A. Börner

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 104 and the number of (GT)n blocks to be 2.3 x 104 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.

Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers

Abstract.A set of 24 wheat microsatellite markers, representing at least one marker from each chromosome, was used for the assessment of genetic diversity in 998 accessions of hexaploid bread wheat (Triticum aestivum L.) which originated from 68 countries of five continents. A total of 470 alleles were detected with an average allele number of 18.1 per locus. The highest number of alleles per locus was detected in the B genome with 19.9, compared to 17.4 and 16.5 for genomes A and D, respectively. The lowest allele number per locus among the seven homoeologous groups was observed in group 4. Greater genetic variation exists in the non-centromeric regions than in the centromeric regions of chromosomes. Allele numbers increased with the repeat number of the microsatellites used and their relative distance from the centromere, and was not dependent on the motif of microsatellites. Gene diversity was correlated with the number of alleles. Gene diversity according to Nei for the 26 microsatellite loci varied from 0.43 to 0.94 with an average of 0.77, and was 0.78, 0.81 and 0.73 for three genomes A, B and D, respectively. Alleles for each locus were present in regular two or three base-pair steps, indicating that the genetic variation during the wheat evolution occurred step by step in a continuous manner. In most cases, allele frequencies showed a normal distribution. Comparative analysis of microsatellite diversity among the eight geographical regions revealed that the accessions from the Near East and the Middle East exhibited more genetic diversity than those from the other regions. Greater diversity was found in Southeast Europe than in North and Southwest Europe. The present study also indicates that microsatellite markers permit the fast and high throughput fingerprinting of large numbers of accessions from a germplasm collection in order to assess genetic diversity.

Optimizing wheat grain yield: effects of Rht (gibberellin-insensitive) dwarfing genes

Four sets of near-isogenic lines carrying different combinations of the alleles Rht-B1b , Rht-D1b and Rht-B1c for gibberellin-insensitive dwarfism in hexaploid wheat ( Triticum aestivum L. ) were compared with tall controls in a series of yield trials in eastern England and central Germany. In all four varietal backgrounds the effects of Rht-B1b and Rht-D1b were similar (plant height ≈ 86 and 83% of tall controls respectively) and in combination reduced plant height to c. 58%. The Rht-B1c allele caused more severe dwarfism ( c. 50%) and, when combined with Rht-D1b , reduced plant height still further to c. 41%. Data from the trials were consistent with a model for height/yield relationships in which the pleiotropic effects of the Rht alleles on yield can be inferred from their primary function: insensitivity to gibberellin limits stem extension growth, decreasing assimilate demand for this organ and diverting it to the developing ear (which is not itself dwarfed). The net balance between the resulting increase in harvest index and the curvilinear relationship observed between plant height and total shoot yield results in optimum grain yields at intermediate plant heights. Yield advantages of shorter plants over tall controls were evident over several trials with mean grain yields ranging from 200 to 760 g m −2 . The optimum plant height for yield improvement in different genetic backgrounds was achieved by different Rht alleles according to the background varietal height, such that intrinsically taller genotypes required more potent Rht alleles to achieve maximum potential grain yield. Ear yield components showed increases in grain number due to Rht pleiotropy, from which it is inferred that the number of grains per ear is limited by supply of assimilates pre-anthesis. Increases in grain number were associated with decreases in mean weight per grain which varied according to severity of dwarfism and varietal background, so that the net effect on grain yield per ear was sometimes positive, sometimes negative, and sometimes neutral in different Rht /variety combinations.

Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality.

BackgroundThe increasingly narrow genetic background characteristic of modern crop germplasm presents a challenge for the breeding of cultivars that require adaptation to the anticipated change in climate. Thus, high priority research aims at the identification of relevant allelic variation present both in the crop itself as well as in its progenitors. This study is based on the characterization of genetic variation in barley, with a view to enhancing its response to terminal drought stress.ResultsThe expression patterns of drought regulated genes were monitored during plant ontogeny, mapped and the location of these genes was incorporated into a comprehensive barley SNP linkage map. Haplotypes within a set of 17 starch biosynthesis/degradation genes were defined, and a particularly high level of haplotype variation was uncovered in the genes encoding sucrose synthase (types I and II) and starch synthase. The ability of a panel of 50 barley accessions to maintain grain starch content under terminal drought conditions was explored.ConclusionThe linkage/expression map is an informative resource in the context of characterizing the response of barley to drought stress. The high level of haplotype variation among starch biosynthesis/degradation genes in the progenitors of cultivated barley shows that domestication and breeding have greatly eroded their allelic diversity in current elite cultivars. Prospective association analysis based on core drought-regulated genes may simplify the process of identifying favourable alleles, and help to understand the genetic basis of the response to terminal drought.

Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.)

Association-based trait mapping is an innovative methodology based on linkage disequilibrium. Studies in plants, especially in cereals, are rare. A genome-wide association study of wheat is reported, in which a large number of diversity array technology markers was used to genotype a winter wheat core collection of 96 accessions. The germplasm was structured into two sub-populations. Twenty agronomic traits were measured in field trials conducted over up to eight growing seasons. Association analysis was performed with two different approaches, the general linear model incorporating the Q-matrix only and the mixed linear model including also the kinship-matrix. In total, 385 marker–trait associations significant in both models were detected. The intrachromosomal location of many of these coincided with those of known major genes or quantitative trait loci, but others were detected in regions where no known genes have been located to date. These latter presumptive loci provide opportunities for further wheat improvement, based on a marker approach.

Salt stress-induced alterations in the root proteome of barley genotypes with contrasting response towards salinity

In addition to drought and extreme temperatures, soil salinity represents a growing threat to crop productivity. Among the cereal crops, barley is considered as notably salt tolerant, and cultivars show considerable variation for tolerance towards salinity stress. In order to unravel the molecular mechanisms underlying salt stress tolerance and to utilize the natural genetic variation of barley accessions, a series of hydroponics-based salinity stress experiments was conducted using two genetic mapping parents, cvs Steptoe and Morex, which display contrasting levels of salinity tolerance. The proteome of roots from both genotypes was investigated as displayed by two-dimensional gel electrophoresis, and comparisons were made between plants grown under non-saline and saline conditions. Multivariate analysis of the resulting protein patterns revealed cultivar-specific and salt stress-responsive protein expression. Mass spectrometry-based identification was successful for 26 out of 39 selected protein spots. Hierarchical clustering was applied to detect similar protein expression patterns. Among those, two proteins involved in the glutathione-based detoxification of reactive oxygen species (ROS) were more abundant in the tolerant genotype, while proteins involved in iron uptake were expressed at a higher level in the sensitive one. This study emphasizes the role of proteins involved in ROS detoxification during salinity stress, and identified potential candidates for increasing salt tolerance in barley.

The influence of photoperiod genes on the adaptability of European winter wheats

Photoperiod response genes play a major role in determining the climatic adaptability of European wheat varieties. Photoperiod insensitivity, in the vast majority of photoperiod insensitive European wheat varieties, is probably determined by a Ppd1 allele originally derived from the old Japanese variety Akakomugi. Analysis of the pleiotropic effects of a Ppd1 allele from the Italian variety Mara shows that, besides accelerating ear emergence time, Ppd1 also reduces plant height, tillering, and spikelet numbers. Increases in spikelet fertilities more than compensate for reduced spikelet numbers, producing increased numbers of grains per ear. In southern Europe, early flowering Ppd1 genotypes produce larger grain and greater yields. In England and Germany, pleiotropic effects of Ppd1 on yield vary annually, depending on prevailing weather conditions, from +9% to −16%, over a 10 year period in the United Kingdom. A possible alternative Ppd1 allele from the CIMMYT variety Ciano 67 was compared to that from Mara. Differences associated with complete substituted chromosomes were found to be due to linked genes rather than different Ppd1 alleles. Examination of an alternative weaker gene for photoperiod insensitivity, Ppd2, shows this to exert similar but less significant pleiotropic effects to Ppd1. In the UK, in each of three years of trialing, Ppd2 increased yield 6% more than Ppd1. Results of 10 years trialing show that in Central European countries, between areas where photoperiod sensitive or photoperiod insensitive varieties have a clear adaptive significance, the annual variations in climate make it extremely difficult for breeders to produce varieties with good adaptability to changing environmental conditions.

Molecular characterization of the genetic integrity of wheat (Triticum aestivum L.) germplasm after long-term maintenance

Abstract The genetic identity of eight wheat (Triticum aestivum L.) accessions maintained in the Gatersleben genebank and regenerated up to 24 times was studied by using wheat microsatellite markers (WMS). It was demonstrated that WMS can be used to analyze bulks of seeds stored more than 50 years in a seed reference collection at room temperature. No contamination due to foreign pollen or incorrect handling during the multiplication cycles was discovered. For one accession (TRI 4599) genetic drift was observed, whereas for TRI 249 a heterogenous situation for two markers was maintained over the years. We were able to show that microsatellites can be used as a simple and reliable marker system for the verification of the integrity and genetic stability of genebank accessions.

The relationships between the dwarfing genes of wheat and rye

SummaryThe improvement of lodging resistance by introducing major dwarfing genes, classified either as GA insensitive or GA sensitive, is one of the main strategies chosen by cereal breeders. In the present paper the current knowledge about the genetics, chromosomal localisation and the homoeoallelic relationships of the dwarfing genes in wheat and rye is reviewed. The confusing system of the symbolisation of the GA insensitive dwarfing genes/alleles in wheat is discussed and a nomenclature based on rules for gene symbolisation in wheat is proposed.

RFLP mapping of genes affecting plant height and growth habit in rye

SummaryRFLP mapping of chromosome 5R in the F3 generation of a rye (Secale cereale L.) cross segregating for gibberellic acid (GA3)-insensitive dwarfness (Ct2/ct2) and spring growth habit (Sp1/sp1) identified RFLP loci close to each of these agronomically important genes. The level of RFLP in the segregating population was high, and thus allowed more than half of the RFLP loci to be mapped, despite partial homozygosity in the parental F2 plant. Eight further loci were mapped in an unrelated F2 rye population, and a further two were placed by inference from equivalent genetic maps of related wheat chromosomes, allowing a consensus map of rye chromosome 5R, consisting of 29 points and spanning 129 cM, to be constructed. The location of the ct2 dwarfing gene was shown to be separated from the segment of the primitive 4RL translocated to 5RL, and thus the gene is probably genetically unrelated to the major GA-insensitive Rht genes of wheat located on chromosome arms 4BS and 4DS. The map position of Sp1 is consistent both with those of wheat Vrn1 and Vrn3, present on chromosome arms 5AL and 5DL, respectively, and with barley Sh2 which is distally located on chromosome arm 7L (= 5HL).