Genome-wide association mapping in elite winter wheat breeding for yield improvement

Increased grain yield (GY) is the primary breeding target of wheat breeders. We performed the genome-wide association study (GWAS) on 168 elite winter wheat lines from an ongoing breeding program to identify the main determinants of grain yield. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 single-nucleotide polymorphism (SNP) and presence-absence variation (PAV) markers. We identified 15 main genomic regions located in ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explained from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker-assisted selection. We found marker-trait associations between three genes involved in starch biosynthesis and grain yield. Two starch synthase genes (TraesCS2B03G1238800 and TraesCS2D03G1048800) and a sucrose synthase gene (TraesCS3D03G0024300) were found in regions of QGy.rut-2B.2, QGy.rut-2D.1, and QGy.rut-3D, respectively. These loci and other significantly associated SNP markers found in this study can be used for pyramiding favorable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.

Population structure and genetic diversity of a germplasm for hybrid breeding in rye (Secale cereale L.) using high-density DArTseq-based silicoDArT and SNP markers

Investigating genetic structure and diversity is crucial for the rye hybrid breeding strategy, leading to improved plant productivity and adaptation. The present study elucidated the population structure and genetic diversity of 188 rye accessions, comprising 94 pollen fertility restoration lines (RF) and 94 cytoplasmic male-sterile (CMS) lines with Pampa sterilizing cytoplasm using SNP and silicoDArT markers from the diversity array technology (DArT)-based sequencing platform (DArTseq). Expected heterozygosity (H_e) and Shanon's diversity (I) indexes varied slightly between marker systems and groups of germplasms (H_e = 0.34, I = 0.51 for RF and CMS lines genotyped using SNPs; H_e = 0.31, I = 0.48, and H_e = 0.35, I = 0.53 for RF and CMS using silicoDArTs, respectively). ANOVA indicated moderate variation (7%) between RF and CMS breeding materials. The same parameter varied when chromosome-assigned markers were used and ranged from 5.8% for 5R to 7.4% for 4R. However, when silicoDArT markers were applied, the respective values varied from 6.4% (1R) to 8.2% (3R and 4R). The model-based (Bayesian) population structure analysis based on the total marker pool identified two major subpopulations for the studied rye germplasm. The first one (P1) encompasses 93 RF accessions, and the second one (P2) encompasses 94 CMS and one RF accession. However, a similar analysis related to markers assigned to selected chromosomes failed to put plant materials into any of the populations in the same way as the total marker pool. Furthermore, the differences in grouping depended on marker types used for analysis.

Genetic variation of Cerastium alpinum L. from Babia Góra, a critically endangered species in Poland

Babia Góra massif is the only site of occurrence of the Cerastium alpinum L. in Poland, an arctic-alpine perennial plant with a wide distribution in North America, northwestern Asia, and Europe. To determine whether the isolated Polish populations are genetically distinct, we have performed an evaluation of C. alpinum from Babia Góra with the use of iPBS markers. A total number of 133 individuals of C. alpinum from seven populations representing four localizations of the species were analyzed, i.e., from Babia Góra (Poland), Alps (Switzerland), Nuolja massif (Sweden), and Kaffiøyra (Svalbard, Norway). Genetic analysis of all C. alpinum samples using eight PBS primers identified 262 bands, 79.4% of which were polymorphic. iPBS markers revealed low genetic diversity (average H_e = 0.085) and high population differentiation (F_ST = 0.617). AMOVA results confirmed that the majority of the genetic variation (62%) was recorded among populations. The grouping revealed by PCoA showed that C. alpinum from Svalbard is the most diverged population, C. alpinum from Switzerland and Sweden form a pair of similar populations, whereas C. alpinum from the Babia Góra form a heterogeneous group of four populations. Results of isolation by distance analysis suggested that the spatial distance is the most probable cause of the observed differentiation among populations. Although significant traces of a bottleneck effect were noted for all populations of C. alpinum from Babia Góra, the populations still maintain a low but significant level of genetic polymorphism. These results are of great importance for developing conservation strategies for this species in Poland.

Triticale Green Plant Regeneration Is Due to DNA Methylation and Sequence Changes Affecting Distinct Sequence Contexts in the Presence of Copper Ions in Induction Medium

Metal ions in the induction medium are essential ingredients allowing green plant regeneration. For instance, Cu(II) and Ag(I) ions may affect the mitochondrial electron transport chain, influencing the Yang cycle and synthesis of S-adenosyl-L-methionine, the prominent donor of the methylation group for all cellular compounds, including cytosines. If the ion concentrations are not balanced, they can interfere with the proper flow of electrons in the respiratory chain and ATP production. Under oxidative stress, methylated cytosines might be subjected to mutations impacting green plant regeneration efficiency. Varying Cu(II) and Ag(I) concentrations in the induction medium and time of anther culture, nine trials of anther culture-derived regenerants of triticale were derived. The methylation-sensitive AFLP approach quantitative characteristics of tissue culture-induced variation, including sequence variation, DNA demethylation, and DNA de novo methylation for all symmetric-CG, CHG, and asymmetric-CHH sequence contexts, were evaluated for all trials. In addition, the implementation of mediation analysis allowed evaluating relationships between factors influencing green plant regeneration efficiency. It was demonstrated that Cu(II) ions mediated relationships between: (1) de novo methylation in the CHH context and sequence variation in the CHH, (2) sequence variation in CHH and green plant regeneration efficiency, (3) de novo methylation in CHH sequences and green plant regeneration, (4) between sequence variation in the CHG context, and green plant regeneration efficiency. Cu(II) ions were not a mediator between de novo methylation in the CG context and green plant regeneration. The latter relationship was mediated by sequence variation in the CG context. On the other hand, we failed to identify any mediating action of Ag(I) ions or the moderating role of time. Furthermore, demethylation in any sequence context seems not to participate in any relationships leading to green plant regeneration, sequence variation, and the involvement of Cu(II) or Ag(I) as mediators.

Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley

The process of anther culture involves numerous abiotic stresses required for cellular reprogramming, microspore developmental switch, and plant regeneration. These stresses affect DNA methylation patterns, sequence variation, and the number of green plants regenerated. Recently, in barley (Hordeum vulgare L.), mediation analysis linked DNA methylation changes, copper (Cu2+) and silver (Ag+) ion concentrations, sequence variation, β-glucans, green plants, and duration of anther culture (Time). Although several models were used to explain particular aspects of the relationships between these factors, a generalized complex model employing all these types of data was not established. In this study, we combined the previously described partial models into a single complex model using the structural equation modeling approach. Based on the evaluated model, we demonstrated that stress conditions (such as starvation and darkness) influence β-glucans employed by cells for glycolysis and the tricarboxylic acid cycle. Additionally, Cu2+ and Ag+ ions affect DNA methylation and induce sequence variation. Moreover, these ions link DNA methylation with green plants. The structural equation model also showed the role of time in relationships between parameters included in the model and influencing plant regeneration via anther culture. Utilization of structural equation modeling may have both scientific and practical implications, as it demonstrates links between biological phenomena (e.g., culture-induced variation, green plant regeneration and biochemical pathways), and provides opportunities for regulating these phenomena for particular biotechnological purposes.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

New PCR-specific markers for pollen fertility restoration QRfp-4R in rye (Secale cereale L.) with Pampa sterilizing cytoplasm

Pampa cytoplasmic male sterility phenomenon is used extensively in the rye hybrid breeding programs. It relies on sterilizing action of the cytoplasm resulting in non-viable pollen of female lines. The sterilizing effect is problematic for reversion, and efficient restores are needed. The most promising QTL is located on chromosome 4R, but other chromosomes may also code the trait. Advanced recombinant inbred lines formed bi-parental mapping population genotyped with DArTseq markers. Genetic mapping allowed the seven linkage groups to construct with numerous markers and represent all rye chromosomes. Single marker analysis and composite interval mapping were conducted to identify markers linked to the pollen fertility. Association mapping was used to detect additional markers associated with the trait. A highly significant QTL (QRfp-4R) that explained 42.3% of the phenotypic variation was mapped to the distal part of the long arm of the 4R chromosome. The markers localized in the QRfp-4R region achieve R² association values up to 0.59. The homology of the 43 marker sequences to the loci responsible for fertility restoration in other species and transcription termination factor (mTERF) linked to Rf genes was established. Ten markers were successfully converted into PCR-specific conditions, and their segregation pattern was identical to that of unconverted DArTs.

Genetic mapping of pollen fertility restoration QTLs in rye (Secale cereale L.) with CMS Pampa

Cytoplasmic male sterility (CMS) is a widely applied plant breeding tool for hybrid seed production. The phenomenon is often caused by chimeric genes with altered open reading frames (ORFs) located in the mitochondrial genomes and expressed as novel genotoxic products that induce pollen abortion. The fertility of CMS plants can be restored by nuclear-encoded genes that inhibit the action of ORFs responsible for pollen sterility. A recombinant inbred line (RIL) mapping population S64/04/01, encompassing 175 individuals, was used for genetic map construction and identification of quantitative trait loci (QTLs) responsible for fertility restoration in rye (Secale cereale L.) with CMS Pampa. The genetic map of all seven rye chromosomes included 15,516 SNP and silicoDArT markers and covered 1070.5 cm. Individual QTLs explaining 60% and 5.5% of the fertility trait’s phenotypic variance were mapped to chromosomes 4R (QRft-4R) and 5R (QRft-5R), respectively. Association mapping identified markers with the highest R² value of 0.58 (p value = 2.21E-28). Markers showing the highest associations with the trait were also mapped to the 4R chromosome within the QRft-4R region. Based on marker sequence homology, putative genes involved in pollen fertility restoration were suggested. Five silicoDArTs were converted into PCR-based markers for further breeding purposes.

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

KEY MESSAGE

The Taguchi method and metAFLP analysis were used to optimise barley regenerants towards maximum and minimum levels of tissue culture-induced variation. The subtle effects of symmetric and asymmetric methylation changes in regenerants were identified. Plant tissue cultures (PTCs) provide researchers with unique materials that accelerate the development of new breeding cultivars and facilitate studies on off-type regenerants. The emerging variability of regenerants derived from PTCs may have both genetic and epigenetic origins, and may be desirable or degrade the value of regenerated plants. Thus, it is crucial to determine how the PTC variation level can be controlled. The easiest way to manipulate total tissue culture-induced variation (TTCIV) is to utilise appropriate stress factors and suitable medium components. This study describes the optimisation of in vitro tissue culture-induced variation in plant regenerants derived from barley anther culture, and maximizes and minimizes regenerant variation compared with the source explants. The approach relied on methylation amplified fragment length polymorphism (metAFLP)-derived TTCIV characteristics, which were evaluated in regenerants derived under distinct tissue culture conditions and analysed via Taguchi statistics. The factors that may trigger TTCIV included CuSO4, AgNO3 and the total time spent on the induction medium. The donor plants prepared for regeneration purposes had 5.75% and 2.01% polymorphic metAFLP loci with methylation and sequence changes, respectively. The level of TTCIV (as the sum of all metAFLP characteristics analyzed) identified in optimisation and verification experiments reached 7.51 and 10.46%, respectively. In the trial designed to produce a minimum number of differences between donor and regenerant plants, CuSO4 and AgNO3 were more crucial than time, which was not a significant factor. In the trial designed to produce a maximum number of differences between donor and regenerant plants, all factors had comparable impact on variation. The Taguchi method reduced the time required for experimental trials compared with a grid method and suggested that medium modifications were required to control regenerant variation. Finally, the effects of symmetric and asymmetric methylation changes on regenerants were identified using novel aspects of the metAFLP method developed for this analysis.

DNA methylation changes and TE activity induced in tissue cultures of barley (Hordeum vulgare L.)

BACKGROUND

In vitro plant regeneration via androgenesis or somatic embryogenesis is capable of inducing (epi)mutations that may affect sexual progenies. While epimutations are associated with DNA methylation, mutations could be due to the movement of transposons. The common notion is that both processes are linked. It is being assumed that demethylation activates transposable elements (TEs). Analysis of methylation changes and their relation with TEs activation in tissue cultures requires uniquely derived donor plants (Ds), their regenerants (Rs) and respective progeny (Ps) that would allow discrimination of processes not related to changes introduced via in vitro cultures. Moreover, a set of methods (RP-HPLC, SSAP, and MSTD) is needed to study whether different TEs families are being activated during in vitro tissue culture plant regeneration and whether their activity could be linked to DNA methylation changes or alternative explanations should be considered.

RESULTS

The in vitro tissue culture plant regeneration in barley was responsible for the induction of DNA methylation in regenerants and conservation of the methylation level in the progeny as shown by the RP-HPLC approach. No difference between andro- and embryo-derived Rs and Ps was observed. The SSAP and MSTD approach revealed that Ds and Rs were more polymorphic than Ps. Moreover, Rs individuals exhibited more polymorphisms with the MSTD than SSAP approach. The differences between Ds, Rs and Ps were also evaluated via ANOVA and AMOVA.

CONCLUSIONS

Stressful conditions during plant regeneration via in vitro tissue cultures affect regenerants and their sexual progeny leading to an increase in global DNA methylation of Rs and Ps compared to Ds in barley. The increased methylation level noted among regenerants remains unchanged in the Ps as indicated via RP-HPLC data. Marker-based experiments suggest that TEs are activated via in vitro tissue cultures and that, independently of the increased methylation, their activity in Rs is greater than in Ps. Thus, the increased methylation level may not correspond to the stabilization of TEs movement at least at the level of regenerants. The presence of TEs variation among Ds that were genetically and epigenetically uniform may suggest that at least some mobile elements may be active, and they may mask variation related to tissue cultures. Thus, tissue cultures may activate some TEs whereas the others remain intact, or their level of movement is changed. Finally, we suggest that sexual reproduction may be responsible for the stabilization of TEs.

Tissue culture-induced genetic and epigenetic variation in triticale (× Triticosecale spp. Wittmack ex A. Camus 1927) regenerants

Plant regeneration via in vitro culture can induce genetic and epigenetic variation; however, the extent of such changes in triticale is not yet understood. In the present study, metAFLP, a variation of methylation-sensitive amplified fragment length polymorphism analysis, was used to investigate tissue culture-induced variation in triticale regenerants derived from four distinct genotypes using androgenesis and somatic embryogenesis. The metAFLP technique enabled identification of both sequence and DNA methylation pattern changes in a single experiment. Moreover, it was possible to quantify subtle effects such as sequence variation, demethylation, and de novo methylation, which affected 19, 5.5, 4.5% of sites, respectively. Comparison of variation in different genotypes and with different in vitro regeneration approaches demonstrated that both the culture technique and genetic background of donor plants affected tissue culture-induced variation. The results showed that the metAFLP approach could be used for quantification of tissue culture-induced variation and provided direct evidence that in vitro plant regeneration could cause genetic and epigenetic variation.

Extended metAFLP approach in studies of tissue culture induced variation (TCIV) in triticale

We present the development of the theoretical background of the metAFLP approach which allows for partition of complex variation into sequence changes, de novo methylation and demethylation of the regenerants derived via in vitro tissue culture methods in the case of triticale. It was demonstrated that, independent of whether andro- or embryogenesis was used for plant regeneration, the level of sequence changes identified between regenerants is about 10 %. Moreover, DNA demethylation prevails over de novo methylation of the regenerants compared to the donor plant. The metAFLP approach allows for the evaluation of numerous quantitative characteristics. For instance, one may quantify the number of sites unaffected by tissue culture approaches, global site DNA methylation etc. It is suggested that the approach could be useful for breeders in order to control plant material uniformity or for the evaluation of modified in vitro tissue culture approaches allowing for control of the (epi)mutation level. The extended metAFLP approach presented here delivers sufficient background for the evaluation of software that could facilitate analyses of the tissue culture induced variation.

Genetic mapping of a 7R Al tolerance QTL in triticale (x Triticosecale Wittmack)

Triticale (x Triticosecale Wittmack) is a relatively new cereal crop. In Poland, triticale is grown on 12 % of arable land ( http://www.stat.gov.pl ). There is an increasing interest in its cultivation due to lowered production costs and increased adaptation to adverse environmental conditions. However, it has an insufficient tolerance to the presence of aluminum ions (Al(3+)) in the soil. The number of genes controlling aluminum tolerance in triticale and their chromosomal location is not known. Two F2 mapping biparental populations (MP1 and MP15) segregating for aluminum (Al) tolerance were tested with AFLP, SSR, DArT, and specific PCR markers. Genetic mapping enabled the construction of linkage groups representing chromosomes 7R, 5R and 2B. Obtained linkage groups were common for both mapping populations and mostly included the same markers. Composite interval mapping (CIM) allowed identification of a single QTL that mapped to the 7R chromosome and explained 25 % (MP1) and 36 % (MP15) of phenotypic variation. The B1, B26 and Xscm150 markers were 0.04 cM and 0.02 cM from the maximum of the LOD function in the MP1 and MP15, respectively and were highly associated with aluminum tolerance as indicated by Kruskal-Wallis nonparametric test. Moreover, the molecular markers B1, B26, Xrems1162 and Xscm92, previously associated with the Alt4 locus that encoded an aluminum-activated malate transporter (ScALMT1) that was involved in Al tolerance in rye (Secale cereale) also mapped within QTL. Biochemical analysis of plants represented MP1 and MP15 mapping populations confirmed that the QTL located on 7R chromosome in both mapping populations is responsible for Al tolerance.

Morphological and genetic distinctiveness of metallicolous and non-metallicolous populations of Armeria maritima s.l. (Plumbaginaceae) in Poland

Patterns of morphological, genetic and epigenetic variation (DNA methylation pattern) were investigated in metallicolous (M) and non-metallicolous (NM) populations of Armeria maritima. A morphological study was carried out using plants from six natural populations grown in a greenhouse. Morphological variation was assessed using seven traits. On the basis of this study, three representative populations were selected for molecular analyses using metAFLP to study sequence- and methylation-based DNA variation. Only one morphological trait (length of outer involucral bracts) was common to both metallicolous populations studied; however, the level of variation was sufficient to differentiate between M and NM populations. Molecular analyses showed the existence of naturally occurring epigenetic variation in A. maritima populations, as well as structuring into distinct between and within population components. We show that patterns of population genetic structure differed depending on the information used in the study. Analysis of sequence-based information data demonstrates the presence of three well-defined and genetically differentiated populations. Methylation-based data show that two major groups of individuals are present, corresponding to the division into M and NM populations. These results were confirmed using different analytical approaches, which suggest that the DNA methylation pattern is similar in both M populations. We hypothesise that epigenetic processes may be involved in microevolution leading to development of M populations in A. maritima.

Genetic map of triticale compiling DArT, SSR, and AFLP markers

A set of 90 doubled haploid (DH) lines derived from F(1) plants that originated from a cross between × Triticosecale Wittm. 'Saka3006' and ×Triticosecale Wittm. 'Modus', via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

Testing cms-P-linked AFLPs for selection of rye hybrid components

Application of AFLPs linked to pollen fertility restoration and non-performing genes evaluated in the C394-F2 hybrid was studied using a set of male sterile lines in the sterilising Pampa cytoplasm, several restorers and maintainer lines and, finally, two inbred lines backcrossed into cms-P, cms-R, cms-S and cms-C cytoplasms each. The set of male sterile lines based on the Pampa cytoplasm exhibited gradual variation in their ability to restore pollen fertility (starting from low and closing with high) in crosses with three unrelated restorers. Variations in the AFLPs between the analysed materials were observed, however, no clustering of the lines according to their sterile and fertile phenotypes was observed. The same markers, when applied to the population restorer (cv. Walet) that formed the C394-F2 cross permitted identification of plants with genotypes that could be recognized as restorers.

The application of the AFLP method to determine the purity of homozygous lines of barley (Horedum vulgare L.)

Amplified fragment length polymorphism of DNA has been used to analyse the equality of plants obtained from isolated microspores. Although the control parental material was regarded as being highly homozygous, the analysis of the banding patterns of single plants showed a certain level of polymorphism. The analysis of regenerants with a doubled chromosome number did not show any diversity within the progeny of a single line. The differences in banding patterns coming from single plants were only observed in microspore donor lines. These results have proven the high purity of homozygous lines obtained via androgenesis from isolated microspores.

Morphological, cytological and BSA-based testing on limited segregation population AFLPs

Cytoplasmic male sterility (cms) in rye (Secale cereale L.), especially cytoplasma PAMPA, is used commercially in hybrid breeding programmes. The development of molecular markers that are tightly linked to the numerous genes coding for pollen fertility is expected to have great impact in the field. Morphological and cytological analyses of plants from a three-way cross C394: [(S67P/94 x S38/94) x CHD296] indicated the presence of at least several genes acting at different stages of pollen grain development, and proved the concurrence of both approaches in plant classification. The AFLP technique combined with the Bulk Segregant Analysis (BSA) were applied to identify DNA fragments linked to the genes of interest. All the 256 possible primer pair combinations based on the MseI and EcoRI restriction sites generated distinct band patterns allowing the identification of 31143 DNA fragments, visualised using the isotopic method. On average, any given primer combination generated 122 fragments. Among 1111 and 431 potential genetic markers respectively identified in the restorer form and the maternal lines, 775 and 295 were present in the F2 population. These numbers were then reduced to 109 and 51. The identified DNA fragments were tested on a limited segregating population, C394-F2, in order to eliminate false signals and to select markers for a future marker-assisted selection programme. Twenty-five markers were selected. Four of these markers were not identified via the BSA approach, indicating that if a highly polymorphic component is used for a cross, or a polygenic trait is studied, then the use of a limited population may be required.

Morphological and AFLP variation of Elymus repens (L.) Gould (Poaceae)

Combined morphological and molecular techniques were used to characterize variation in Elymus repens. We studied the morphological variability of E. repens in relation to the degree of its genetic differentiation, in order to unravel the causes of conspicuous intraspecific morphological variation. Four populations of E. repens from different habitats were analyzed for 35 morphological characters, and their genetic differentiation was assessed by Amplified Fragment Length Polymorphism (AFLP). Four pairs of selective primers were used to detect a total of 279 AFLP bands, of which 104 (37.28%) were polymorphic between populations. Cluster analysis based on AFLP fingerprint data showed that individuals were arranged in population-specific groups. The analyses of variance (ANOVA and AMOVA) indicated significant morphological and genetic differentiation among populations (P<0.01). This study revealed low levels of AFLP variation, which suggests that conspicuous morphological variation of E. repens is caused by plasticity. E. repens is an evolutionarily young species, of hybrid origin, in which microevolutionary processes continue. This study showed that common analysis of genetic diversity and morphology is a powerful tool in low-level taxonomy.

AFLP-profiling of long-term stored and regenerated rye Genebank samples

The aim of these studies was to analyse the genetic changes induced by natural aging during long-term seed storage of rye. For this purpose, the AFLP (Amplified Fragment Length Polymorphism) technique was applied. In the experiment, DNA variation was demonstrated in seven-day-old seedlings of four seed samples of cv. Dańkowskie Złote, showing different levels of viability following long-term storage. Among the 362 AFLP fragments analysed, 73 had significantly different frequencies in at least one of the series. Principle Coordinate Analysis (PCA) based on molecular data revealed differences between the progenies of naturally aged seed samples with variable initial viability. It was clearly shown that materials with low viability differed in structure from highly viable ones, and that the population changes exhibited in the first case are preserved through regenerations. Although changes that were observed for initially viable samples were not so significant, they still occurred - probably as a result of genetic shift

Studies on changes in specific rye genome regions due to seed aging and regeneration

The aim of this study was to identify the genetic changes in rye seeds induced by natural aging during long-term storage and successive regeneration cycles under gene bank conditions. Genomic DNA from four rye samples (cv. Dańkowskie Złote), varying in their initial viability and having gone through one or three reproduction cycles, were analysed using specific PCR targeting of a secalin locus, and various repetitive fragments defined by the R173 sequence. A statistical analysis of the band frequencies for both secalin and R173.3 primer pairs revealed no changes in their frequencies. Similar data on R173.1 demonstrated significant changes between samples of different initial viability showing a lack of a band of the expected length (987 bp) in progeny originating from low viability seeds lots. These changes were inherited even after three regeneration cycles. Our results may indicate that long-term storage that leads to loss of viability also generates heritable changes in the preserved germplasm. However, it remains to be discovered where these changes occur and whether they are connected with coding or with non-coding DNA regions.

The chromosomal location of rye AFLP bands

23 AFLP bands were assigned to different rye chromosomes by means of two different sets of wheat-rye addition lines. Only one AFLP band could be assigned to 4R, and no specific AFLPs were found on the 5R chromosome. Only one AFLP band was explicitly assigned to 4R, and no specific AFLPs were found on the 5R chromosome. At least seven co-migrating AFLPs showed the same chromosomal location in both sets of addition lines. A total of 22 AFLPs were assigned to chromosome 1R using wheat-rye substitution lines. Six of them have counterparts in one of the addition lines analyzed, but only four have the same chromosomal location. Six and four of the total AFLPs located using addition (23) and substitution (22) lines segregated in the mapping population DS2 x RXL10, but only six were simultaneously assigned to the same chromosome by both approaches. Although co-migrating AFLPs could be located on different rye chromosomes using addition and substitution lines, we believe that AFLPs can be useful as rye chromosome markers.