syntheticxcultivated wheat cross (ITMI mapping population) under different environmental conditions it was shown that the expression of the genes determining anthocyanin pigmentation of the coleoptiles varies. One additional locus was detected on chromosome 4BL. Beside the mapping data, results of a screening for red coleoptile color genes in 468 mainly European wheat varieties are presented.

Microsatellite polymorphism in natural populations of wild emmer wheat, Triticum dicoccoides, in Israel

Diversity in 20 microsatellite loci of wild emmer wheat, Triticum dicoccoides, was examined in 15 populations (135 genotypes) representing a wide range of ecological conditions of soil, temperature, and water availability, in Israel and Turkey. An extensive amount of diversity at microsatellite loci was observed despite the predominantly selfing nature of this plant species. The 20 Gatersleben wheat microsatellites (GWM), representing 13 chromosomes of genomes A and B of wheat, revealed a total of 364 alleles, with an average of 18 alleles per GWM marker (range: 5-26). The proportion of polymorphic loci per population averaged 0.90 (range: 0.45- 1.00); genic diversity, He, averaged 0.50 (range 0.094- 0.736); and Shannon's information index averaged 0.84 (range 0.166-1.307). The coefficients of genetic distance between populations were high and averaged D=1.862 (range 0.876-3.320), an indication of sharp genetic divergence over short distances. Interpopulation genetic distances showed no association with geographic distance between the population sites of origin, which ruled out a simple isolation by distance model. Genetic dissimilarity values between genotypes were used to produce a dendrogram of the relationships among wild wheat populations by the unweighted pair-group method with arithmetic averages (UPGMA). The results showed that all the wild emmer wheat populations could be distinguished. Microsatellite analysis was found to be highly effective in distinguishing genotypes of T. dicoccoides, originating from diverse ecogeographical sites in Israel and Turkey, with 88% of the 135 genotypes correctly classified into sites of origin by discriminant analysis. Our present microsatellite results are non-random and in agreement with the previously obtained allozyme and RAPD patterns, although the genetic-diversity values obtained with microsatellites are much higher. Significant correlates of microsatellite markers with various climatic and soil factors suggest that, as in allozymes and RAPDs, natural selection causes adaptive microsatellite ecogeographical differentiation, not only in coding, but most importantly in non-coding genomic regions. Hence, the concept of "junk DNA" needs to be replaced by at least partly regulatory DNA. The obtained results suggest that microsatellite markers are useful for the estimation of genetic diversity in natural populations of T. dicoccoidesand for the tagging of agronomically important traits derived from wild emmer wheat.

Construction of a YAC library from barley cultivar Franka and identification of YAC-derived markers linked to the Rh2 gene conferring resistance to scald (Rhynchosporium secalis)

The Rh2 resistance gene of barley (Hordeum vulgare) confers resistance against the scald pathogen (Rhynchosporium secalis). A high-resolution genetic map of the Rh2 region on chromosome I (7H) was established by the use of molecular markers. Tightly linked markers from this region were used to screen existing and a newly constructed yeast artificial chromosome (YAC) library of barley cv. Franka composed of 45,000 clones representing approximately two genome equivalents. Corresponding YAC clones were identified for most markers, indicating that the combined YAC library has good representation of the barley genome. The contiguous sets of YAC clones with the most tightly linked molecular markers represent entry points for map-based cloning of this resistance gene.

Isolation of a chromosomally engineered durum wheat line carrying the Aegilops ventricosa Pch1 gene for resistance to eyespot

The chromosome 7Dv of Aegilops ventricosa (syn. Triticum ventricosum, 2n = 4x = 28, genome DvDvMvMv) carries the gene Pch1 for resistance to eyespot. This gene has previously been transferred to chromosome 7D of bread wheat, T. aestivum (2n = 6x = 42, genome AABBDD). To (1) enhance the level of resistance of bread wheat by increasing the copy number of Pch1, and (2) create eyespot-resistant triticales, meiotically stable Pch1-carrying durum lines were selected from the backcross progenies of a cross between Ae. ventricosa and T. durum cv. Creso ph1c (2n = 4x = 28, genome AABB). The Pch1 transfer, likely resulting from homoeologous recombination, was located at the distal position on the long arm of chromosome 7A. The 7A microsatellite marker Xgwm 698 was found closely linked in repulsion to the introgression in the resistant recombination lines, and the endopeptidase allele located on chromosome 7A of cv. Creso ph1c was lost.Key words: eyespot, introgression, homoeologous recombination, mapping, wheat.

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.]

Isolation and mapping of microsatellite markers specific for the D genome of bread wheat

The potential of Aegilops tauschii, the diploid progenitor of the D genome of wheat, as a source of microsatellite markers for hexaploid bread wheat was investigated. By screening lambda phage and plasmid libraries of Ae. tauschii genomic DNA, dinucleotide microsatellites containing GA and GT motifs were isolated and a total of 65 functional microsatellite markers were developed. All primer pairs that were functional in Ae. tauschii amplified well in hexaploid wheat. Fifty-five loci amplified by 48 primer sets were placed onto a genetic framework map of the reference population of the International Triticeae Mapping Initiative (ITMI) 'Opata 85' × 'W7984'. The majority of microsatellite markers could be assigned to the chromosomes of the D genome of wheat. The distribution of the markers along the chromosomes is random. Chromosomal location of 22 loci nonpolymorphic in the reference population was determined using nullitetrasomic lines of Triticum aestivum 'Chinese Spring'. The results of this study demonstrate the value of microsatellite markers isolated from Ae. tauschii for the study of bread wheat. The microsatellite markers developed improve the existing wheat microsatellite map and can be used in a wide range of genetic studies and breeding programs.Key words: Aegilops tauschii, wheat, molecular markers, genetic map, simple sequence repeats.

Isolation and mapping of microsatellite markers specific for the D genome of bread wheat

The potential of Aegilops tauschii, the diploid progenitor of the D genome of wheat, as a source of microsatellite markers for hexaploid bread wheat was investigated. By screening lambda phage and plasmid libraries of Ae. tauschii genomic DNA, dinucleotide microsatellites containing GA and GT motifs were isolated and a total of 65 functional microsatellite markers were developed. All primer pairs that were functional in Ae. tauschii amplified well in hexaploid wheat. Fifty-five loci amplified by 48 primer sets were placed onto a genetic framework map of the reference population of the International Triticeae Mapping Initiative (ITMI) 'Opata 85' x 'W7984'. The majority of microsatellite markers could be assigned to the chromosomes of the D genome of wheat. The distribution of the markers along the chromosomes is random. Chromosomal location of 22 loci nonpolymorphic in the reference population was determined using nullitetrasomic lines of Triticum aestivum 'Chinese Spring'. The results of this study demonstrate the value of microsatellite markers isolated from Ae. tauschii for the study of bread wheat. The microsatellite markers developed improve the existing wheat microsatellite map and can be used in a wide range of genetic studies and breeding programs.

Microsatellite diversity correlated with ecological-edaphic and genetic factors in three microsites of wild emmer wheat in North Israel

This study was conducted to test the effects of internal (genetic) and external factors on allelic diversity at 27 dinucleotide microsatellite (simple sequence repeat [SSR]) loci in three Israeli natural populations of Triticum dicoccoides from Ammiad, Tabigha, and Yehudiyya, north of the Sea of Galilee. The results demonstrated that SSR diversity is correlated with the interaction of ecological and genetic factors. Genetic factors, including genome (A vs. B), chromosome, motif, and locus, affected average repeat number (ARN), variance in repeat number (sigma), and number of alleles (NA) of SSRs, but the significance of some factors varied among populations. Genome effect on SSR variation may result from different motif types, particularly compound (or imperfect) versus perfect motifs, which may be related to different evolutionary histories of genomes A and B. Ecological factors significantly affected SSR variation. Soil-unique and soil-specific alleles were found in two edaphic groups dwelling on terra rossa and basalt soils across macro- and microgeographical scales. The largest contributions of genetic and ecological effects were found for diversity of ARN and NA, respectively. Multiple regression indicated that replication slippage and unequal crossing over could be important mutational mechanisms, but their significance varied among motifs. Edaphic stresses may affect the probability of replication errors and recombination intermediates and thus control diversity level and divergence of SSRs. The results may indicate that SSR diversity is adaptive, channeled by natural selection and influenced by both internal and external factors and their interactions.

Isolation of microsatellite and RAPD markers flanking the Yr15 gene of wheat using NILs and bulked segregant analysis

Microsatellite and random amplified polymorphic DNA (RAPD) primers were used to identify molecular markers linked to the Yr15 gene which confer resistance to stripe rust (Puccina striiformis Westend) in wheat. By using near isogenic lines (NILs) for the Yr15 gene and a F2 mapping population derived from crosses of these lines and phenotyped for resistance, we identified one microsatellite marker (GWM33) and one RAPD marker (OPA19(800)) linked to Yr15. Then, bulked segregant analysis was used in addition to the NILs to identify RAPD markers linked to the target gene. Using this approach, two RAPD markers linked to Yr15 were identified, one in coupling (UBC199(700)) and one in repulsion phase (UBC212(1200)). After MAPMAKER linkage analysis on the F2 population, the two closest markers were shown to be linked to Yr15 within a distance of about 12 cM. The recombination rates were recalculated using the maximum likelihood technique to take into account putative escaped individuals from the stripe rust resistance test and obtain unbiased distance estimates. As a result of this study, the stripe rust resistance gene Yr15 is surrounded by two flanking PCR markers, UBC199(700) and GWM33, at about 5 cM from each side.

A microsatellite map of wheat

Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 x W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

A microsatellite map of wheat

Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 x W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

Detection of genetic diversity in closely related bread wheat using microsatellite markers

Wheat microsatellites (WMS) were used to estimate the extent of genetic diversity among 40 wheat cultivars and lines, including mainly European elite material. The 23 WMS used were located on 15 different chromosomes, and revealed a total of 142 alleles. The number of alleles ranged from 3 to 16, with an average of 6.2 alleles per WMS. The average dinucleotide repeat number ranged from 13 to 41. The correlation coefficient between the number of alleles and the average number of repeats was only slight (r s = 0.55). Based on percentage difference a dendrogram is presented, calculated by the WMS-derived data. All but two of the wheat cultivars and lines could be distinguished. Some of the resulting groups are strongly related to the pedigrees of the appropriate cultivars. Values for co-ancestry (f) of 179 pairs of cultivars related by their pedigrees (f[Symbol: see text]0.1) averaged 0.29. Genetic similarity (GS) based on WMS of the same pairs averaged 0.44. The rank correlation for these pairs was slight, with r s = 0.55, but highly significant (P<0.001). The results suggest that a relatively small number of microsatellites can be used for the estimation of genetic diversity and cultivar identification in elite material of hexaploid bread wheat.

Barley telomeres are associated with two different types of satellite DNA sequences

The genomic organization of two different types of satellite DNA sequences was analysed by means of fluorescence in situ hybridization (FISH) and pulsed-field gel electrophoresis (PFGE) in barley. Satellite HvT01 was detected at all chromosome ends except the long arms of chromosomes 2 and 7. The unrelated satellite pAS1 was found at all chromosome ends except the long arm of chromosome 7 and at two interstitial sites, both located on the long arm of chromosome 4 on the standard karyotype. Southern and in situ hybridization further indicate that pAS1 also occurs interspersed in the barley genome. For most chromosome ends, the linear order of HvT01 and pAS1 could not be determined by in situ hybridization except at the short arms of chromosomes 2 and 6, where HvT01 is more distal than pAS1. This is confirmed by PFGE analysis, HvT01 being frequently associated with the telomeric repeat but not pAS1. Furthermore, we found that HvT01 occurred in clusters up to 1000 kb in size, whereas the pAS1 cluster had a maximum size of 500 kb. Sequence comparison revealed that both satellites are completely unrelated and differ considerably in their G + C contents.

RFLP markers linked to scald (Rhynchosporium secalis) resistance gene Rh2 in barley

Rhynchosporium secalis is the causal organism of barley scald disease. A number of resistance genes against the fungus are well known; one of them, the single dominant Rh2 resistance gene, has been mapped on the linkage map of barley using RFLP (restriction fragment length polymorphism) markers. The Rh2 gene was located on the distal part of chromosome arm 1S co-segregating with the RFLP marker CDO545 in 85 doubled-haploid progeny plants. The spring barley test population used was a cross between the 6-rowed American spring barley cv Atlas, C.I. 4118, carrying the Rh2 resistance gene, and a Bavarian 2-rowed malting barley cv Steffi, susceptible for R. secalis. The assessment of resistance versus susceptibility was based on artificial infections with a one-spore inoculum in greenhouse tests and with pathotype mixtures in field tests. By testing a pathotype mixture of German origin good resistance was found for the Rh2 gene in the field.

Abundance, variability and chromosomal location of microsatellites in wheat

The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)n blocks was estimated to be 3.6 x 10(4) and the number of (GT)n blocks to be 2.3 x 10(4) per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated microsatellites, it was found that wheat microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.

Pulsed-field gel analysis of 5S and satellite DNA in barley

Pulsed-field gel electrophoresis was used to study the variability of clustered tandemly repeated sequences in barley. Twelve spring barley cultivars were investigated with a heterologous 5S DNA probe and the 118 base pair barley satellite DNA probe HVT01. On a per fragment basis, the 5S probe was 5 times and the barley satellite probe 6.7 times more variable than single- or low-copy RFLP markers, demonstrating their usefulness for cultivar distinction.

Genetic and physical mapping of barley telomeres

Barley (Hordeum vulgare L.) telomeres were investigated by means of pulsed field gel electrophoresis (PFGE) and in situ hybridization. In situ hybridization showed that a tandemly repeated satellite sequence has a subtelomeric location, and is present at thirteen of the fourteen chromosome ends. PFGE revealed that this satellite sequence is physically close to the telomeric repeat. Pulsed field gel electrophoresis was then used for segregation analysis and linkage mapping of several telomeric and satellite loci in a segregating doubled-haploid population. The telomeric repeat displayed a hypervariable segregation pattern with new alleles occurring in the progeny. Eight satellite and telomeric sites were mapped on an restriction fragment length polymorphism (RFLP)-map of barley, defining the ends of chromosome arms 1L, 2S, 3L, 4S, 4L, 5S and 6. One satellite locus mapped to an interstitial site on the long arm of chromosome 3. The physical location of this locus was confirmed by in situ hybridization to wheat/barley addition line 3.

5S ribosomal gene clusters in wheat: pulsed field gel electrophoresis reveals a high degree of polymorphism

The long-range structure of 5S rRNA gene clusters has been investigated in wheat (Triticum aestivum L.) by means of pulsed field gel electrophoresis. Using aneuploid stocks, 5S rRNA gene clusters were assigned to sites on chromosomes 1B, 1D, 5B and 5D. Cluster sizes were evaluated and the copy number of 5S DNA repeats was estimated at 4700-5200 copies for the short repeating unit (410 bp) and about 3100 copies for the long repeat (500 bp) per haploid genome. A comparison of wheat cultivars revealed extremely high levels of polymorphism in the 5S rRNA gene clusters. With one restriction enzyme digest all varieties tested gave unique banding patterns and, on a per fragment basis, 21-fold more polymorphism was detected among cultivars for 5S DNA compared to standard restriction fragment length polymorphisms (RFLPs) detected with single copy clones. Experiments with aneuploid stocks suggest that the 5S rRNA gene clusters at several chromosomal sites contribute to this polymorphism. A number of previous reports have shown that wheat cultivars are not easily distinguished by isozymes or RFLPs. The high level of variation detected in 5S rRNA gene clusters therefore offers the possibility of a sensitive fingerprinting method for wheat. 5S DNA and other macro-satellite sequences may also serve as hypervariable Mendelian markers for genetic and breeding experiments in wheat.