Genotyping by sequencing (GBS) is an efficient method of genotyping in numerous plant species. One of the crucial steps toward the application of GBS markers in crop improvement is anchoring them on particular chromosomes. In rye (Secale cereale L.), chromosomal localization of GBS markers has not yet been reported. In this paper, the application of GBS markers generated by the DArTseq platform for extending the high-density map of rye is presented. Additionally, their application is used for the localization of the Rfc1 gene that restores male fertility in plants with the C source of sterility-inducing cytoplasm. The total number of markers anchored on the current version of the map is 19,081, of which 18,132 were obtained from the DArTseq platform. Numerous markers co-segregated within the studied mapping population, so, finally, only 3397 unique positions were located on the map of all seven rye chromosomes. The total length of the map is 1593 cM and the average distance between markers is 0.47 cM. In spite of the resolution of the map being not very high, it should be a useful tool for further studies of the Secale cereale genome because of the presence on this map of numerous GBS markers anchored for the first time on rye chromosomes. The Rfc1 gene was located on high-density maps of the long arm of the 4R chromosome obtained for two mapping populations. Genetic maps were composed of DArT, DArTseq, and PCR-based markers. Consistent mapping results were obtained and DArTs tightly linked to the Rfc1 gene were successfully applied for the development of six new PCR-based markers useful in marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1007/s13353-016-0347-4) contains supplementary material, which is available to authorized users.

The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene. In the population developed from the 541×2020LM intercross, numerous markers tightly linked with the restorer gene were identified. This group contained 91 DArT markers and three SCARs additionally analyzed in the study. All these markers were mapped in the distance not exceeding 6 cM from the gene of interest. In the second mapping population (541×Ot1-3 intercross), only 9 DArT markers located closely to the Rfc1 gene were identified. Five of these DArT markers were polymorphic in both populations.

The sterilising cytoplasm from Triticum timopheevii is presently considered to be the most promising as regards to the seed production of triticale hybrid cultivars. This study was aimed at the utilisation of Diversity Arrays Technology (DArT) for the preliminary identification of genomic regions with loci controlling male sterility/fertility in the field-grown F2 generation of the interline hybrid between male sterile line CMS-Salvo 15/1 and restorer line Stan I. The fertility of plants was examined by visual scoring as well as by the assessment of seed setting within bagged spikes. For DNA analyses, 92 individuals representing opposite phenotypes (male sterile vs. fully male fertile) were chosen from the whole F2 population, which consisted of 414 plants. The constructed genetic map consists of 759 DArT markers distributed in 24 linkage groups that cover a distance of 974.4 cM. Application of the interval mapping method and the Kruskal–Wallis test enabled the identification of six genomic regions engaged in the restoration of male fertility within the mapping population. The most effective restorer genes were found on chromosomes of the sixth homeologic group, i.e. on 6R (the most efficient), 6A and 6B. Additionally, linkage groups assigned to chromosomes 1BS, 3A and 3A/3B were important for the determination of male fertility.

The development of genetic maps is, nowadays, one of the most intensive research activities of plant geneticists. One of the major goals of genome mapping is the localisation of quantitative trait loci (QTLs). This study was aimed at the identification of QTLs controlling morphological traits of rye and comparison of their localisation on genetic maps constructed with the use of genetically different germplasms. For QTL analyses, two high-density consensus maps of two populations (RIL-S and RIL-M) of recombinant inbred lines (RIL) were applied. Plant height (Ph), length of spikes (Sl) and the number of spikelets per spike (Sps) were studied in both populations. Additionally, the number of kernels per spike under isolation (Kps), the weight of kernels per spike (Kw) and thousand kernel weight (Tkw) were assessed in the RIL-M population. Except for Tkw, the majority of the traits were correlated to each other. The non-parametric Kruskal–Wallis (K-W) test and composite interval mapping (CIM) revealed 18/48 and 24/18 regions of rye chromosomes engaged in the determination of Ph, Sl and Sps in the RIL-S and RIL-M populations, respectively. An additional 18/15 QTLs controlling Kps, Kw and Tkw were detected on a map of the RIL-M population. A numerous group of QTLs detected via CIM remained in agreement with the genomic regions found when the K-W test was applied. Frequently, the intervals indicated by CIM were narrower.Electronic supplementary materialThe online version of this article (doi:10.1007/s13353-013-0186-5) contains supplementary material, which is available to authorized users.

Dwarfing genes play a major role in development of semi-dwarf cultivars of various cereals, but in rye this type of cultivar is still not common. Several recessive and dominant dwarfing genes in rye have been reported. Among the known dominant dwarfing genes in rye, two are well characterised: Ddw1 from the 5RL chromosome and Ddw2 located on 7R. This study was aimed at characterisation of the K11 source of dominantly inherited dwarfism found in plant materials grown in the Plant Breeding and Acclimatization Institute (Radzików, Poland). Mapping analyses in this study indicate that the dominant dwarf gene under investigation is located on the 1RL chromosome and is independent from previously known genes. The gene was named Ddw3. Phenotypic effect of the Ddw3 was tested on two pairs of nearisogenic lines. Six morphological traits were analysed in two or three growing seasons: plant height, length of the second internode from the base, number of internodes, tillering, spike length, and number of spikelets per spike. No negative or weak influences on yield-related traits were observed. The examination of the dwarf plants' reaction to seedling treatment by gibberellic acid solution revealed sensitivity of Ddw3 to this growth regulator. This report is the first evidence of the dominant Ddw3 gene in rye and its presence on the 1R chromosome.