T. Lelley

SciRoKo: a new tool for whole genome microsatellite search and investigation

UNLABELLED SciRoKo is a user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo an excellent tool for full genome analysis. Compared to other already existing tools, SciRoKo also allows the analysis of compound microsatellites. AVAILABILITY free for use: www.kofler.or.at/Bioinformatics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Seed quality QTLs identified in a molecular map of early maturing soybean

Abstract This study identified QTLs influencing seed quality characters in a cross of two early maturing soybean (Glycine max [L.] Merr.) cultivars (Ma.Belle and Proto) adapted to the short growing seasons of Central Europe. A molecular linkage map was constructed by using 113 SSR, 6 RAPD and 1 RFLP markers segregating in 82 individuals of an F2 population. The map consists of 23 linkage groups and corresponds wellto previously published soybean maps. Using phenotypic data of the F2-derived lines grown in five environments, four markers for protein content, three for oil content and eight for seed weight were identified. Four from fifteen seed quality QTL-regions identified in the present study were also found by other authors. Markers associated with seed weight QTLs were consistent across all environments and proved to have effects large enough to be useful in a marker-assisted breeding program, whereas protein and oil QTLs showed environmental interactions.

Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use

Abstract For studying genetic differentiation caused by selection for adaptation and end-use, the allele frequencies of 42 microsatellites (MS), representative of the three wheat genomes, were analysed in a total of 60 wheat cultivars. The cultivars originate from three agroecological areas (AEAs) – Germany, Austria and Hungary – and represent equal numbers of ’quality wheats’ and ’feed wheats’ for each country. For the 42 loci, 202 alleles were detected using PAGE and silver staining. The average number of alleles per locus was 4.8, including four monomorphic loci. For 16 loci, null alleles were detected. Cluster analysis clearly differentiated the varieties according to the three AEAs and, within each AEA, into quality wheats from feed wheats. Analysis of variance revealed highly significant differences of distance data between AEAs as well as between quality groups. The correlation between genetic distance (GD) and pedigree data (coefficient of diversity, COD) was rs=0.45. The results have proven the excellent resolving power of MS in varietal differentiation, which arises through breeding under specific environmental conditions, and for different end-use.

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

BackgroundRye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding.ResultsHere, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers.ConclusionThis work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.

Effect of Nitrogen Fertilization on Quantity of Flour Protein Components, Dough Properties, and Breadmaking Quality of Wheat

ABSTRACT Three winter wheat varieties with differing breadmaking quality were grown at two locations in two years at 0 or 3 × 60 kg of nitrogen application. The effect of nitrogen on amount of different components of gluten proteins was determined by reverse-phase HPLC. A high amount of nitrogen led generally to a significant increase of total protein content. However, this increase was obvious only for the gluten proteins; albumins and globulins remained nearly unaffected. The effect of increased protein content on gliadin to glutenin (gli-glu) ratio was inconsistent. While increased protein content increased the gli-glu ratio in the variety Capo, the opposite was true for the variety Renan. Gli-glu ratio of the variety Lindos showed no discernible tendency. As total protein content increased, the ratio of low molecular weight (LMW) to high molecular weight (HMW) glutenins decreased consistently, i.e., in all varieties, in both years and locations. Change of LMW to HMW ratio showed a significant negative...

Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication.

A consensus map for Cucurbita pepo

Using random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), and morphological traits, the first genetic maps for Cucurbita pepo (2n=2x=40) were constructed and compared. The two mapping populations consisted of 92 F2 individuals each. One map was developed from a cross between an oil-seed pumpkin breeding line and a zucchini accession, into which genes for resistance to Zucchini Yellow Mosaic Virus (ZYMV) from a related species, C. moschata, had been introgressed. The other map was developed from a cross between an oil-seed pumpkin and a crookneck variety. A total of 332 and 323 markers were mapped in the two populations. Markers were distributed in each map over 21 linkage groups and covered an average of 2,200 cM of the C. pepo genome. The two maps had 62 loci in common, which enabled identification of 14 homologous linkage groups. Polyacrylamide gel analyses allowed detection of a high number of markers suitable for mapping, 10% of which were co-dominant RAPD loci. In the Pumpkin-Zucchini population, bulked segregant analysis (BSA) identified seven markers less than 7 cM distant from the locus n, affecting lignification of the seed coat. One of these markers, linked to the recessive hull-less allele (AW11-420), was also found in the Pumpkin-Crookneck population, 4 cM from n. In the Pumpkin-Zucchini population, 24 RAPD markers, previously introduced into C. pepo from C. moschata, were mapped in two linkage groups (13 and 11 markers in LGpz1 and LGpz2, respectively), together with two sequence characterized amplified region (SCAR) markers linked to genes for resistance to ZYMV.

Genetic and physical mapping of sequence-specific amplified polymorphic (SSAP) markers on the 1RS chromosome arm of rye in a wheat background

Abstract Three rye-specific repeated sequences, pSc10C, pSc20H and R173-1, were used to design sequence-specific anchored primers. These primers and 16 restriction site-specific adaptor primers were used in all possible combinations to establish sequence-specific amplified polymorphic (SSAP) markers for the 1RS chromosome arm of rye in a wheat background. Thirty 1RS-specific SSAP markers were detected in 19 primer combinations. Along with six markers localised previously on 1RS, 26 of the SSAP markers were mapped genetically in wheat genotypes carrying recombinant 1BL.1RS translocations. A clear decrease in recombination frequency from distal to proximal regions was observed. Wheat-rye addition lines for the 1R chromosome with different-sized deletions of the short arm were used to physically localise these markers. Physical mapping suggested an even distribution of the SSAP markers along the total length of the 1RS chromosome arm.

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

BackgroundGenomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C~7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation.ResultsWe demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using Hin dIII and Eco RI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning.ConclusionWe present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.

Genetic mapping of sequence-specific PCR-based markers on the short arm of the 1BL.1RS wheat-rye translocation

Wheat cultivars carrying the 1BL.1RStranslocation were crossed with newly synthesised octoploid triticale lines involving four rye genotypes having ο-secalin banding patterns different from each other and from that of the 1BL.1RS translocation. Homologous recombination was expected between the short arm of the 1R chromosomes of the rye genotypes and the 1RS arm of the 1BL.1RSwheat/rye translocation. Seven sequence-specific PCR-based markers:Xiag95, RMS13, Bmac0213, GPI, Xpsr960, 5Sand SCM9, and ο-secalinproteins were used to detect recombination events in the BC1F2 generation. Segregation analysis demonstrated that a barley SSR marker (Bmac0213) locus was present on the 1RS chromosome arm. Of 834plants tested in four different BC1F2 populations, 246individuals were found to carry recombined1BL.1RS translocation chromosomes. Genetic linkage analysis was performed on the eight markers in the four different mapping populations. The physical positions of the markers are discussed.