Transfer of sequence tagged site PCR markers between wheat and barley

Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 other Vicia species

The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.

Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa

BACKGROUND

Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology.

RESULTS

Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology.

CONCLUSIONS

Two transcriptome sets were built that are valuable resources for marker development, comparative genomic studies and candidate gene approaches. Next generation sequencing of leaf transcriptome is very effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative studies.

Characterization of alien chromosomes in backcross derivatives of Triticum aestivum × Elymus rectisetus hybrids by using molecular markers and sequential multicolor FISH/GISH

Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Based on DNA sequences of genome-specific RAPD markers, sequence-tagged site (STS) markers specific for W and Y genomes have been obtained. Coupling with the use of genomic in situ hybridization, these STS markers enabled the identification of the W- and Y-genome chromosomes in backcross derivatives from hybrids of bread wheat Triticum aestivum L. (2n = 42; AABBDD) and Elymus rectisetus (Nees in Lehm.) Á. Löve & Connor (2n = 42; StStWWYY). The detection of six different alien chromosomes in five of these derivatives was ascertained by quantitative PCR of STS markers, simple sequence repeat markers, rDNA genes, and (or) multicolor florescence in situ hybridization. Disomic addition line 4687 (2n = 44) has the full complement of 42 wheat chromosomes and a pair of 1Y chromosomes that carry genes for resistance to tan spot (caused by Pyrenophora tritici-repentis (Died.) Drechs.) and Stagonospora nodorum blotch (caused by Stagonospora nodorum (Berk.) Castellani and Germano). The disomic addition line 4162 has a pair of 1St chromosomes and 21 pairs of wheat chromosomes. Lines 4319 and 5899 are two triple substitution lines (2n = 42) having the same chromosome composition, with 2A, 4B, and 6D of wheat substituted by one pair of W- and two pairs of St-genome chromosomes. Line 4434 is a substitution–addition line (2n = 44) that has the same W- and St-genome chromosomes substituting 2A, 4B, and 6D of wheat as in lines 4319 and 5899 but differs by having an additional pair of Y-genome chromosome, which is not the 1Y as in line 4687. The production and identification of these alien cytogenetic stocks may help locate and isolate genes for useful agronomic traits.

CAPS markers specific to Eb, Ee, and R genomes in the tribe Triticeae

Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Understanding their genome compositions is pivotal for efficient use of this vast gene pool in germplasm-enhancement programs. Several cleaved amplified polymorphic sequence (CAPS) markers were developed to distinguish the Eb, Ee, and R genomes. With the aid of disomic addition lines of wheat, it was confirmed that all 7 chromosomes of Eb, Ee, and R genomes carry these genome-specific CAPS markers. Thus, the identified CAPS markers are useful in detecting and monitoring the chromosomes of these 3 genomes. This study also provides evidence suggesting that some Purdue and Chinese germplasm lines developed for barley yellow dwarf virus (BYDV) resistance are different from those developed in Australia. Furthermore, Thinopyrum intermedium and Thinopyrum ponticum were shown to have different genome constitutions. Sequence analyses of the 1272 bp sequences, containing Ty3/gypsy retrotransposons, from the Eb, Ee, and R genomes also shed light on the evolution of these 3 genomes.

Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.)

In order to develop simple sequence repeat (SSR) markers in Italian ryegrass, we constructed a genomic library enriched for (CA)n-containing SSR repeats. A total of 1,544 clones were sequenced, of which 1,044 (67.6%) contained SSR motifs, and 395 unique clones were chosen for primer design. Three hundred and fifty-seven of these clones amplified products of the expected size in both parents of a two-way pseudo-testcross F(1) mapping population, and 260 primer pairs detected genetic polymorphism in the F(1) population. Genetic loci detected by a total of 218 primer pairs were assigned to locations on seven linkage groups, representing the seven chromosomes of the haploid Italian ryegrass karyotype. The SSR markers covered 887.8 cM of the female map and 795.8 cM of the male map. The average distance between two flanking SSR markers was 3.2 cM. The SSR markers developed in this study will be useful in cultivar discrimination, linkage analysis, and marker-assisted selection of Italian ryegrass and closely related species.

PCR-based markers for the powdery mildew resistance gene Pm4a in wheat

Gene tagging is the basis of marker-assisted selection and map-based cloning. To develop PCR-based markers for Pm4a, a dominant powdery mildew resistance gene of wheat, we surveyed 46 group 2 microsatellite markers between Pm4a near-isogenic line (NIL) CI 14124 and the recurrent parent Chancellor (Cc). One of the markers, gwm356, detected polymorphism and was used for genotyping an F(2) population of 85 plants derived from CI 14124 x Cc. Linkage mapping indicated that Xgwm356 was linked to Pm4a at a distance of 4.8 cM. To identify more PCR-based markers for Pm4a, we also converted the restriction fragment length polymorphism marker BCD1231 linked to it into a sequence-tagged site (STS) marker. The STS primer designed based on the end sequences of BCD1231 amplified an approximately 1.6-kb monomorphic band in both parents. Following digestion of the products with the four-cutter enzymes HaeIII and MspI, it was discovered that the band from CI 14124 consisted of at least two products, one of which had a digestion pattern different from the band from Cc. In the F(2) population, the cleaved polymorphism revealed by the STS marker between the parents co-segregated with powdery mildew resistance. To design Pm4a-specific PCR markers, the 1.6-kb band from Cc and the fragment associated with Pm4a in CI 14124 were sequenced and compared. Based on these sequences a new PCR marker was identified, which detected a 470-bp product only in the Pm4a-containing lines. These PCR-based markers provide a cost-saving option for marker-assisted selection of Pm4a.

Genetic diversity in wild Spanish populations of Thinopyrum junceum and Thinopyrum junceiforme using endosperm proteins and PCR-based markers

The genetic variation of sixteen wild, Spanish populations of Thinopyrum junceum and Thinopyrumjunceiforme and their interspecific relationships were analyzed. The relationships between these species and the diploids T. bessarabicum and T. elongatum were also investigated. The number of phenotypes and the composition of bands yielded by the electrophoretic separation of endosperm proteins were used to estimate intra- and interpopulational variability. DNA polymorphism generated by 24 arbitrary 10-mer primers and 14 specific 20-mer primers was used to determine interpopulational variability and interspecific relationships. Jaccard's coefficient of similarity was used to analyze presence and absence data in the DNA polymorphism and endosperm protein determinations of individual plants. Pearson's product-moment correlation coefficient was used to analyse interpopulational variation using endosperm protein band frequency data. Dendrograms were constructed using an unweighted pair group method with arithmetical average (UPGMA). The high level of intrapopulational variability found in T. junceum and T. junceiforme was inconsistent with the traditional classification of these species as self-pollinating. The level of interpopulational variation varied according to the degree of polymorphism of the corresponding markers. The endosperm proteins and random amplified polymorphic DNAs (RAPDs) proved to be the most polymorphic markers to those used although only the former were able to distinguish between the different populations. Interspecific relationships were consistently confirmed by all the PCR-based markers, and were also in agreement with the results of other authors.

Development and transferability of apricot and grape EST microsatellite markers across taxa

EST microsatellite markers were developed in apricot (Prunus armeniaca L.) and grape (Vitis vinifera L.). cDNA libraries from either apricot leaves or grape roots were used in an enrichment procedure for GA and CA repeats. The transferability of EST simple sequence repeat (SSR) markers from apricot and grapevine to other related and unrelated species was examined. Overall, grape primers amplified products in most of the Vitaceae accessions while the apricot primers amplified polymorphic alleles only in closely related species of the Rosaceae. In this taxonomic family, ten EST SSR loci were tested, and one single primer pair, PacB22, was amplified across species and sections in the Prunoideae and Maloideae. Sequencing of EST SSR loci in other species and genera confirmed a higher level of conservation in the microsatellite motif and flanking regions in the Vitaceae compared to the Rosaceae. Two distinct fragments of the PacB22 locus amplified across the Malus and Pyrus genera; however, while the coding region was highly conserved, the microsatellite repeat motif was no longer present. The banding pattern was explained by base substitution and insertion/deletion events in the intronic region of PacB22. This study includes the determination of the degree of polymorphism detected among species and genera in two unrelated taxonomic families and the evaluation of the information provided by the microsatellite repeats and the flanking regions.

Cross-species amplification of the Hordeum chilense genome using barley sequence-tagged-sites (STSs)

A selection of 51 barley Sequence-Tagged Sites (STSs) were studied for their utility in Hordeum chilense. They included four primer sets from wheat origin and six primer sets from oat origin. Forty-four primer pairs amplified H. chilense products consistently. Five primer pairs were suitable for studying the introgression of H. chilense in wheat because they amplified H. chilense products of distinct size. Six of the STSs showed polymorphism between different H. chilense accessions. The results showed that barley STSs could be useful for the genetic characterization of H. chilense, tritordeums and derived introgression lines.

Rapid verification of wheat-Hordeum introgressions by direct staining of SCAR, STS, and SSR amplicons

A range of single tagged site (STS), simple sequence repeat (SSR), and sequence-characterized amplified region (SCAR) markers were screened for their utility in detecting Hordeum vulgare and H. chilense chromosomes in a wheat background. PCR conditions were optimized for specific amplification of the targeted sequences and to avoid cross-species amplification. Two H. vulgare derived STSs, six H. vulgare derived SSRs, and nine H. chilense derived SCARs were usable for the detection of five H. vulgare and three H. chilense chromosomes by direct ethidium bromide staining of the PCR products in test tubes, avoiding the more costly and time-consuming DNA electrophoresis step. The practical application of the method is illustrated by the identification of a monotelosomic substitution of H. vulgare chromosome 6HS in tritordeum and a monosomic addition of H. chilense chromosome 6Hch in durum wheat.

Identification of barley genome segments introgressed into wheat using PCR markers

Barley has several important traits that might be used in the genetic improvement of wheat. For this report, we have produced wheat-barley recombinants involving barley chromosomes 4 (4H) and 7 (5H). Wheat-barley disomic addition lines were crossed with 'Chinese Spring' wheat carrying the ph1b mutation to promote homoeologous pairing. Selection was performed using polymerase chain reaction (PCR) markers to identify lines with the barley chromosome in the ph1b background. These lines were self pollinated, and recombinants were identified using sequence-tagged-site (STS) primer sets that allowed differentiation between barley and wheat chromosomes. Several recombinant lines were isolated that involved different STS-PCR markers. Recombination was confirmed by allowing the lines to self pollinate and rescreening the progeny via STS-PCR. Progeny testing confirmed 9 recombinants involving barley chromosome 4 (4H) and 11 recombinants involving barley chromosome 7 (5H). Some recombinants were observed cytologically to eliminate the possibility of broken chromosomes. Since transmission of the recombinant chromosomes was lower than expected and since seed set was reduced in recombinant lines, the utility of producing recombinants with this method is uncertain.Key words: introgression, sequence-tagged-site, recombination.

Barley allele-specific amplicons useful for identifying wheat-barley recombinant chromosomes

Barley (Hordeum vulgare L.) is potentially a new source of genes for wheat (Triticum aestivum L.) improvement. Wheat-barley chromosome recombinant lines provide a means for introgressing barley genes to wheat genome by chromosome engineering, and since these are expected to occur only rarely in special cytogenetic stocks, an efficient selection skill is necessary to identify them. To convert RFLP markers to barley allele-specific PCR markers useful for effective production of wheat-barley recombinant lines, 91 primer sets derived from RFLP clones which were previously mapped to the barley chromosomes were examined for PCR amplification using 'Chinese Spring' wheat, 'Betzes' barley and the wheat-barley chromosome addition lines. The polymorphisms were detected by an agarose gel electrophoresis of the PCR products without digestion with restriction enzymes. Out of 81 primer sets producing polymorphisms between the wheat and barley genomes, 26 amplified barley chromosome-specific DNAs which were confirmed to be located on the same chromosome as the RFLP markers by using the wheat-barley chromosome addition lines. These amplified DNAs represent barley allele-specific amplicons, which distinguish barley alleles from their wheat homoeologous counterparts. The present investigation revealed a higher probability for obtaining allele-specific amplicons from genomic DNA-derived RFLP markers than from cDNA-derived ones. The barley allele-specific amplicons developed in this study, namely, four for chromosome 2H, two for 3H, seven for 4H, eight for 5H, one for 6H and four for 7H, are suitable for identifying 'Chinese Spring' wheat- 'Betzes' barley recombinant chromosomes. However, one out of eight barley allele-specific amplicons on chromosome 5H did not detect a unique barley band in a 'New Golden' barley chromosome 5H addition line of 'Shinchunaga' wheat, indicating there may be a need to reconstruct allele-specific amplicons with different barley cultivars.

Properties of sequence-tagged-site primer sets influencing repeatability

The polymerase chain reaction (PCR) has become a standard procedure in plant genetics, and is the basis for many emerging genomics approaches to mapping and gene identification. One advantage of PCR is that sequence information for primer sets can be exchanged between laboratories, obviating the need for exchange and maintenance of biological materials. Repeatability of primer sets, whereby the same products are amplified in different laboratories using the same primer set, is important to successful exchange and utilization. We have developed several hundred sequence-tagged site (STS) primer sets for wheat and barley. The ability of the primer sets to generate reproducible amplifications in other laboratories has been variable. We wished to empirically determine the properties of the primer sets that most influenced repeatability. A total of 96 primer sets were tested with four genomic DNA samples on each of four thermocyclers. All major bands were repeatable across all four thermocyclers for approximately 50% of the primer sets. Characteristics most often associated with differences in repeatability included primer GC content and 3'-end stability of the primers. The propensity for primer-dimer formation was not a factor in repeatability. Our results provide empirical direction for the development of repeatable primer sets. Key words: STS-PCR primers, wheat, barley.

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.

More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA

Allohexaploid bread wheat is grown on more acreage than any other cereal crop, yet variation at the DNA level seems to be less than that observed in many diploid crop species. A common explanation for the small amount of DNA-level variation is that a severe bottleneck event resulted from the polyploidization events that gave rise to hexaploid wheat, whereby wheat was genetically separated from its progenitors. In this report, we test the extent of the bottleneck separating wheat from its D-genome progenitor, Triticum tauschii, by comparative DNA sequence analysis. Restriction site variation of low-copy DNA sequences amplified by PCR showed an average of 2.9 and 2.4 alleles per primer set in T. tauschii and wheat, respectively. Two different restriction patterns were present in T. tauschii for DNA amplified with a primer set for the A1 locus. Both alleles were also present in wheat. Alleles at the A1 locus were cloned and 527 bp of sequence obtained from 12 and 13 diverse accessions of wheat and T. tauschii, respectively. Average genetic distance among the wheat alleles was similar to that among the T. tauschii alleles (0.0127 and 0.0133, respectively). Nucleotide differences indicated that two distinct alleles existed in T. tauschii, both of which were present in wheat. These data suggest that hexaploid wheat formed at least twice, and that the bottleneck separating wheat from T. tauschii may be less constrictive than previously supposed.Key words: wheat, evolution, DNA.